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Spada SJ, Rose KM, Sette P, O'Connor SK, Dussupt V, Siddartha Yerramilli V, Nagashima K, Sjoelund VH, Cruz P, Kabat J, Ganesan S, Smelkinson M, Nita-Lazar A, Hoyt F, Scarlata S, Hirsch V, Best SM, Grigg ME, Bouamr F. Human ESCRT-I and ALIX function as scaffolding helical filaments in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592080. [PMID: 38903125 PMCID: PMC11188096 DOI: 10.1101/2024.05.01.592080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The Endosomal Sorting Complex Required for Transport (ESCRT) is an evolutionarily conserved machinery that performs reverse-topology membrane scission in cells universally required from cytokinesis to budding of enveloped viruses. Upstream acting ESCRT-I and ALIX control these events and link recruitment of viral and cellular partners to late-acting ESCRT-III CHMP4 through incompletely understood mechanisms. Using structure-function analyses combined with super-resolution imaging, we show that ESCRT-I and ALIX function as distinct helical filaments in vivo . Together, they are essential for optimal structural scaffolding of HIV-1 nascent virions, the retention of viral and human genomes through defined functional interfaces, and recruitment of CHMP4 that itself assembles into corkscrew-like filaments intertwined with ESCRT-I or ALIX helices. Disruption of filament assembly or their conformationally clustered RNA binding interfaces in human cells impaired membrane abscission, resulted in major structural instability and leaked nucleic acid from nascent virions and nuclear envelopes. Thus, ESCRT-I and ALIX function as helical filaments in vivo and serve as both nucleic acid-dependent structural scaffolds as well as ESCRT-III assembly templates. Significance statement When cellular membranes are dissolved or breached, ESCRT is rapidly deployed to repair membranes to restore the integrity of intracellular compartments. Membrane sealing is ensured by ESCRT-III filaments assembled on the inner face of membrane; a mechanism termed inverse topology membrane scission. This mechanism, initiated by ESCRT-I and ALIX, is universally necessary for cytokinesis, wound repair, budding of enveloped viruses, and more. We show ESCRT-I and ALIX individually oligomerize into helical filaments that cluster newly discovered nucleic acid-binding interfaces and scaffold-in genomes within nascent virions and nuclear envelopes. These oligomers additionally appear to serve as ideal templates for ESCRT-III polymerization, as helical filaments of CHMP4B were found intertwined ESCRT-I or ALIX filaments in vivo . Similarly, corkscrew-like filaments of ALIX are also interwoven with ESCRT-I, supporting a model of inverse topology membrane scission that is synergistically reinforced by inward double filament scaffolding.
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2
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How HIV-1 Gag Manipulates Its Host Cell Proteins: A Focus on Interactors of the Nucleocapsid Domain. Viruses 2020; 12:v12080888. [PMID: 32823718 PMCID: PMC7471995 DOI: 10.3390/v12080888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/27/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) polyprotein Gag (Group-specific antigen) plays a central role in controlling the late phase of the viral lifecycle. Considered to be only a scaffolding protein for a long time, the structural protein Gag plays determinate and specific roles in HIV-1 replication. Indeed, via its different domains, Gag orchestrates the specific encapsidation of the genomic RNA, drives the formation of the viral particle by its auto-assembly (multimerization), binds multiple viral proteins, and interacts with a large number of cellular proteins that are needed for its functions from its translation location to the plasma membrane, where newly formed virions are released. Here, we review the interactions between HIV-1 Gag and 66 cellular proteins. Notably, we describe the techniques used to evidence these interactions, the different domains of Gag involved, and the implications of these interactions in the HIV-1 replication cycle. In the final part, we focus on the interactions involving the highly conserved nucleocapsid (NC) domain of Gag and detail the functions of the NC interactants along the viral lifecycle.
