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Gao Y, Raghavan A, Espinosa Garcia SA, Deng B, Hurtado de Mendoza D, Liang B. In vitro higher-order oligomeric assembly of the respiratory syncytial virus M2-1 protein with longer RNAs. J Virol 2024:e0104624. [PMID: 39016557 DOI: 10.1128/jvi.01046-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Abstract
The respiratory syncytial virus (RSV) M2-1 protein is a transcriptional antitermination factor crucial for efficiently synthesizing multiple full-length viral mRNAs. During RSV infection, M2-1 exists in a complex with mRNA within cytoplasmic compartments called inclusion body-associated granules (IBAGs). Prior studies showed that M2-1 can bind along the entire length of viral mRNAs instead of just gene-end (GE) sequences, suggesting that M2-1 has more sophisticated RNA recognition and binding characteristics. Here, we analyzed the higher oligomeric complexes formed by M2-1 and RNAs in vitro using size exclusion chromatography (SEC), electrophoretic mobility shift assays (EMSA), negative stain electron microscopy (EM), and mutagenesis. We observed that the minimal RNA length for such higher oligomeric assembly is about 14 nucleotides for polyadenine sequences, and longer RNAs exhibit distinct RNA-induced binding modality to M2-1, leading to enhanced particle formation frequency and particle homogeneity as the local RNA concentration increases. We showed that particular cysteine residues of the M2-1 cysteine-cysteine-cystine-histidine (CCCH) zinc-binding motif are essential for higher oligomeric assembly. Furthermore, complexes assembled with long polyadenine sequences remain unaffected when co-incubated with ribonucleases or a zinc chelation agent. Our study provided new insights into the higher oligomeric assembly of M2-1 with longer RNA.IMPORTANCERespiratory syncytial virus (RSV) causes significant respiratory infections in infants, the elderly, and immunocompromised individuals. The virus forms specialized compartments to produce genetic material, with the M2-1 protein playing a pivotal role. M2-1 acts as an anti-terminator in viral transcription, ensuring the creation of complete viral mRNA and associating with both viral and cellular mRNA. Our research focuses on understanding M2-1's function in viral mRNA synthesis by modeling interactions in a controlled environment. This approach is crucial due to the challenges of studying these compartments in vivo. Reconstructing the system in vitro uncovers structural and biochemical aspects and reveals the potential functions of M2-1 and its homologs in related viruses. Our work may contribute to identifying targets for antiviral inhibitors and advancing RSV infection treatment.
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Affiliation(s)
- Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Anirudh Raghavan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Bowei Deng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
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2
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Sibert BS, Kim JY, Yang JE, Ke Z, Stobart CC, Moore ML, Wright ER. Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers. Nat Commun 2024; 15:5923. [PMID: 39004634 PMCID: PMC11247094 DOI: 10.1038/s41467-024-50162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Respiratory syncytial virus (RSV) is an enveloped, filamentous, negative-strand RNA virus that causes significant respiratory illness worldwide. RSV vaccines are available, however there is still significant need for research to support the development of vaccines and therapeutics against RSV and related Mononegavirales viruses. Individual virions vary in size, with an average diameter of ~130 nm and ranging from ~500 nm to over 10 µm in length. Though the general arrangement of structural proteins in virions is known, we use cryo-electron tomography and sub-tomogram averaging to determine the molecular organization of RSV structural proteins. We show that the peripheral membrane-associated RSV matrix (M) protein is arranged in a packed helical-like lattice of M-dimers. We report that RSV F glycoprotein is frequently observed as pairs of trimers oriented in an anti-parallel conformation to support potential interactions between trimers. Our sub-tomogram averages indicate the positioning of F-trimer pairs is correlated with the underlying M lattice. These results provide insight into RSV virion organization and may aid in the development of RSV vaccines and anti-viral targets.
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Affiliation(s)
- Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Joseph Y Kim
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zunlong Ke
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | | | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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Passchier TC, White JBR, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 2024; 14:14099. [PMID: 38890308 PMCID: PMC11189427 DOI: 10.1038/s41598-024-58243-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 06/20/2024] Open
Abstract
We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound N protein ring assembly exhibiting D14 symmetry. The structure of the HeV N protein adopts the common bi-lobed paramyxoviral N protein fold; the N-terminal and C-terminal globular domains are bisected by an RNA binding cleft containing six RNA nucleotides and are flanked by the N-terminal and C-terminal arms, respectively. In common with other paramyxoviral nucleocapsids, the lateral interface between adjacent Ni and Ni+1 protomers involves electrostatic and hydrophobic interactions mediated primarily through the N-terminal arm and globular domains with minor contribution from the C-terminal arm. However, the HeV N multimeric assembly uniquely identifies an additional protomer-protomer contact between the Ni+1 N-terminus and Ni-1 C-terminal arm linker. The model presented here broadens the understanding of RNA-bound paramyxoviral nucleocapsid architectures and provides a platform for further insight into the molecular biology of HeV, as well as the development of antiviral interventions.
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Affiliation(s)
- Tim C Passchier
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Department of Biology, University of York, York, YO10 5DD, UK.
| | - Joshua B R White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Daniel P Maskell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew J Byrne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Exscientia, The Schrödinger Building Oxford Science Park, Oxford, OX4 4GE, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- College of Biomedical Sciences, Larkin University, 18301 N Miami Avenue, Miami, FL, 33169, USA.
| | - John N Barr
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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Parsons EL, Kim JS, Malloy AMW. Development of innate and adaptive immunity to RSV in young children. Cell Immunol 2024; 399-400:104824. [PMID: 38615612 DOI: 10.1016/j.cellimm.2024.104824] [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: 12/24/2023] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
Infection of the respiratory tract with respiratory syncytial virus (RSV) is common and occurs repeatedly throughout life with most severe disease occurring at the extremes of age: in young infants and the elderly. Effective anti-viral therapeutics are not available and therefore prevention has been the primary strategy for reducing the disease burden. Our current understanding of respiratory mucosal cell biology and the immune response within the respiratory tract is inadequate to prevent infection caused by a pathogen like RSV that does not disseminate outside of this environment. Gaps in our understanding of the activation of innate and adaptive immunity in response to RSV and the role of age upon infection also limit improvements in the design of therapeutics and vaccines for young infants. However, advancements in structural biology have improved our ability to characterize antibodies against viral proteins and in 2023 the first vaccines for those over 60 years and pregnant women became available, potentially reducing the burden of disease. This review will examine our current understanding of the critical facets of anti-RSV immune responses in infants and young children as well as highlight areas where more research is needed.
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Affiliation(s)
| | - Jisung S Kim
- Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation, Bethesda, MD, USA
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Zhang Q, Ye H, Liu C, Zhou H, He M, Liang X, Zhou Y, Wang K, Qin Y, Li Z, Chen M. PABP-driven secondary condensed phase within RSV inclusion bodies activates viral mRNAs for ribosomal recruitment. Virol Sin 2024; 39:235-250. [PMID: 38072230 PMCID: PMC11074649 DOI: 10.1016/j.virs.2023.12.001] [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: 11/18/2023] [Accepted: 12/03/2023] [Indexed: 01/12/2024] Open
Abstract
Inclusion bodies (IBs) of respiratory syncytial virus (RSV) are formed by liquid-liquid phase separation (LLPS) and contain internal structures termed "IB-associated granules" (IBAGs), where anti-termination factor M2-1 and viral mRNAs are concentrated. However, the mechanism of IBAG formation and the physiological function of IBAGs are unclear. Here, we found that the internal structures of RSV IBs are actual M2-1-free viral messenger ribonucleoprotein (mRNP) condensates formed by secondary LLPS. Mechanistically, the RSV nucleoprotein (N) and M2-1 interact with and recruit PABP to IBs, promoting PABP to bind viral mRNAs transcribed in IBs by RNA-recognition motif and drive secondary phase separation. Furthermore, PABP-eIF4G1 interaction regulates viral mRNP condensate composition, thereby recruiting specific translation initiation factors (eIF4G1, eIF4E, eIF4A, eIF4B and eIF4H) into the secondary condensed phase to activate viral mRNAs for ribosomal recruitment. Our study proposes a novel LLPS-regulated translation mechanism during viral infection and a novel antiviral strategy via targeting on secondary condensed phase.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanzhe Ye
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Cong Liu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haiwu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mingbin He
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaodong Liang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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Jobe F, Kelly JT, Simpson J, Wells J, Armstrong SD, Spick M, Lacey E, Logan L, Geifman N, Hawes P, Bailey D. Viral PIC-pocketing: RSV sequestration of translational preinitiation complexes into bi-phasic biomolecular condensates. J Virol 2024; 98:e0015324. [PMID: 38421168 PMCID: PMC10949503 DOI: 10.1128/jvi.00153-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Orthopneumoviruses characteristically form membrane-less cytoplasmic inclusion bodies (IBs) wherein RNA replication and transcription occur. Here, we report a strategy whereby the orthopneumoviruses sequester various components of the translational preinitiation complex machinery into viral inclusion bodies to facilitate translation of their own mRNAs-PIC-pocketing. Electron microscopy of respiratory syncytial virus (RSV)-infected cells revealed bi-phasic organization of IBs, specifically, spherical "droplets" nested within the larger inclusion. Using correlative light and electron microscopy, combined with fluorescence in situ hybridization, we showed that the observed bi-phasic morphology represents functional compartmentalization of the inclusion body and that these domains are synonymous with the previously reported inclusion body-associated granules (IBAGs). Detailed analysis demonstrated that IBAGs concentrate nascent viral mRNA, the viral M2-1 protein as well as components of eukaryotic translation initiation factors (eIF), eIF4F and eIF3, and 40S complexes involved in translation initiation. Interestingly, although ribopuromycylation-based imaging indicates that the majority of viral mRNA translation occurs in the cytoplasm, there was some evidence for intra-IBAG translation, consistent with the likely presence of ribosomes in a subset of IBAGs imaged by electron microscopy. Mass spectrometry analysis of sub-cellular fractions from RSV-infected cells identified significant modification of the cellular translation machinery; however, interestingly, ribopuromycylation assays showed no changes to global levels of translation. The mechanistic basis for this pathway was subsequently determined to involve the viral M2-1 protein interacting with eIF4G, likely to facilitate its transport between the cytoplasm and the separate phases of the viral inclusion body. In summary, our data show that these viral organelles function to spatially regulate early steps in viral translation within a highly selective bi-phasic biomolecular condensate. IMPORTANCE Respiratory syncytial viruses (RSVs) of cows and humans are a significant cause of morbidity and mortality in their respective populations. These RNA viruses replicate in the infected cells by compartmentalizing the cell's cytoplasm into distinct viral microdomains called inclusion bodies (IBs). In this paper, we show that these IBs are further compartmentalized into smaller structures that have significantly different density, as observed by electron microscopy. Within smaller intra-IB structures, we observed ribosomal components and evidence for active translation. These findings highlight that RSV may additionally compartmentalize translation to favor its own replication in the cell. These data contribute to our understanding of how RNA viruses hijack the cell to favor replication of their own genomes and may provide new targets for antiviral therapeutics in vivo.