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Characterization of influenza H1N1 Gag virus-like particles and extracellular vesicles co-produced in HEK-293SF. Vaccine 2019; 37:7100-7107. [DOI: 10.1016/j.vaccine.2019.07.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/06/2019] [Accepted: 07/05/2019] [Indexed: 01/02/2023]
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Bieniasz P, Telesnitsky A. Multiple, Switchable Protein:RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly. Annu Rev Virol 2018; 5:165-183. [PMID: 30048218 DOI: 10.1146/annurev-virology-092917-043448] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) particle assembly requires several protein:RNA interactions that vary widely in their character, from specific recognition of highly conserved and structured viral RNA elements to less specific interactions with variable RNA sequences. Genetic, biochemical, biophysical, and structural studies have illuminated how virion morphogenesis is accompanied by dramatic changes in the interactions among the protein and RNA virion components. The 5' leader RNA element drives RNA recognition by Gag upon initiation of HIV-1 assembly and can assume variable conformations that influence translation, dimerization, and Gag recognition. As Gag multimerizes on the plasma membrane, forming immature particles, its RNA binding specificity transiently changes, enabling recognition of the A-rich composition of the viral genome. Initiation of assembly may also be regulated by occlusion of the membrane binding surface of Gag by tRNA. Finally, recent work has suggested that RNA interactions with viral enzymes may activate and ensure the accuracy of virion maturation.
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Affiliation(s)
- Paul Bieniasz
- Laboratory of Retrovirology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA;
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Sci Rep 2017; 7:16965. [PMID: 29208937 PMCID: PMC5717263 DOI: 10.1038/s41598-017-16793-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/17/2017] [Indexed: 02/05/2023] Open
Abstract
HIV-1 replication requires myriad interactions between cellular proteins and the viral unspliced RNA. These interactions are important in archetypal RNA processes such as transcription and translation as well as for more specialized functions including alternative splicing and packaging of unspliced genomic RNA into virions. We present here a hybridization capture strategy for purification of unspliced full-length HIV RNA-protein complexes preserved in vivo by formaldehyde crosslinking, and coupled with mass spectrometry to identify HIV RNA-protein interactors in HIV-1 infected cells. One hundred eighty-nine proteins were identified to interact with unspliced HIV RNA including Rev and Gag/Gag-Pol, 24 host proteins previously shown to bind segments of HIV RNA, and over 90 proteins previously shown to impact HIV replication. Further analysis using siRNA knockdown techniques against several of these proteins revealed significant changes to HIV expression. These results demonstrate the utility of the approach for the discovery of host proteins involved in HIV replication. Additionally, because this strategy only requires availability of 30 nucleotides of the HIV-RNA for hybridization with a capture oligonucleotide, it is readily applicable to any HIV system of interest regardless of cell type, HIV-1 virus strain, or experimental perturbation.
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Lago S, Tosoni E, Nadai M, Palumbo M, Richter SN. The cellular protein nucleolin preferentially binds long-looped G-quadruplex nucleic acids. Biochim Biophys Acta Gen Subj 2017; 1861:1371-1381. [PMID: 27913192 PMCID: PMC5466061 DOI: 10.1016/j.bbagen.2016.11.036] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants. METHODS Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding. RESULTS The purified full-length human NCL was initially tested on telomeric G4 target sequences to allow for modulation of loop, conformation, length, G-tract number, stability. G4s in promoter regions with more complex sequences were next employed. We found that NCL binding to G4s heavily relies on G4 loop length, independently of the conformation and oligonucleotide/loop sequence. Low stability G4s are preferred. When alternative G4 conformations are possible, those with longer loops are preferred upon binding to NCL, even if G-tracts need to be spared from G4 folding. CONCLUSIONS Our data provide insight into how G4s and the associated proteins may control the ON/OFF molecular switch to several pathological processes, including neurodegeneration, tumor and virus activation. Understanding these regulatory determinants is the first step towards the development of targeted therapies. GENERAL SIGNIFICANCE The indication that NCL binding preferentially stimulates and induces folding of G4s containing long loops suggests NCL ability to modify the overall structure and steric hindrance of the involved nucleic acid regions. This protein-induced modification of the G4 structure may represent a cellular mechanosensor mechanism to molecular signaling and disease pathogenesis. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Elena Tosoni
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical Sciences, University of Padua, via Marzolo 5, 35131 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
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7
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Zivcec M, Scholte FEM, Spiropoulou CF, Spengler JR, Bergeron É. Molecular Insights into Crimean-Congo Hemorrhagic Fever Virus. Viruses 2016; 8:106. [PMID: 27110812 PMCID: PMC4848600 DOI: 10.3390/v8040106] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 01/11/2023] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne pathogen that causes high morbidity and mortality. Efficacy of vaccines and antivirals to treat human CCHFV infections remains limited and controversial. Research into pathology and underlying molecular mechanisms of CCHFV and other nairoviruses is limited. Significant progress has been made in our understanding of CCHFV replication and pathogenesis in the past decade. Here we review the most recent molecular advances in CCHFV-related research, and provide perspectives on future research.