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Affiliation(s)
| | | | | | - Joanna Wells
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Stuart D. Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Matt Spick
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Emily Lacey
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Leanne Logan
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Nophar Geifman
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Dalan Bailey
- The Pirbright Institute, Woking, Surrey, United Kingdom
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7
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Sun BW, Zhang PP, Wang ZH, Yao X, He ML, Bai RT, Che H, Lin J, Xie T, Hui Z, Ye XY, Wang LW. Prevention and Potential Treatment Strategies for Respiratory Syncytial Virus. Molecules 2024; 29:598. [PMID: 38338343 PMCID: PMC10856762 DOI: 10.3390/molecules29030598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a significant viral pathogen that causes respiratory infections in infants, the elderly, and immunocompromised individuals. RSV-related illnesses impose a substantial economic burden worldwide annually. The molecular structure, function, and in vivo interaction mechanisms of RSV have received more comprehensive attention in recent times, and significant progress has been made in developing inhibitors targeting various stages of the RSV replication cycle. These include fusion inhibitors, RSV polymerase inhibitors, and nucleoprotein inhibitors, as well as FDA-approved RSV prophylactic drugs palivizumab and nirsevimab. The research community is hopeful that these developments might provide easier access to knowledge and might spark new ideas for research programs.
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Affiliation(s)
- Bo-Wen Sun
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Peng-Peng Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Zong-Hao Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Xia Yao
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Meng-Lan He
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rui-Ting Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Hao Che
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Jing Lin
- Drug Discovery, Hangzhou Haolu Pharma Co., Hangzhou 311121, China;
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Zi Hui
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Li-Wei Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (B.-W.S.); (P.-P.Z.); (Z.-H.W.); (X.Y.); (M.-L.H.); (R.-T.B.); (H.C.); (T.X.); (Z.H.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
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Zhuang X, Gallo G, Sharma P, Ha J, Magri A, Borrmann H, Harris JM, Tsukuda S, Bentley E, Kirby A, de Neck S, Yang H, Balfe P, Wing PA, Matthews D, Harris AL, Kipar A, Stewart JP, Bailey D, McKeating JA. Hypoxia inducible factors inhibit respiratory syncytial virus infection by modulation of nucleolin expression. iScience 2024; 27:108763. [PMID: 38261926 PMCID: PMC10797196 DOI: 10.1016/j.isci.2023.108763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/13/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a global healthcare problem, causing respiratory illness in young children and elderly individuals. Our knowledge of the host pathways that define susceptibility to infection and disease severity are limited. Hypoxia inducible factors (HIFs) define metabolic responses to low oxygen and regulate inflammatory responses in the lower respiratory tract. We demonstrate a role for HIFs to suppress RSV entry and RNA replication. We show that hypoxia and HIF prolyl-hydroxylase inhibitors reduce the expression of the RSV entry receptor nucleolin and inhibit viral cell-cell fusion. We identify a HIF regulated microRNA, miR-494, that regulates nucleolin expression. In RSV-infected mice, treatment with the clinically approved HIF prolyl-hydroxylase inhibitor, Daprodustat, reduced the level of infectious virus and infiltrating monocytes and neutrophils in the lung. This study highlights a role for HIF-signalling to limit multiple aspects of RSV infection and associated inflammation and informs future therapeutic approaches for this respiratory pathogen.
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Affiliation(s)
- Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jiyeon Ha
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrea Magri
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helene Borrmann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James M. Harris
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Senko Tsukuda
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleanor Bentley
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Simon de Neck
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, 8057 Zurich, Switzerland
| | - Hongbing Yang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter A.C. Wing
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - David Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | | | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, 8057 Zurich, Switzerland
| | - James P. Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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9
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Zhang C, Wu H, Feng H, Zhang YA, Tu J. Grass carp reovirus VP56 and VP35 induce formation of viral inclusion bodies for replication. iScience 2024; 27:108684. [PMID: 38188516 PMCID: PMC10767200 DOI: 10.1016/j.isci.2023.108684] [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: 08/23/2023] [Revised: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Viral inclusion bodies (VIBs) are subcellular structures required for efficient viral replication. How type II grass carp reovirus (GCRV-II), the mainly prevalent strain, forms VIBs is unknown. In this study, we found that GCRV-II infection induced punctate VIBs in grass carp ovary (GCO) cells and that non-structural protein 38 (NS38) functioned as a participant in VIB formation. Furthermore, VP56 and VP35 induced VIBs and recruited other viral proteins via the N-terminal of VP56 and the middle domain of VP35. Additionally, we found that the newly synthesized viral RNAs co-localized with VP56 and VP35 in VIBs during infection. Taken together, VP56 and VP35 induce VIB formation and recruit other viral proteins and viral RNAs to the VIBs for viral replication, which helps identify new targets for developing anti-GCRV-II drugs to disrupt viral replication.
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Affiliation(s)
- Chu Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jiagang Tu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
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10
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Zou G, Cao S, Gao Z, Yie J, Wu JZ. Current state and challenges in respiratory syncytial virus drug discovery and development. Antiviral Res 2024; 221:105791. [PMID: 38160942 DOI: 10.1016/j.antiviral.2023.105791] [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: 11/21/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Human respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections (LRTI) in young children and elderly people worldwide. Recent significant progress in our understanding of the structure and function of RSV proteins has led to the discovery of several clinical candidates targeting RSV fusion and replication. These include both the development of novel small molecule interventions and the isolation of potent monoclonal antibodies. In this review, we summarize the state-of-the-art of RSV drug discovery, with a focus on the characteristics of the candidates that reached the clinical stage of development. We also discuss the lessons learned from failed and discontinued clinical developments and highlight the challenges that remain for development of RSV therapies.
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Affiliation(s)
- Gang Zou
- Shanghai Ark Biopharmaceutical Co., Ltd, Shanghai, 201203, China.
| | - Sushan Cao
- Shanghai Ark Biopharmaceutical Co., Ltd, Shanghai, 201203, China
| | - Zhao Gao
- Shanghai Ark Biopharmaceutical Co., Ltd, Shanghai, 201203, China
| | - Junming Yie
- Shanghai Ark Biopharmaceutical Co., Ltd, Shanghai, 201203, China
| | - Jim Zhen Wu
- Shanghai Ark Biopharmaceutical Co., Ltd, Shanghai, 201203, China
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11
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Le Rouzic A, Fix J, Vinck R, Kappler-Gratias S, Volmer R, Gallardo F, Eléouët JF, Keck M, Cintrat JC, Barbier J, Gillet D, Galloux M. A New Derivative of Retro-2 Displays Antiviral Activity against Respiratory Syncytial Virus. Int J Mol Sci 2023; 25:415. [PMID: 38203585 PMCID: PMC10778932 DOI: 10.3390/ijms25010415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Human respiratory syncytial virus (hRSV) is the most common cause of bronchiolitis and pneumonia in newborns, with all children being infected before the age of two. Reinfections are very common throughout life and can cause severe respiratory infections in the elderly and immunocompromised adults. Although vaccines and preventive antibodies have recently been licensed for use in specific subpopulations of patients, there is still no therapeutic treatment commonly available for these infections. Here, we investigated the potential antiviral activity of Retro-2.2, a derivative of the cellular retrograde transport inhibitor Retro-2, against hRSV. We show that Retro-2.2 inhibits hRSV replication in cell culture and impairs the ability of hRSV to form syncytia. Our results suggest that Retro-2.2 treatment affects virus spread by disrupting the trafficking of the viral de novo synthetized F and G glycoproteins to the plasma membrane, leading to a defect in virion morphogenesis. Taken together, our data show that targeting intracellular transport may be an effective strategy against hRSV infection.
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Affiliation(s)
- Adrien Le Rouzic
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Jenna Fix
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
| | - Robin Vinck
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, 91191 Gif-sur-Yvette, France;
| | | | - Romain Volmer
- INRAE, IHAP, UMR 1225, ENVT, 31300 Toulouse, France;
| | - Franck Gallardo
- NeoVirTech SAS, 1 Place Pierre Potier, 31000 Toulouse, France; (S.K.-G.); (F.G.)
| | - Jean-François Eléouët
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
| | - Mathilde Keck
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Jean-Christophe Cintrat
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, 91191 Gif-sur-Yvette, France;
| | - Julien Barbier
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Daniel Gillet
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Marie Galloux
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
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12
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Bodmer BS, Vallbracht M, Ushakov DS, Wendt L, Chlanda P, Hoenen T. Ebola virus inclusion bodies are liquid organelles whose formation is facilitated by nucleoprotein oligomerization. Emerg Microbes Infect 2023; 12:2223727. [PMID: 37306660 PMCID: PMC10288931 DOI: 10.1080/22221751.2023.2223727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Viral RNA synthesis of several non-segmented, negative-sense RNA viruses (NNSVs) takes place in inclusion bodies (IBs) that show properties of liquid organelles, which are formed by liquid-liquid phase separation of scaffold proteins. It is believed that this is driven by intrinsically disordered regions (IDRs) and/or multiple copies of interaction domains, which for NNSVs are usually located in their nucleo - and phosphoproteins. In contrast to other NNSVs, the Ebola virus (EBOV) nucleoprotein NP alone is sufficient to form IBs without the need for a phosphoprotein, and to facilitate the recruitment of other viral proteins into these structures. While it has been proposed that also EBOV IBs are liquid organelles, this has so far not been formally demonstrated. Here we used a combination of live cell microscopy, fluorescence recovery after photobleaching assays, and mutagenesis approaches together with reverse genetics-based generation of recombinant viruses to study the formation of EBOV IBs. Our results demonstrate that EBOV IBs are indeed liquid organelles, and that oligomerization but not IDRs of the EBOV nucleoprotein plays a key role in their formation. Additionally, VP35 (often considered the phosphoprotein-equivalent of EBOV) is not essential for IB formation, but alters their liquid behaviour. These findings define the molecular mechanism for the formation of EBOV IBs, which play a central role in the life cycle of this deadly virus.
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Affiliation(s)
- Bianca S. Bodmer
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Melina Vallbracht
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dmitry S. Ushakov
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Lisa Wendt
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
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13
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Whitehead JD, Decool H, Leyrat C, Carrique L, Fix J, Eléouët JF, Galloux M, Renner M. Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus. Nat Commun 2023; 14:7627. [PMID: 37993464 PMCID: PMC10665349 DOI: 10.1038/s41467-023-43434-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9 Å resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.
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Affiliation(s)
- Jack D Whitehead
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Hortense Decool
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Loic Carrique
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jenna Fix
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | | | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
| | - Max Renner
- Department of Chemistry, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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14
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Merritt TN, Pei J, Leung DW. Pathogenicity and virulence of human respiratory syncytial virus: Multifunctional nonstructural proteins NS1 and NS2. Virulence 2023:2283897. [PMID: 37964591 DOI: 10.1080/21505594.2023.2283897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Human respiratory syncytial virus (hRSV) is a major cause of acute lower respiratory tract infections in children under the age of two as well as in the elderly and immunocompromised worldwide. Despite its discovery over 60 years ago and the global impact on human health, limited specific and effective prophylactic or therapeutic options have been available for hRSV infections. Part of the lack of treatment options is attributed to the legacy of vaccine failure in the 1960s using a formalin-inactivated RSV (FI-RSV), which led to enhancement of disease post exposure to hRSV infection and hampered subsequent development of vaccine candidates. Recent FDA approval of a vaccine for older adults and impending approval for a maternal vaccine are major advancements but leaves children between 6 months and 5 years of age unprotected. Part of this limitation can be attributed to a lack of complete understanding of the factors that contribute to hRSV pathogenesis. The nonstructural proteins NS1 and NS2 are multifunctional virulence factors that are unique to hRSV and that play critical roles during hRSV infection, including antagonizing interferon (IFN) signalling to modulate host responses to hRSV infection. However, the molecular mechanisms by which the nonstructural proteins mediate their IFN inhibitory functions have not been completely defined. Current progress on the characterization of NS1 and NS2 during infection provides deeper insight into their roles. Furthermore, reverse genetics systems for hRSV provide a viable strategy to generate attenuated viruses by introduction of select mutations while maintaining immunogenicity required to elicit a long-term protective response. Here we will review the current state of knowledge of the nonstructural proteins, their contributions to RSV pathogenesis, and their potential as targets for therapeutic development.
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Affiliation(s)
- Trudy N Merritt
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jingjing Pei
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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15
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Swain J, Bierre M, Veyrié L, Richard CA, Eleouet JF, Muriaux D, Bajorek M. Selective targeting and clustering of phosphatidylserine lipids by RSV M protein is critical for virus particle production. J Biol Chem 2023; 299:105323. [PMID: 37805138 PMCID: PMC10641529 DOI: 10.1016/j.jbc.2023.105323] [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: 03/04/2023] [Revised: 09/16/2023] [Accepted: 09/23/2023] [Indexed: 10/09/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of infantile bronchiolitis in the developed world and of childhood deaths in resource-poor settings. The elderly and the immunosuppressed are also affected. It is a major unmet target for vaccines and antiviral drugs. RSV assembles and buds from the host cell plasma membrane by forming infectious viral particles which are mostly filamentous. A key interaction during RSV assembly is the interaction of the matrix (M) protein with cell plasma membrane lipids forming a layer at assembly sites. Although the structure of RSV M protein dimer is known, it is unclear how the viral M proteins interact with cell membrane lipids, and with which one, to promote viral assembly. Here, we demonstrate that M proteins are able to cluster at the plasma membrane by selectively binding with phosphatidylserine (PS). Our in vitro studies suggest that M binds PS lipid as a dimer and upon M oligomerization, PS clustering is observed. In contrast, the presence of other negatively charged lipids like PI(4, 5)P2 does not enhance M binding beyond control zwitterionic lipids, while cholesterol negatively affects M interaction with membrane lipids. Moreover, we show that the initial binding of the RSV M protein with PS lipids is independent of the cytoplasmic tail of the fusion (F) glycoprotein (FCT). Here, we highlight that M binding on membranes occurs directly through PS lipids, this interaction is electrostatic in nature, and M oligomerization generates PS clusters.
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Affiliation(s)
- Jitendriya Swain
- Virology and Molecular Immunology Unit (VIM), Animal Health Department, INRAE, IRIM, Montpellier, France
| | - Maxime Bierre
- INRAE, UVSQ, VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Laura Veyrié
- Virology and Molecular Immunology Unit (VIM), Animal Health Department, INRAE, IRIM, Montpellier, France
| | | | | | - Delphine Muriaux
- Virology and Molecular Immunology Unit (VIM), Animal Health Department, INRAE, IRIM, Montpellier, France.
| | - Monika Bajorek
- INRAE, UVSQ, VIM, Université Paris-Saclay, Jouy-en-Josas, France.
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16
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El Najjar F, Castillo SR, Moncman CL, Wu CY, Isla E, Velez Ortega AC, Frolenkov GI, Cifuentes-Munoz N, Dutch RE. Imaging analysis reveals budding of filamentous human metapneumovirus virions and direct transfer of inclusion bodies through intercellular extensions. mBio 2023; 14:e0158923. [PMID: 37681946 PMCID: PMC10653870 DOI: 10.1128/mbio.01589-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 09/09/2023] Open
Abstract
IMPORTANCE Human metapneumovirus is an important respiratory pathogen that causes significant morbidity and mortality, particularly in the very young, the elderly, and the immunosuppressed. However, the molecular details of how this virus spreads to new target cells are unclear. This work provides important new information on the formation of filamentous structures that are consistent with virus particles and adds critical new insight into the structure of extensions between cells that form during infection. In addition, it demonstrates for the first time the movement of viral replication centers through these intercellular extensions, representing a new mode of direct cell-to-cell spread that may be applicable to other viral systems.
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Affiliation(s)
- Farah El Najjar
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Santiago Restrepo Castillo
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Carole L. Moncman
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Cheng-Yu Wu
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Eduardo Isla
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | | | - Gregory I. Frolenkov
- Department of Physiology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Nicolas Cifuentes-Munoz
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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17
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Li Q, Gao P. Phase separation in cGAS-STING signaling. Front Med 2023; 17:855-866. [PMID: 37906339 DOI: 10.1007/s11684-023-1026-6] [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: 04/18/2023] [Accepted: 08/16/2023] [Indexed: 11/02/2023]
Abstract
Biomolecular condensates formed by phase separation are widespread and play critical roles in many physiological and pathological processes. cGAS-STING signaling functions to detect aberrant DNA signals to initiate anti-infection defense and antitumor immunity. At the same time, cGAS-STING signaling must be carefully regulated to maintain immune homeostasis. Interestingly, exciting recent studies have reported that biomolecular phase separation exists and plays important roles in different steps of cGAS-STING signaling, including cGAS condensates, STING condensates, and IRF3 condensates. In addition, several intracellular and extracellular factors have been proposed to modulate the condensates in cGAS-STING signaling. These studies reveal novel activation and regulation mechanisms of cGAS-STING signaling and provide new opportunities for drug discovery. Here, we summarize recent advances in the phase separation of cGAS-STING signaling and the development of potential drugs targeting these innate immune condensates.
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Affiliation(s)
- Quanjin Li
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Pu Gao
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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18
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Agac A, Kolbe SM, Ludlow M, Osterhaus ADME, Meineke R, Rimmelzwaan GF. Host Responses to Respiratory Syncytial Virus Infection. Viruses 2023; 15:1999. [PMID: 37896776 PMCID: PMC10611157 DOI: 10.3390/v15101999] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Respiratory syncytial virus (RSV) infections are a constant public health problem, especially in infants and older adults. Virtually all children will have been infected with RSV by the age of two, and reinfections are common throughout life. Since antigenic variation, which is frequently observed among other respiratory viruses such as SARS-CoV-2 or influenza viruses, can only be observed for RSV to a limited extent, reinfections may result from short-term or incomplete immunity. After decades of research, two RSV vaccines were approved to prevent lower respiratory tract infections in older adults. Recently, the FDA approved a vaccine for active vaccination of pregnant women to prevent severe RSV disease in infants during their first RSV season. This review focuses on the host response to RSV infections mediated by epithelial cells as the first physical barrier, followed by responses of the innate and adaptive immune systems. We address possible RSV-mediated immunomodulatory and pathogenic mechanisms during infections and discuss the current vaccine candidates and alternative treatment options.