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Affiliation(s)
- Marko Zivcec
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Florine E M Scholte
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Li Y, Frederick KM, Haverland NA, Ciborowski P, Belshan M. Investigation of the HIV-1 matrix interactome during virus replication. Proteomics Clin Appl 2015; 10:156-63. [PMID: 26360636 DOI: 10.1002/prca.201400189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 07/15/2015] [Accepted: 09/07/2015] [Indexed: 12/18/2022]
Abstract
PURPOSE Like all viruses, human immunodeficiency virus type 1 (HIV-1) requires host cellular factors for productive replication. Identification of these factors may lead to the development of novel cell-based inhibitors. EXPERIMENTAL DESIGN A Strep-tag was inserted into the C-terminus of the matrix (MA) region of the HIV-1 gag gene. The resultant virus was replication competent and used to infect Jurkat T-cells. MA complexes were affinity purified with Strep-Tactin agarose. Protein quantification was performed using sequential window acquisition of all theoretical fragment ion spectra (SWATH) MS, data were log2 -transformed, and Student t-tests with Bonferroni correction used to determine statistical significance. Several candidate proteins were validated by immunoblot and investigated for their role in virus infection by siRNA knockdown assays. RESULTS A total of 17 proteins were found to be statistically different between the infected versus uninfected and untagged control samples. X-ray repair cross-complementing protein 6 (Ku70), X-ray repair cross-complementing protein 5 (Ku80), and Y-box binding protein 1 (YB-1) were confirmed to interact with MA by immunoblot. Knockdown of two candidates, EZRIN and Y-box binding protein 1, enhanced HIV infection in vitro. CONCLUSIONS AND CLINICAL RELEVANCE The Strep-tag allowed for the capture of viral protein complexes in the context of virus replication. Several previously described factors were identified and at least two candidate proteins were found to play a role in HIV-1 infection. These data further increase our understanding of HIV host -cell interactions.
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Affiliation(s)
- Yan Li
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA
| | - Kristin M Frederick
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nicole A Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.,The Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA.,The Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
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9
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Tosoni E, Frasson I, Scalabrin M, Perrone R, Butovskaya E, Nadai M, Palù G, Fabris D, Richter SN. Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription. Nucleic Acids Res 2015; 43:8884-97. [PMID: 26354862 PMCID: PMC4605322 DOI: 10.1093/nar/gkv897] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 01/26/2023] Open
Abstract
Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy.
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Affiliation(s)
- Elena Tosoni
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Elena Butovskaya
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Dan Fabris
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
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10
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DeBoer J, Jagadish T, Haverland NA, Madson CJ, Ciborowski P, Belshan M. Alterations in the nuclear proteome of HIV-1 infected T-cells. Virology 2014; 468-470:409-420. [PMID: 25240327 DOI: 10.1016/j.virol.2014.08.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/17/2023]
Abstract
Virus infection of a cell involves the appropriation of host factors and the innate defensive response of the cell. The identification of proteins critical for virus replication may lead to the development of novel, cell-based inhibitors. In this study we mapped the changes in T-cell nuclei during human immunodeficiency virus type 1 (HIV-1) at 20 hpi. Using a stringent data threshold, a total of 13 and 38 unique proteins were identified in infected and uninfected cells, respectively, across all biological replicates. An additional 15 proteins were found to be differentially regulated between infected and control nuclei. STRING analysis identified four clusters of protein-protein interactions in the data set related to nuclear architecture, RNA regulation, cell division, and cell homeostasis. Immunoblot analysis confirmed the differential expression of several proteins in both C8166-45 and Jurkat E6-1 T-cells. These data provide a map of the response in host cell nuclei upon HIV-1 infection.
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Affiliation(s)
- Jason DeBoer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Teena Jagadish
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nicole A Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Christian J Madson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA.
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11
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Proteome analysis of the HIV-1 Gag interactome. Virology 2014; 460-461:194-206. [PMID: 25010285 DOI: 10.1016/j.virol.2014.04.038] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/06/2014] [Accepted: 04/19/2014] [Indexed: 11/22/2022]
Abstract
Human immunodeficiency virus Gag drives assembly of virions in infected cells and interacts with host factors which facilitate or restrict viral replication. Although several Gag-binding proteins have been characterized, understanding of virus-host interactions remains incomplete. In a series of six affinity purification screens, we have identified protein candidates for interaction with HIV-1 Gag. Proteins previously found in virions or identified in siRNA screens for host factors influencing HIV-1 replication were recovered. Helicases, translation factors, cytoskeletal and motor proteins, factors involved in RNA degradation and RNA interference were enriched in the interaction data. Cellular networks of cytoskeleton, SR proteins and tRNA synthetases were identified. Most prominently, components of cytoplasmic RNA transport granules were co-purified with Gag. This study provides a survey of known Gag-host interactions and identifies novel Gag binding candidates. These factors are associated with distinct molecular functions and cellular pathways relevant in host-pathogen interactions.
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12
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Gao W, Li M, Zhang J. Tandem immunoprecipitation approach to identify HIV-1 Gag associated host factors. J Virol Methods 2014; 203:116-9. [PMID: 24690621 DOI: 10.1016/j.jviromet.2014.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/06/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
Abstract
HIV-1 Gag by itself is able to assemble and release from host cells and thus serves as a simplified model to identify host factors involved in this stage of the HIV-1 life cycle. In this study, a tandem immunoprecipitation approach is taken to immunoprecipitate Gag-interacting host proteins from transfected 293T cells. It is demonstrated that with the tandem immunoprecipitation method Gag-interacting host factors can be precipitated more efficiently than by single-step immunoprecipitation. Gag proteins are found to interact with multiple RNA-binding proteins such as hnRNPs, nucleolin, EF1a and ribosomal proteins. Such interactions are mediated by cellular RNAs and the Gag Nuclear Capsid (NC) domain. Deletion of the NC domain results in removal of most of the RNA-binding proteins, as well as a reduction of the Gag releasing capability, which can be restored by replacing the deleted NC domain with another multimerization motif. Importantly, interactions between Gag and host factors are relevant functionally, as evidenced by significantly increased nucleolin protein in the cytoplasm where it is recruited into the Gag complex, and enhanced Gag release when nucleolin is over-expressed.
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Affiliation(s)
- Wei Gao
- Liaoning Medical University, First Affiliated Hospital, Jinzhou, Liaoning 121001, China
| | - Min Li
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jingxin Zhang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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13
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Balinsky CA, Schmeisser H, Ganesan S, Singh K, Pierson TC, Zoon KC. Nucleolin interacts with the dengue virus capsid protein and plays a role in formation of infectious virus particles. J Virol 2013; 87:13094-106. [PMID: 24027323 PMCID: PMC3838225 DOI: 10.1128/jvi.00704-13] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 09/03/2013] [Indexed: 01/24/2023] Open
Abstract
Dengue virus (DENV) is a mosquito-transmitted flavivirus that can cause severe disease in humans and is considered a reemerging pathogen of significant importance to public health. The DENV capsid (C) protein functions as a structural component of the infectious virion; however, it may have additional functions in the virus replicative cycle. Here, we show that the DENV C protein interacts and colocalizes with the multifunctional host protein nucleolin (NCL). Furthermore, we demonstrate that this interaction can be disrupted by the addition of an NCL binding aptamer (AS1411). Knockdown of NCL with small interfering RNA (siRNA) or treatment of cells with AS1411 results in a significant reduction of viral titers after DENV infection. Western blotting and quantitative RT-PCR (qRT-PCR) analysis revealed no differences in viral RNA or protein levels at early time points postinfection, suggesting a role for NCL in viral morphogenesis. We support this hypothesis by showing that treatment with AS1411 alters the migration characteristics of the viral capsid, as visualized by native electrophoresis. Here, we identify a critical interaction between DENV C protein and NCL that represents a potential new target for the development of antiviral therapeutics.
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Affiliation(s)
- Corey A. Balinsky
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Hana Schmeisser
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kavita Singh
- Structural Biology Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Theodore C. Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kathryn C. Zoon
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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14
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Nucleolar trafficking of the mouse mammary tumor virus gag protein induced by interaction with ribosomal protein L9. J Virol 2012; 87:1069-82. [PMID: 23135726 DOI: 10.1128/jvi.02463-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mouse mammary tumor virus (MMTV) Gag protein directs the assembly in the cytoplasm of immature viral capsids, which subsequently bud from the plasma membranes of infected cells. MMTV Gag localizes to discrete cytoplasmic foci in mouse mammary epithelial cells, consistent with the formation of cytosolic capsids. Unexpectedly, we also observed an accumulation of Gag in the nucleoli of infected cells derived from mammary gland tumors. To detect Gag-interacting proteins that might influence its subcellular localization, a yeast two-hybrid screen was performed. Ribosomal protein L9 (RPL9 or L9), an essential component of the large ribosomal subunit and a putative tumor suppressor, was identified as a Gag binding partner. Overexpression of L9 in cells expressing the MMTV(C3H) provirus resulted in specific, robust accumulation of Gag in nucleoli. Förster resonance energy transfer (FRET) and coimmunoprecipitation analyses demonstrated that Gag and L9 interact within the nucleolus, and the CA domain was the major site of interaction. In addition, the isolated NC domain of Gag localized to the nucleolus, suggesting that it contains a nucleolar localization signal (NoLS). To determine whether L9 plays a role in virus assembly, small interfering RNA (siRNA)-mediated knockdown was performed. Although Gag expression was not reduced with L9 knockdown, virus production was significantly impaired. Thus, our data support the hypothesis that efficient MMTV particle assembly is dependent upon the interaction of Gag and L9 in the nucleoli of infected cells.