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Affiliation(s)
| | | | | | | | | | - Guus F. Rimmelzwaan
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (A.A.); (S.M.K.); (M.L.); (A.D.M.E.O.); (R.M.)
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19
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Gonnin L, Desfosses A, Bacia-Verloop M, Chevret D, Galloux M, Éléouët JF, Gutsche I. Structural landscape of the respiratory syncytial virus nucleocapsids. Nat Commun 2023; 14:5732. [PMID: 37714861 PMCID: PMC10504348 DOI: 10.1038/s41467-023-41439-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
Human Respiratory Syncytial Virus (HRSV) is a prevalent cause of severe respiratory infections in children and the elderly. The helical HRSV nucleocapsid is a template for the viral RNA synthesis and a scaffold for the virion assembly. This cryo-electron microscopy analysis reveals the non-canonical arrangement of the HRSV nucleocapsid helix, composed of 16 nucleoproteins per asymmetric unit, and the resulting systematic variations in the RNA accessibility. We demonstrate that this unique helical symmetry originates from longitudinal interactions by the C-terminal arm of the HRSV nucleoprotein. We explore the polymorphism of the nucleocapsid-like assemblies, report five structures of the full-length particles and two alternative arrangements formed by a C-terminally truncated nucleoprotein mutant, and demonstrate the functional importance of the identified longitudinal interfaces. We put all these findings in the context of the HRSV RNA synthesis machinery and delineate the structural basis for its further investigation.
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Affiliation(s)
- Lorène Gonnin
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
- VIM, Paris-Saclay University, INRAE, 78350, Jouy-en-Josas, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Didier Chevret
- VIM, Paris-Saclay University, INRAE, 78350, Jouy-en-Josas, France
| | - Marie Galloux
- VIM, Paris-Saclay University, INRAE, 78350, Jouy-en-Josas, France
| | | | - Irina Gutsche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
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20
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Diot C, Richard CA, Risso-Ballester J, Martin D, Fix J, Eléouët JF, Sizun C, Rameix-Welti MA, Galloux M. Hardening of Respiratory Syncytial Virus Inclusion Bodies by Cyclopamine Proceeds through Perturbation of the Interactions of the M2-1 Protein with RNA and the P Protein. Int J Mol Sci 2023; 24:13862. [PMID: 37762166 PMCID: PMC10531356 DOI: 10.3390/ijms241813862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/20/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Respiratory syncytial virus (RSV) RNA synthesis takes place in cytoplasmic viral factories also called inclusion bodies (IBs), which are membrane-less organelles concentrating the viral RNA polymerase complex. The assembly of IBs is driven by liquid-liquid phase separation promoted by interactions between the viral nucleoprotein N and the phosphoprotein P. We recently demonstrated that cyclopamine (CPM) inhibits RSV multiplication by disorganizing and hardening IBs. Although a single mutation in the viral transcription factor M2-1 induced resistance to CPM, the mechanism of action of CPM still remains to be characterized. Here, using FRAP experiments on reconstituted pseudo-IBs both in cellula and in vitro, we first demonstrated that CPM activity depends on the presence of M2-1 together with N and P. We showed that CPM impairs the competition between P and RNA binding to M2-1. As mutations on both P and M2-1 induced resistance against CPM activity, we suggest that CPM may affect the dynamics of the M2-1-P interaction, thereby affecting the relative mobility of the proteins contained in RSV IBs. Overall, our results reveal that stabilizing viral protein-protein interactions is an attractive new antiviral approach. They pave the way for the rational chemical optimization of new specific anti-RSV molecules.
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Affiliation(s)
- Cédric Diot
- Institut Pasteur, Université Paris Cité, M3P, F-75015 Paris, France;
- INSERM, UMR 1173 (2I), Université Paris-Saclay-Versailles St. Quentin, M3P, F-78180 Versailles, France;
| | - Charles-Adrien Richard
- INRAE, Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St. Quentin, F-78350 Jouy-en-Josas, France; (C.-A.R.); (D.M.); (J.F.); (J.-F.E.)
| | - Jennifer Risso-Ballester
- INSERM, UMR 1173 (2I), Université Paris-Saclay-Versailles St. Quentin, M3P, F-78180 Versailles, France;
| | - Davy Martin
- INRAE, Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St. Quentin, F-78350 Jouy-en-Josas, France; (C.-A.R.); (D.M.); (J.F.); (J.-F.E.)
| | - Jenna Fix
- INRAE, Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St. Quentin, F-78350 Jouy-en-Josas, France; (C.-A.R.); (D.M.); (J.F.); (J.-F.E.)
| | - Jean-François Eléouët
- INRAE, Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St. Quentin, F-78350 Jouy-en-Josas, France; (C.-A.R.); (D.M.); (J.F.); (J.-F.E.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France;
| | - Marie-Anne Rameix-Welti
- INSERM, UMR 1173 (2I), Université Paris-Saclay-Versailles St. Quentin, M3P, F-78180 Versailles, France;
- Laboratoire de Microbiologie, Hôpital Ambroise Paré, Assistance Publique des Hôpitaux de Paris, DMU15, F-75015 Paris, France
| | - Marie Galloux
- INRAE, Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St. Quentin, F-78350 Jouy-en-Josas, France; (C.-A.R.); (D.M.); (J.F.); (J.-F.E.)
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21
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Salgueiro M, Camporeale G, Visentin A, Aran M, Pellizza L, Esperante SA, Corbat A, Grecco H, Sousa B, Esperón R, Borkosky SS, de Prat-Gay G. Molten Globule Driven and Self-downmodulated Phase Separation of a Viral Factory Scaffold. J Mol Biol 2023; 435:168153. [PMID: 37210029 DOI: 10.1016/j.jmb.2023.168153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
Viral factories of liquid-like nature serve as sites for transcription and replication in most viruses. The respiratory syncytial virus factories include replication proteins, brought together by the phosphoprotein (P) RNA polymerase cofactor, present across non-segmented negative stranded RNA viruses. Homotypic liquid-liquid phase separation of RSV-P is governed by an α-helical molten globule domain, and strongly self-downmodulated by adjacent sequences. Condensation of P with the nucleoprotein N is stoichiometrically tuned, defining aggregate-droplet and droplet-dissolution boundaries. Time course analysis show small N-P nuclei gradually coalescing into large granules in transfected cells. This behavior is recapitulated in infection, with small puncta evolving to large viral factories, strongly suggesting that P-N nucleation-condensation sequentially drives viral factories. Thus, the tendency of P to undergo phase separation is moderate and latent in the full-length protein but unleashed in the presence of N or when neighboring disordered sequences are deleted. This, together with its capacity to rescue nucleoprotein-RNA aggregates suggests a role as a "solvent-protein".
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Affiliation(s)
- Mariano Salgueiro
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Gabriela Camporeale
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Araceli Visentin
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Martin Aran
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Leonardo Pellizza
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | | | - Agustín Corbat
- Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, and IFIBA, CONICET, Buenos Aires, Argentina
| | - Hernán Grecco
- Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, and IFIBA, CONICET, Buenos Aires, Argentina
| | - Belén Sousa
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Ramiro Esperón
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Silvia S Borkosky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina.
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22
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Zhang S, Pei G, Li B, Li P, Lin Y. Abnormal phase separation of biomacromolecules in human diseases. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1133-1152. [PMID: 37475546 PMCID: PMC10423695 DOI: 10.3724/abbs.2023139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Membrane-less organelles (MLOs) formed through liquid-liquid phase separation (LLPS) are associated with numerous important biological functions, but the abnormal phase separation will also dysregulate the physiological processes. Emerging evidence points to the importance of LLPS in human health and diseases. Nevertheless, despite recent advancements, our knowledge of the molecular relationship between LLPS and diseases is frequently incomplete. In this review, we outline our current understanding about how aberrant LLPS affects developmental disorders, tandem repeat disorders, cancers and viral infection. We also examine disease mechanisms driven by aberrant condensates, and highlight potential treatment approaches. This study seeks to expand our understanding of LLPS by providing a valuable new paradigm for understanding phase separation and human disorders, as well as to further translate our current knowledge regarding LLPS into therapeutic discoveries.
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Affiliation(s)
- Songhao Zhang
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Gaofeng Pei
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Boya Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Pilong Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Yi Lin
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
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23
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Xie E, Ahmad S, Smyth RP, Sieben C. Advanced fluorescence microscopy in respiratory virus cell biology. Adv Virus Res 2023; 116:123-172. [PMID: 37524480 DOI: 10.1016/bs.aivir.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.
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Affiliation(s)
- Enyu Xie
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany; Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Christian Sieben
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany.
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24
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Liu Y, Yao Z, Lian G, Yang P. Biomolecular phase separation in stress granule assembly and virus infection. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1099-1118. [PMID: 37401177 PMCID: PMC10415189 DOI: 10.3724/abbs.2023117] [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: 12/28/2022] [Accepted: 05/06/2023] [Indexed: 07/05/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a crucial mechanism for cellular compartmentalization. One prominent example of this is the stress granule. Found in various types of cells, stress granule is a biomolecular condensate formed through phase separation. It comprises numerous RNA and RNA-binding proteins. Over the past decades, substantial knowledge has been gained about the composition and dynamics of stress granules. SGs can regulate various signaling pathways and have been associated with numerous human diseases, such as neurodegenerative diseases, cancer, and infectious diseases. The threat of viral infections continues to loom over society. Both DNA and RNA viruses depend on host cells for replication. Intriguingly, many stages of the viral life cycle are closely tied to RNA metabolism in human cells. The field of biomolecular condensates has rapidly advanced in recent times. In this context, we aim to summarize research on stress granules and their link to viral infections. Notably, stress granules triggered by viral infections behave differently from the canonical stress granules triggered by sodium arsenite (SA) and heat shock. Studying stress granules in the context of viral infections could offer a valuable platform to link viral replication processes and host anti-viral responses. A deeper understanding of these biological processes could pave the way for innovative interventions and treatments for viral infectious diseases. They could potentially bridge the gap between basic biological processes and interactions between viruses and their hosts.
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Affiliation(s)
- Yi Liu
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Zhiying Yao
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Guiwei Lian
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Peiguo Yang
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
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25
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Visentin A, Demitroff N, Salgueiro M, Borkosky SS, Uversky VN, Camporeale G, de Prat-Gay G. Assembly of the Tripartite and RNA Condensates of the Respiratory Syncytial Virus Factory Proteins In Vitro: Role of the Transcription Antiterminator M 2-1. Viruses 2023; 15:1329. [PMID: 37376628 DOI: 10.3390/v15061329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
A wide variety of viruses replicate in liquid-like viral factories. Non-segmented negative stranded RNA viruses share a nucleoprotein (N) and a phosphoprotein (P) that together emerge as the main drivers of liquid-liquid phase separation. The respiratory syncytial virus includes the transcription antiterminator M2-1, which binds RNA and maximizes RNA transcriptase processivity. We recapitulate the assembly mechanism of condensates of the three proteins and the role played by RNA. M2-1 displays a strong propensity for condensation by itself and with RNA through the formation of electrostatically driven protein-RNA coacervates based on the amphiphilic behavior of M2-1 and finely tuned by stoichiometry. M2-1 incorporates into tripartite condensates with N and P, modulating their size through an interplay with P, where M2-1 is both client and modulator. RNA is incorporated into the tripartite condensates adopting a heterogeneous distribution, reminiscent of the M2-1-RNA IBAG granules within the viral factories. Ionic strength dependence indicates that M2-1 behaves differently in the protein phase as opposed to the protein-RNA phase, in line with the subcompartmentalization observed in viral factories. This work dissects the biochemical grounds for the formation and fate of the RSV condensates in vitro and provides clues to interrogate the mechanism under the highly complex infection context.
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Affiliation(s)
- Araceli Visentin
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Nicolás Demitroff
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Mariano Salgueiro
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Silvia Susana Borkosky
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Gabriela Camporeale
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Gonzalo de Prat-Gay
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
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26
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Li Z, Zheng M, He Z, Qin Y, Chen M. Morphogenesis and functional organization of viral inclusion bodies. CELL INSIGHT 2023; 2:100103. [PMID: 37193093 PMCID: PMC10164783 DOI: 10.1016/j.cellin.2023.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/18/2023]
Abstract
Eukaryotic viruses are obligate intracellular parasites that rely on the host cell machinery to carry out their replication cycle. This complex process involves a series of steps, starting with virus entry, followed by genome replication, and ending with virion assembly and release. Negative strand RNA and some DNA viruses have evolved to alter the organization of the host cell interior to create a specialized environment for genome replication, known as IBs, which are precisely orchestrated to ensure efficient viral replication. The biogenesis of IBs requires the cooperation of both viral and host factors. These structures serve multiple functions during infection, including sequestering viral nucleic acids and proteins from innate immune responses, increasing the local concentration of viral and host factors, and spatially coordinating consecutive replication cycle steps. While ultrastructural and functional studies have improved our understanding of IBs, much remains to be learned about the precise mechanisms of IB formation and function. This review aims to summarize the current understanding of how IBs are formed, describe the morphology of these structures, and highlight the mechanism of their functions. Given that the formation of IBs involves complex interactions between the virus and the host cell, the role of both viral and cellular organelles in this process is also discussed.
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Affiliation(s)
- Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Miaomiao Zheng
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Zhicheng He
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, 430200, China
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27
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Yang S, Shen W, Hu J, Cai S, Zhang C, Jin S, Guan X, Wu J, Wu Y, Cui J. Molecular mechanisms and cellular functions of liquid-liquid phase separation during antiviral immune responses. Front Immunol 2023; 14:1162211. [PMID: 37251408 PMCID: PMC10210139 DOI: 10.3389/fimmu.2023.1162211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Spatiotemporal separation of cellular components is vital to ensure biochemical processes. Membrane-bound organelles such as mitochondria and nuclei play a major role in isolating intracellular components, while membraneless organelles (MLOs) are accumulatively uncovered via liquid-liquid phase separation (LLPS) to mediate cellular spatiotemporal organization. MLOs orchestrate various key cellular processes, including protein localization, supramolecular assembly, gene expression, and signal transduction. During viral infection, LLPS not only participates in viral replication but also contributes to host antiviral immune responses. Therefore, a more comprehensive understanding of the roles of LLPS in virus infection may open up new avenues for treating viral infectious diseases. In this review, we focus on the antiviral defense mechanisms of LLPS in innate immunity and discuss the involvement of LLPS during viral replication and immune evasion escape, as well as the strategy of targeting LLPS to treat viral infectious diseases.
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Affiliation(s)
- Shuai Yang
- The First Affiliated Hospital of Sun Yat-sen University, Ministry of Education MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Weishan Shen
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiajia Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Sihui Cai
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chenqiu Zhang
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shouheng Jin
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiangdong Guan
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jianfeng Wu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yaoxing Wu
- The First Affiliated Hospital of Sun Yat-sen University, Ministry of Education MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jun Cui
- The First Affiliated Hospital of Sun Yat-sen University, Ministry of Education MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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28
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Brodrick AJ, Broadbent AJ. The Formation and Function of Birnaviridae Virus Factories. Int J Mol Sci 2023; 24:ijms24108471. [PMID: 37239817 DOI: 10.3390/ijms24108471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
The use of infectious bursal disease virus (IBDV) reverse genetics to engineer tagged reporter viruses has revealed that the virus factories (VFs) of the Birnaviridae family are biomolecular condensates that show properties consistent with liquid-liquid phase separation (LLPS). Although the VFs are not bound by membranes, it is currently thought that viral protein 3 (VP3) initially nucleates the formation of the VF on the cytoplasmic leaflet of early endosomal membranes, and likely drives LLPS. In addition to VP3, IBDV VFs contain VP1 (the viral polymerase) and the dsRNA genome, and they are the sites of de novo viral RNA synthesis. Cellular proteins are also recruited to the VFs, which are likely to provide an optimal environment for viral replication; the VFs grow due to the synthesis of the viral components, the recruitment of other proteins, and the coalescence of multiple VFs in the cytoplasm. Here, we review what is currently known about the formation, properties, composition, and processes of these structures. Many open questions remain regarding the biophysical nature of the VFs, as well as the roles they play in replication, translation, virion assembly, viral genome partitioning, and in modulating cellular processes.
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Affiliation(s)
- Andrew J Brodrick
- Department of Animal and Avian Sciences, University of Maryland, 8127 Regents Drive, College Park, MD 20742, USA
| | - Andrew J Broadbent
- Department of Animal and Avian Sciences, University of Maryland, 8127 Regents Drive, College Park, MD 20742, USA
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29
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Quek RT, Hardy KS, Walker SG, Nguyen DT, de Almeida
Magalhães T, Salic A, Gopalakrishnan SM, Silver PA, Mitchison TJ. Screen for Modulation of Nucleocapsid Protein Condensation Identifies Small Molecules with Anti-Coronavirus Activity. ACS Chem Biol 2023; 18:583-594. [PMID: 36795767 PMCID: PMC9942534 DOI: 10.1021/acschembio.2c00908] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
Biomolecular condensates formed by liquid-liquid phase separation have been implicated in multiple diseases. Modulation of condensate dynamics by small molecules has therapeutic potential, but so far, few condensate modulators have been disclosed. The SARS-CoV-2 nucleocapsid (N) protein forms phase-separated condensates that are hypothesized to play critical roles in viral replication, transcription, and packaging, suggesting that N condensation modulators might have anti-coronavirus activity across multiple strains and species. Here, we show that N proteins from all seven human coronaviruses (HCoVs) vary in their tendency to undergo phase separation when expressed in human lung epithelial cells. We developed a cell-based high-content screening platform and identified small molecules that both promote and inhibit condensation of SARS-CoV-2 N. Interestingly, these host-targeted small molecules exhibited condensate-modulatory effects across all HCoV Ns. Some have also been reported to exhibit antiviral activity against SARS-CoV-2, HCoV-OC43, and HCoV-229E viral infections in cell culture. Our work reveals that the assembly dynamics of N condensates can be regulated by small molecules with therapeutic potential. Our approach allows for screening based on viral genome sequences alone and might enable rapid paths to drug discovery with value for confronting future pandemics.
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Affiliation(s)
- Rui Tong Quek
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | - Kierra S. Hardy
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | - Stephen G. Walker
- Drug Discovery Science and Technology,
AbbVie Inc., North Chicago, Illinois 60064, United
States
| | - Dan T. Nguyen
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | | | - Adrian Salic
- Department of Cell Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
| | | | - Pamela A. Silver
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | - Timothy J. Mitchison
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
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30
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Sagan SM, Weber SC. Let's phase it: viruses are master architects of biomolecular condensates. Trends Biochem Sci 2023; 48:229-243. [PMID: 36272892 DOI: 10.1016/j.tibs.2022.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/15/2022]
Abstract
Viruses compartmentalize their replication and assembly machinery to both evade detection and concentrate the viral proteins and nucleic acids necessary for genome replication and virion production. Accumulating evidence suggests that diverse RNA and DNA viruses form replication organelles and nucleocapsid assembly sites using phase separation. In general, the biogenesis of these compartments is regulated by two types of viral protein, collectively known as antiterminators and nucleocapsid proteins, respectively. Herein, we discuss how RNA viruses establish replication organelles and nucleocapsid assembly sites, and the evidence that these compartments form through phase separation. While this review focuses on RNA viruses, accumulating evidence suggests that all viruses rely on phase separation and form biomolecular condensates important for completing the infectious cycle.