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15
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NC-mediated nucleolar localization of retroviral gag proteins. Virus Res 2012; 171:304-18. [PMID: 23036987 DOI: 10.1016/j.virusres.2012.09.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 08/13/2012] [Accepted: 09/22/2012] [Indexed: 11/21/2022]
Abstract
The assembly and release of retrovirus particles from the cell membrane is directed by the Gag polyprotein. The Gag protein of Rous sarcoma virus (RSV) traffics through the nucleus prior to plasma membrane localization. We previously reported that nuclear localization of RSV Gag is linked to efficient packaging of viral genomic RNA, however the intranuclear activities of RSV Gag are not well understood. To gain insight into the properties of the RSV Gag protein within the nucleus, we examined the subnuclear localization and dynamic trafficking of RSV Gag. Restriction of RSV Gag to the nucleus by mutating its nuclear export signal (NES) in the p10 domain or interfering with CRM1-mediated nuclear export of Gag by leptomycin B (LMB) treatment led to the accumulation of Gag in nucleoli and discrete nucleoplasmic foci. Retention of RSV Gag in nucleoli was reduced with cis-expression of the 5' untranslated RU5 region of the viral RNA genome, suggesting the psi (Ψ) packaging signal may alter the subnuclear localization of Gag. Fluorescence recovery after photobleaching (FRAP) demonstrated that the nucleolar fraction of Gag was highly mobile, indicating that there was rapid exchange with Gag proteins in the nucleoplasm. RSV Gag is targeted to nucleoli by a nucleolar localization signal (NoLS) in the NC domain, and similarly, the human immunodeficiency virus type 1 (HIV-1) NC protein also contains an NoLS consisting of basic residues. Interestingly, co-expression of HIV-1 NC or Rev with HIV-1 Gag resulted in accumulation of Gag in nucleoli. Moreover, a subpopulation of HIV-1 Gag was detected in the nucleoli of HeLa cells stably expressing the entire HIV-1 genome in a Rev-dependent fashion. These findings suggest that the RSV and HIV-1 Gag proteins undergo nucleolar trafficking in the setting of viral infection.
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Cancio-Lonches C, Yocupicio-Monroy M, Sandoval-Jaime C, Galvan-Mendoza I, Ureña L, Vashist S, Goodfellow I, Salas-Benito J, Gutiérrez-Escolano AL. Nucleolin interacts with the feline calicivirus 3' untranslated region and the protease-polymerase NS6 and NS7 proteins, playing a role in virus replication. J Virol 2011; 85:8056-68. [PMID: 21680514 PMCID: PMC3147956 DOI: 10.1128/jvi.01878-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 05/29/2011] [Indexed: 12/19/2022] Open
Abstract
Cellular proteins play many important roles during the life cycle of all viruses. Specifically, host cell nucleic acid-binding proteins interact with viral components of positive-stranded RNA viruses and regulate viral translation, as well as RNA replication. Here, we report that nucleolin, a ubiquitous multifunctional nucleolar shuttling phosphoprotein, interacts with the Norwalk virus and feline calicivirus (FCV) genomic 3' untranslated regions (UTRs). Nucleolin can also form a complex in vitro with recombinant Norwalk virus NS6 and -7 (NS6/7) and can be copurified with the analogous protein from feline calicivirus (p76 or NS6/7) from infected feline kidney cells. Nucleolin RNA levels or protein were not modified during FCV infection; however, as a consequence of the infection, nucleolin was seen to relocalize from the nucleoli to the nucleoplasm, as well as to the perinuclear area where it colocalizes with the feline calicivirus NS6/7 protein. In addition, antibodies to nucleolin were able to precipitate viral RNA from feline calicivirus-infected cells, indicating a direct or indirect association of nucleolin with the viral RNA during virus replication. Small interfering RNA (siRNA)-mediated knockdown of nucleolin resulted in a reduction of the cytopathic effect and virus yield in CrFK cells. Taken together, these results demonstrate that nucleolin is a nucleolar component that interacts with viral RNA and NS6/7 and is required for feline calicivirus replication.