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Affiliation(s)
- Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada.
| | - Stephanie C Weber
- Department of Biology, McGill University, Montreal, QC, Canada; Department of Physics, McGill University, Montreal, QC, Canada
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31
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Scrima N, Le Bars R, Nevers Q, Glon D, Chevreux G, Civas A, Blondel D, Lagaudrière-Gesbert C, Gaudin Y. Rabies virus P protein binds to TBK1 and interferes with the formation of innate immunity-related liquid condensates. Cell Rep 2023; 42:111949. [PMID: 36640307 DOI: 10.1016/j.celrep.2022.111949] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 07/27/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
Viruses must overcome the interferon-mediated antiviral response to replicate and propagate into their host. Rabies virus (RABV) phosphoprotein P is known to inhibit interferon induction. Here, using a global mass spectrometry approach, we show that RABV P binds to TBK1, a kinase located at the crossroads of many interferon induction pathways, resulting in innate immunity inhibition. Mutations of TBK1 phosphorylation sites abolish P binding. Importantly, we demonstrate that upon RABV infection or detection of dsRNA by innate immunity sensors, TBK1 and its adaptor proteins NAP1 and SINTBAD form dynamic cytoplasmic condensates that have liquid properties. These condensates can form larger aggregates having ring-like structures in which NAP1 and TBK1 exhibit locally restricted movement. P binding to TBK1 interferes with the formation of these structures. This work demonstrates that proteins of the signaling pathway leading to interferon induction transiently form liquid organelles that can be targeted by viruses.
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Affiliation(s)
- Nathalie Scrima
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Romain Le Bars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Quentin Nevers
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Damien Glon
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | | | - Ahmet Civas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Danielle Blondel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
| | - Yves Gaudin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
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32
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Sutto-Ortiz P, Eléouët JF, Ferron F, Decroly E. Biochemistry of the Respiratory Syncytial Virus L Protein Embedding RNA Polymerase and Capping Activities. Viruses 2023; 15:v15020341. [PMID: 36851554 PMCID: PMC9960070 DOI: 10.3390/v15020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
The human respiratory syncytial virus (RSV) is a negative-sense, single-stranded RNA virus. It is the major cause of severe acute lower respiratory tract infection in infants, the elderly population, and immunocompromised individuals. There is still no approved vaccine or antiviral treatment against RSV disease, but new monoclonal prophylactic antibodies are yet to be commercialized, and clinical trials are in progress. Hence, urgent efforts are needed to develop efficient therapeutic treatments. RSV RNA synthesis comprises viral transcription and replication that are catalyzed by the large protein (L) in coordination with the phosphoprotein polymerase cofactor (P), the nucleoprotein (N), and the M2-1 transcription factor. The replication/transcription is orchestrated by the L protein, which contains three conserved enzymatic domains: the RNA-dependent RNA polymerase (RdRp), the polyribonucleotidyl transferase (PRNTase or capping), and the methyltransferase (MTase) domain. These activities are essential for the RSV replicative cycle and are thus considered as attractive targets for the development of therapeutic agents. In this review, we summarize recent findings about RSV L domains structure that highlight how the enzymatic activities of RSV L domains are interconnected, discuss the most relevant and recent antivirals developments that target the replication/transcription complex, and conclude with a perspective on identified knowledge gaps that enable new research directions.
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Affiliation(s)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, F78350 Jouy en Josas, France
| | - François Ferron
- Aix Marseille Université, CNRS, AFMB, UMR, 7257 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB, UMR, 7257 Marseille, France
- Correspondence:
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Liaisons dangereuses: Intrinsic Disorder in Cellular Proteins Recruited to Viral Infection-Related Biocondensates. Int J Mol Sci 2023; 24:ijms24032151. [PMID: 36768473 PMCID: PMC9917183 DOI: 10.3390/ijms24032151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is responsible for the formation of so-called membrane-less organelles (MLOs) that are essential for the spatio-temporal organization of the cell. Intrinsically disordered proteins (IDPs) or regions (IDRs), either alone or in conjunction with nucleic acids, are involved in the formation of these intracellular condensates. Notably, viruses exploit LLPS at their own benefit to form viral replication compartments. Beyond giving rise to biomolecular condensates, viral proteins are also known to partition into cellular MLOs, thus raising the question as to whether these cellular phase-separating proteins are drivers of LLPS or behave as clients/regulators. Here, we focus on a set of eukaryotic proteins that are either sequestered in viral factories or colocalize with viral proteins within cellular MLOs, with the primary goal of gathering organized, predicted, and experimental information on these proteins, which constitute promising targets for innovative antiviral strategies. Using various computational approaches, we thoroughly investigated their disorder content and inherent propensity to undergo LLPS, along with their biological functions and interactivity networks. Results show that these proteins are on average, though to varying degrees, enriched in disorder, with their propensity for phase separation being correlated, as expected, with their disorder content. A trend, which awaits further validation, tends to emerge whereby the most disordered proteins serve as drivers, while more ordered cellular proteins tend instead to be clients of viral factories. In light of their high disorder content and their annotated LLPS behavior, most proteins in our data set are drivers or co-drivers of molecular condensation, foreshadowing a key role of these cellular proteins in the scaffolding of viral infection-related MLOs.
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [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] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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35
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Brownsword MJ, Locker N. A little less aggregation a little more replication: Viral manipulation of stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1741. [PMID: 35709333 PMCID: PMC10078398 DOI: 10.1002/wrna.1741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Matthew J. Brownsword
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
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36
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Nevers Q, Scrima N, Glon D, Le Bars R, Decombe A, Garnier N, Ouldali M, Lagaudrière-Gesbert C, Blondel D, Albertini A, Gaudin Y. Properties of rabies virus phosphoprotein and nucleoprotein biocondensates formed in vitro and in cellulo. PLoS Pathog 2022; 18:e1011022. [PMID: 36480574 PMCID: PMC9767369 DOI: 10.1371/journal.ppat.1011022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 12/20/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Rabies virus (RABV) transcription and replication take place within viral factories having liquid properties, called Negri bodies (NBs), that are formed by liquid-liquid phase separation (LLPS). The co-expression of RABV nucleoprotein (N) and phosphoprotein (P) in mammalian cells is sufficient to induce the formation of cytoplasmic biocondensates having properties that are like those of NBs. This cellular minimal system was previously used to identify P domains that are essential for biocondensates formation. Here, we constructed fluorescent versions of N and analyzed by FRAP their dynamics inside the biocondensates formed in this minimal system as well as in NBs of RABV-infected cells using FRAP. The behavior of N appears to be different of P as there was no fluorescence recovery of N proteins after photobleaching. We also identified arginine residues as well as two exposed loops of N involved in condensates formation. Corresponding N mutants exhibited distinct phenotypes in infected cells ranging from co-localization with NBs to exclusion from them associated with a dominant-negative effect on infection. We also demonstrated that in vitro, in crowded environments, purified P as well as purified N0-P complex (in which N is RNA-free) form liquid condensates. We identified P domains required for LLPS in this acellular system. P condensates were shown to associate with liposomes, concentrate RNA, and undergo a liquid-gel transition upon ageing. Conversely, N0-P droplets were disrupted upon incubation with RNA. Taken together, our data emphasize the central role of P in NBs formation and reveal some physicochemical features of P and N0-P droplets relevant for explaining NBs properties such as their envelopment by cellular membranes at late stages of infection and nucleocapsids ejections from the viral factories.
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Affiliation(s)
- Quentin Nevers
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nathalie Scrima
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Damien Glon
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Romain Le Bars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alice Decombe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nathalie Garnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Danielle Blondel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Albertini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Gaudin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail:
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37
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Li H, Ernst C, Kolonko-Adamska M, Greb-Markiewicz B, Man J, Parissi V, Ng BWL. Phase separation in viral infections. Trends Microbiol 2022; 30:1217-1231. [PMID: 35902318 DOI: 10.1016/j.tim.2022.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 01/13/2023]
Abstract
Viruses rely on the reprogramming of cellular processes to enable efficient viral replication; this often requires subcompartmentalization within the host cell. Liquid-liquid phase separation (LLPS) has emerged as a fundamental principle to organize and subdivide cellular processes, and plays an important role in viral life cycles. Despite substantial advances in the field, elucidating the exact organization and function of these organelles remains a major challenge. In this review, we summarize the biochemical basis of condensate formation, the role of LLPS during viral infection, and interplay of LLPS with innate immune responses. Finally, we discuss possible strategies and molecules to modulate LLPS during viral infections.
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Affiliation(s)
- Haohua Li
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christina Ernst
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marta Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jackie Man
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong; Faculty of Medicine, Imperial College, London, UK
| | - Vincent Parissi
- Microbiologie Fondamentale et Pathogénicité Laboratory (MPF), UMR 5234, « Mobility of pathogenic genomes and chromatin dynamics » team (MobilVIR), CNRS-University of Bordeaux, Bordeaux, France
| | - Billy Wai-Lung Ng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
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38
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BenDavid E, Pfaller CK, Pan Y, Samuel CE, Ma D. Host 5'-3' Exoribonuclease XRN1 Acts as a Proviral Factor for Measles Virus Replication by Downregulating the dsRNA-Activated Kinase PKR. J Virol 2022; 96:e0131922. [PMID: 36300942 PMCID: PMC9683022 DOI: 10.1128/jvi.01319-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 11/20/2022] Open
Abstract
Many negative-sense RNA viruses, including measles virus (MeV), are thought to carry out much of their viral replication in cytoplasmic membraneless foci known as inclusion bodies (IBs). The mechanisms by which IBs facilitate efficient viral replication remain largely unknown but may involve an intricate network of regulation at the host-virus interface. Viruses are able to modulate such interactions by a variety of strategies including adaptation of their genomes and "hijacking" of host proteins. The latter possibility broadens the molecular reservoir available for a virus to enhance its replication and/or antagonize host antiviral responses. Here, we show that the cellular 5'-3' exoribonuclease, XRN1, is a host protein hijacked by MeV. We found that upon MeV infection, XRN1 is translocated to cytoplasmic IBs where it acts in a proviral manner by preventing the accumulation of double-stranded RNA (dsRNA) within the IBs. This leads to the suppression of the dsRNA-induced innate immune responses mediated via the protein kinase R (PKR)-integrated stress response (ISR) pathway. IMPORTANCE Measles virus remains a major global health threat due to its high transmissibility and significant morbidity in children and immunocompromised individuals. Although there is an effective vaccine against MeV, a large population in the world remains without access to the vaccine, contributing to more than 7,000,000 measles cases and 60,000 measles deaths in 2020 (CDC). For negative-sense RNA viruses including MeV, one active research area is the exploration of virus-host interactions occurring at cytoplasmic IBs where viral replication takes place. In this study we present evidence suggesting a model in which MeV IBs antagonize host innate immunity by recruiting XRN1 to reduce dsRNA accumulation and subsequent PKR kinase activation/ISR induction. In the absence of XRN1, the increased dsRNA level acts as a potent activator of the antiviral PKR/ISR pathway leading to suppression of global cap-dependent mRNA translation and inhibition of viral replication.
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Affiliation(s)
- Ethan BenDavid
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
| | | | - Yue Pan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Charles E. Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
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Rahman SK, Ampah KK, Roy P. Role of NS2 specific RNA binding and phosphorylation in liquid-liquid phase separation and virus assembly. Nucleic Acids Res 2022; 50:11273-11284. [PMID: 36259663 DOI: 10.1093/nar/gkac904] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/13/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) has assumed a prominent role in biological cell systems, where it underpins the formation of subcellular compartments necessary for cell function. We investigated the underlying mechanism of LLPS in virus infected cells, where virus inclusion bodies are formed by an RNA-binding phosphoprotein (NS2) of Bluetongue virus to serve as sites for subviral particle assembly and virus maturation. We show that NS2 undergoes LLPS that is dependent on protein phosphorylation and RNA-binding and that LLPS occurrence is accompanied by a change in protein secondary structure. Site-directed mutagenesis identified two critical arginine residues in NS2 responsible for specific RNA binding and thus for NS2-RNA complex driven LLPS. Reverse genetics identified the same residues as essential for VIB assembly in infected cells and virus viability. Our findings suggest that a specific arginine-RNA interaction in the context of a phosphorylated state drives LLPS in this, and possibly other, virus infections.
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Affiliation(s)
- Shah Kamranur Rahman
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT UK
| | - Khamal Kwesi Ampah
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT UK
| | - Polly Roy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT UK
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40
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Wu C, Holehouse AS, Leung DW, Amarasinghe GK, Dutch RE. Liquid Phase Partitioning in Virus Replication: Observations and Opportunities. Annu Rev Virol 2022; 9:285-306. [PMID: 35709511 DOI: 10.1146/annurev-virology-093020-013659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus replication is poorly understood. Recent research supports phase separation as a foundational principle for organization of cellular components with the potential to influence viral replication. In this review, phase separation is described in the context of formation of viral replication centers, with an emphasis on the nonsegmented negative-strand RNA viruses. Consideration is given to the interplay between phase separation and the critical processes of viral transcription and genome replication, and the role of these regions in pathogen-host interactions is discussed. Finally, critical questions that must be addressed to fully understand how phase separation influences viral replication and the viral life cycle are presented, along with information about new approaches that could be used to make important breakthroughs in this emerging field.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Science and Engineering Living Systems, Washington University, St. Louis, Missouri, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA;
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41
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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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42
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Wei W, Bai L, Yan B, Meng W, Wang H, Zhai J, Si F, Zheng C. When liquid-liquid phase separation meets viral infections. Front Immunol 2022; 13:985622. [PMID: 36016945 PMCID: PMC9395683 DOI: 10.3389/fimmu.2022.985622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic cells have both membranous and membraneless organelles. While the formation mechanism of membranous organelles is well understood, the formation mechanism of membraneless organelles remains unknown. Many biomolecules in the cytoplasm transition from the liquid phase to the agglutinated phase are known as liquid-liquid phase separation (LLPS). The biomolecular agglomerates’ physical properties enable them to function as dynamic compartments that respond to external pressures and stimuli. Scientists have gradually recognized the importance of phase separation during viral infections. LLPS provides a powerful new framework for understanding the viral life cycle from viral replication to evasion of host immune surveillance. As a result, this review focuses on the progress of LLPS research in viral infection and immune regulation to provide clues for antiviral therapeutic strategies.
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Affiliation(s)
- Wenqiang Wei
- Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Lu Bai
- Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Bing Yan
- Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Weiquan Meng
- Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Hongju Wang
- Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Jingbo Zhai
- Medical College, Inner Mongolia Minzu University, Tongliao, China
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao, China
| | - Fusheng Si
- Institute of Animal Science and Veterinary Medicine, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Chunfu Zheng, ; Fusheng Si,
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- *Correspondence: Chunfu Zheng, ; Fusheng Si,
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43
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Gonnin L, Richard CA, Gutsche I, Chevret D, Troussier J, Vasseur JJ, Debart F, Eléouët JF, Galloux M. Importance of RNA length for in vitro encapsidation by the nucleoprotein of human Respiratory Syncytial Virus. J Biol Chem 2022; 298:102337. [PMID: 35931116 PMCID: PMC9436823 DOI: 10.1016/j.jbc.2022.102337] [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: 04/23/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
Respiratory syncytial virus has a negative-sense single-stranded RNA genome constitutively encapsidated by the viral nucleoprotein N, forming a helical nucleocapsid which is the template for viral transcription and replication by the viral polymerase L. Recruitment of L onto the nucleocapsid depends on the viral phosphoprotein P, which is an essential L cofactor. A prerequisite for genome and antigenome encapsidation is the presence of the monomeric, RNA-free, neosynthesized N protein, named N0. Stabilization of N0 depends on the binding of the N-terminal residues of P to its surface, which prevents N oligomerization. However, the mechanism involved in the transition from N0-P to nucleocapsid assembly, and thus in the specificity of viral genome encapsidation, is still unknown. Furthermore, the specific role of N oligomerization and RNA in the morphogenesis of viral factories, where viral transcription and replication occur, have not been elucidated although the interaction between P and N complexed to RNA has been shown to be responsible for this process. Here, using a chimeric protein comprising N and the first 40 N-terminal residues of P, we succeeded in purifying a recombinant N0-like protein competent for RNA encapsidation in vitro. Our results showed the importance of RNA length for stable encapsidation and revealed that the nature of the 5′ end of RNA does not explain the specificity of encapsidation. Finally, we showed that RNA encapsidation is crucial for the in vitro reconstitution of pseudo-viral factories. Together, our findings provide insight into respiratory syncytial virus viral genome encapsidation specificity.
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Affiliation(s)
- Lorène Gonnin
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Irina Gutsche
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Didier Chevret
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Joris Troussier
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Françoise Debart
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France.
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44
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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45
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Cosentino G, Marougka K, Desquesnes A, Welti N, Sitterlin D, Gault E, Rameix-Welti MA. Respiratory syncytial virus ribonucleoproteins hijack microtubule Rab11 dependent transport for intracellular trafficking. PLoS Pathog 2022; 18:e1010619. [PMID: 35797399 PMCID: PMC9262236 DOI: 10.1371/journal.ppat.1010619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/25/2022] [Indexed: 01/31/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the primary cause of severe respiratory infection in infants worldwide. Replication of RSV genomic RNA occurs in cytoplasmic inclusions generating viral ribonucleoprotein complexes (vRNPs). vRNPs then reach assembly and budding sites at the plasma membrane. However, mechanisms ensuring vRNPs transportation are unknown. We generated a recombinant RSV harboring fluorescent RNPs allowing us to visualize moving vRNPs in living infected cells and developed an automated imaging pipeline to characterize the movements of vRNPs at a high throughput. Automatic tracking of vRNPs revealed that around 10% of the RNPs exhibit fast and directed motion compatible with transport along the microtubules. Visualization of vRNPs moving along labeled microtubules and restriction of their movements by microtubule depolymerization further support microtubules involvement in vRNPs trafficking. Approximately 30% of vRNPs colocalize with Rab11a protein, a marker of the endosome recycling (ER) pathway and we observed vRNPs and Rab11-labeled vesicles moving together. Transient inhibition of Rab11a expression significantly reduces vRNPs movements demonstrating Rab11 involvement in RNPs trafficking. Finally, Rab11a is specifically immunoprecipitated with vRNPs in infected cells suggesting an interaction between Rab11 and the vRNPs. Altogether, our results strongly suggest that RSV RNPs move on microtubules by hijacking the ER pathway.
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Affiliation(s)
- Gina Cosentino
- Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Versailles, France
| | - Katherine Marougka
- Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Versailles, France
| | - Aurore Desquesnes
- Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Versailles, France
| | - Nicolas Welti
- Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Versailles, France
| | - Delphine Sitterlin
- Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Versailles, France
| | - Elyanne Gault
- Université Paris-Saclay, Université de Versailles St. Quentin; UMR 1173 (2I), INSERM; Assistance Publique des Hôpitaux de Paris, Hôpital Ambroise Paré, Laboratoire de Microbiologie, DMU15; Versailles, France
| | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, Université de Versailles St. Quentin; UMR 1173 (2I), INSERM; Assistance Publique des Hôpitaux de Paris, Hôpital Ambroise Paré, Laboratoire de Microbiologie, DMU15; Versailles, France
- * E-mail:
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Abstract
Filovirus-infected cells are characterized by typical cytoplasmic inclusion bodies (IBs) located in the perinuclear region. The formation of these IBs is induced mainly by the accumulation of the filoviral nucleoprotein NP, which recruits the other nucleocapsid proteins, the polymerase co-factor VP35, the polymerase L, the transcription factor VP30 and VP24 via direct or indirect protein-protein interactions. Replication of the negative-strand RNA genomes by the viral polymerase L and VP35 occurs in the IBs, resulting in the synthesis of positive-strand genomes, which are encapsidated by NP, thus forming ribonucleoprotein complexes (antigenomic RNPs). These newly formed antigenomic RNPs in turn serve as templates for the synthesis of negative-strand RNA genomes that are also encapsidated by NP (genomic RNPs). Still in the IBs, genomic RNPs mature into tightly packed transport-competent nucleocapsids (NCs) by the recruitment of the viral protein VP24. NCs are tightly coiled left-handed helices whose structure is mainly determined by the multimerization of NP at its N-terminus, and these helices form the inner layer of the NCs. The RNA genome is fixed by 2 lobes of the NP N-terminus and is thus guided by individual NP molecules along the turns of the helix. Direct interaction of the NP C-terminus with the VP35 and VP24 molecules forms the outer layer of the NCs. Once formed, NCs that are located at the border of the IBs recruit actin polymerization machinery to one of their ends to drive their transport to budding sites for their envelopment and final release. Here, we review the current knowledge on the structure, assembly, and transport of filovirus NCs.
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Affiliation(s)
- Olga Dolnik
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
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47
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Boggs KB, Edmonds K, Cifuentes-Munoz N, El Najjar F, Ossandón C, Roe M, Wu C, Moncman CL, Creamer TP, Amarasinghe GK, Leung DW, Dutch RE. Human Metapneumovirus Phosphoprotein Independently Drives Phase Separation and Recruits Nucleoprotein to Liquid-Like Bodies. mBio 2022; 13:e0109922. [PMID: 35536005 PMCID: PMC9239117 DOI: 10.1128/mbio.01099-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Human metapneumovirus (HMPV) inclusion bodies (IBs) are dynamic structures required for efficient viral replication and transcription. The minimum components needed to form IB-like structures in cells are the nucleoprotein (N) and the tetrameric phosphoprotein (P). HMPV P binds to the following two versions of the N protein in infected cells: N-terminal P residues interact with monomeric N (N0) to maintain a pool of protein to encapsidate new RNA and C-terminal P residues interact with oligomeric, RNA-bound N (N-RNA). Recent work on other negative-strand viruses has suggested that IBs are, at least in part, liquid-like phase-separated membraneless organelles. Here, HMPV IBs in infected or transfected cells were shown to possess liquid organelle properties, such as fusion and fission. Recombinant versions of HMPV N and P proteins were purified to analyze the interactions required to drive phase separation in vitro. Purified HMPV P was shown to form liquid droplets in isolation. This observation is distinct from other viral systems that also form IBs. Partial removal of nucleic acid from purified P altered phase-separation dynamics, suggesting that nucleic acid interactions play a role in IB formation. HMPV P also recruits monomeric N (N0-P) and N-RNA to droplets in vitro. These findings suggest that HMPV P may also act as a scaffold protein to mediate multivalent interactions with monomeric and oligomeric N, as well as RNA, to promote phase separation of IBs. Together, these findings highlight an additional layer of regulation in HMPV replication by the viral P and N proteins. IMPORTANCE Human metapneumovirus (HMPV) is a leading cause of respiratory disease among children, immunocompromised individuals, and the elderly. Currently, no vaccines or antivirals are available for the treatment of HMPV infections. Cytoplasmic inclusion bodies (IBs), where HMPV replication and transcription occur, represent a promising target for the development of novel antivirals. The HMPV nucleoprotein (N) and phosphoprotein (P) are the minimal components needed for IB formation in eukaryotic cells. However, interactions that regulate the formation of these dynamic structures are poorly understood. Here, we showed that HMPV IBs possess the properties of liquid organelles and that purified HMPV P phase separates independently in vitro. Our work suggests that HMPV P phase-separation dynamics are altered by nucleic acid. We provide strong evidence that, unlike results reported from other viral systems, HMPV P alone can serve as a scaffold for multivalent interactions with monomeric (N0) and oligomeric (N-RNA) HMPV N for IB formation.
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Affiliation(s)
- Kerri Beth Boggs
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Kearstin Edmonds
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Nicolas Cifuentes-Munoz
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Farah El Najjar
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Conny Ossandón
- Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - McKenna Roe
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carole L. Moncman
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Trevor P. Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daisy W. Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
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Sourimant J, Lieber CM, Yoon JJ, Toots M, Govindarajan M, Udumula V, Sakamoto K, Natchus MG, Patti J, Vernachio J, Plemper RK. Orally efficacious lead of the AVG inhibitor series targeting a dynamic interface in the respiratory syncytial virus polymerase. SCIENCE ADVANCES 2022; 8:eabo2236. [PMID: 35749502 PMCID: PMC9232112 DOI: 10.1126/sciadv.abo2236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Respiratory syncytial virus (RSV) is a leading cause of lower respiratory infections in infants and the immunocompromised, yet no efficient therapeutic exists. We have identified the AVG class of allosteric inhibitors of RSV RNA synthesis. Here, we demonstrate through biolayer interferometry and in vitro RNA-dependent RNA polymerase (RdRP) assays that AVG compounds bind to the viral polymerase, stalling the polymerase in initiation conformation. Resistance profiling revealed a unique escape pattern, suggesting a discrete docking pose. Affinity mapping using photoreactive AVG analogs identified the interface of polymerase core, capping, and connector domains as a molecular target site. A first-generation lead showed nanomolar potency against RSV in human airway epithelium organoids but lacked in vivo efficacy. Docking pose-informed synthetic optimization generated orally efficacious AVG-388, which showed potent efficacy in the RSV mouse model when administered therapeutically. This study maps a druggable target in the RSV RdRP and establishes clinical potential of the AVG chemotype against RSV disease.
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Affiliation(s)
- Julien Sourimant
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Carolin M. Lieber
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Jeong-Joong Yoon
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Mart Toots
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | | | - Venkata Udumula
- Emory Institute for Drug Development, Emory University, Atlanta, GA 30322, USA
| | - Kaori Sakamoto
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Michael G. Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, GA 30322, USA
| | - Joseph Patti
- Aviragen Therapeutics Inc, Alpharetta, GA 30009, USA
| | | | - Richard K. Plemper
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
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49
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Phase-Separated Subcellular Compartmentation and Related Human Diseases. Int J Mol Sci 2022; 23:ijms23105491. [PMID: 35628304 PMCID: PMC9141834 DOI: 10.3390/ijms23105491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
In live cells, proteins and nucleic acids can associate together through multivalent interactions, and form relatively isolated phases that undertake designated biological functions and activities. In the past decade, liquid–liquid phase separation (LLPS) has gradually been recognized as a general mechanism for the intracellular organization of biomolecules. LLPS regulates the assembly and composition of dozens of membraneless organelles and condensates in cells. Due to the altered physiological conditions or genetic mutations, phase-separated condensates may undergo aberrant formation, maturation or gelation that contributes to the onset and progression of various diseases, including neurodegenerative disorders and cancers. In this review, we summarize the properties of different membraneless organelles and condensates, and discuss multiple phase separation-regulated biological processes. Based on the dysregulation and mutations of several key regulatory proteins and signaling pathways, we also exemplify how aberrantly regulated LLPS may contribute to human diseases.
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50
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Fang XD, Gao Q, Zang Y, Qiao JH, Gao DM, Xu WY, Wang Y, Li D, Wang XB. Host casein kinase 1-mediated phosphorylation modulates phase separation of a rhabdovirus phosphoprotein and virus infection. eLife 2022; 11:74884. [PMID: 35191833 PMCID: PMC8887900 DOI: 10.7554/elife.74884] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) plays important roles in forming cellular membraneless organelles. However, how host factors regulate LLPS of viral proteins during negative-sense RNA (NSR) virus infection is largely unknown. Here, we used barley yellow striate mosaic virus (BYSMV) as a model to demonstrate regulation of host casein kinase 1 (CK1) in phase separation and infection of NSR viruses. We first found that the BYSMV phosphoprotein (P) formed spherical granules with liquid properties and recruited viral nucleotide (N) and polymerase (L) proteins in vivo. Moreover, the P-formed granules were tethered to the ER/actin network for trafficking and fusion. BYSMV P alone formed droplets and incorporated the N protein and the 5′ trailer of genomic RNA in vitro. Interestingly, phase separation of BYSMV P was inhibited by host CK1-dependent phosphorylation of an intrinsically disordered P protein region. Genetic assays demonstrated that the unphosphorylated mutant of BYSMV P exhibited condensed phase, which promoted viroplasm formation and virus replication. Whereas, the phosphorylation-mimic mutant existed in diffuse phase state for virus transcription. Collectively, our results demonstrate that host CK1 modulates phase separation of the viral P protein and virus infection.
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Affiliation(s)
- Xiao-Dong Fang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiang Gao
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Zang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ji-Hui Qiao
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dong-Min Gao
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Ya Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Xian-Bing Wang
- College of Biological Sciences, China Agricultural University, Beijing, China
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