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Affiliation(s)
- Clotilde Cancio-Lonches
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
- Departamento de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, IPN, Distrito Federal, México
| | - Martha Yocupicio-Monroy
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Distrito Federal, México
| | - Carlos Sandoval-Jaime
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
| | - Iván Galvan-Mendoza
- Laboratorios Centrales, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
| | - Luis Ureña
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Surender Vashist
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Ian Goodfellow
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Juan Salas-Benito
- Departamento de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, IPN, Distrito Federal, México
| | - Ana Lorena Gutiérrez-Escolano
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
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Vallejos M, Deforges J, Plank TDM, Letelier A, Ramdohr P, Abraham CG, Valiente-Echeverría F, Kieft JS, Sargueil B, López-Lastra M. Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors. Nucleic Acids Res 2011; 39:6186-200. [PMID: 21482538 PMCID: PMC3152342 DOI: 10.1093/nar/gkr189] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The 5′ leader of the human immunodeficiency virus type 1 (HIV-1) genomic RNA harbors an internal ribosome entry site (IRES) that is functional during the G2/M phase of the cell cycle. Here we show that translation initiation mediated by the HIV-1 IRES requires the participation of trans-acting cellular factors other than the canonical translational machinery. We used ‘standard’ chemical and enzymatic probes and an ‘RNA SHAPE’ analysis to model the structure of the HIV-1 5′ leader and we show, by means of a footprinting assay, that G2/M extracts provide protections to regions previously identified as crucial for HIV-1 IRES activity. We also assessed the impact of mutations on IRES function. Strikingly, mutations did not significantly affect IRES activity suggesting that the requirement for pre-formed stable secondary or tertiary structure within the HIV-1 IRES may not be as strict as has been described for other viral IRESes. Finally, we used a proteomic approach to identify cellular proteins within the G2/M extracts that interact with the HIV-1 5′ leader. Together, data show that HIV-1 IRES-mediated translation initiation is modulated by cellular proteins.
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Affiliation(s)
- Maricarmen Vallejos
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
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Muriaux D, Darlix JL. Properties and functions of the nucleocapsid protein in virus assembly. RNA Biol 2010; 7:744-53. [PMID: 21157181 DOI: 10.4161/rna.7.6.14065] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
HIV-1 nucleocapsid protein (NC) is a small basic protein generated by the cleavage of the Gag structural polyprotein precusor by the viral protease during virus assembly in the infected cell. HIV-1 NC possesses two copies of a highly conserved CCHC zinc finger (ZnF), flanked by basic residues. HIV-1 NC and more generally retroviral NC proteins are nucleic acid binding proteins possessing potent nucleic acid condensing and chaperoning activities. As such NC protein drives critical structural rearrangements of the genomic RNA, notably RNA dimerization in the course of virus assembly and viral nucleic acid annealing required for genomic RNA replication by the viral reverse transcriptase (RT). Here we review the relationships between the 3D structure of HIV-1 NC, notably the central globular domain encompassing the two zinc fingers and the basic linker and NC functions in the early and late phases of virus replication. One of the salient feature of the NC central globular domain is an hydrophobic plateau which appears to orchestrate the NC functions, such as chaperoning the conversion of the genomic RNA into viral DNA by RT during the early phase, and driving the selection and dimerization of the genomic RNA at the initial stage of viral particle assembly. This ensures a bona fide trafficking of early GagNC-genomic RNA complexes to the plasma membrane of the infected cell and ultimately virion formation and budding.
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Jiang Y, Li Z, Nagy PD. Nucleolin/Nsr1p binds to the 3' noncoding region of the tombusvirus RNA and inhibits replication. Virology 2010; 396:10-20. [PMID: 19861225 PMCID: PMC2788044 DOI: 10.1016/j.virol.2009.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 06/13/2009] [Accepted: 10/03/2009] [Indexed: 01/11/2023]
Abstract
Previous genome-wide screens identified >100 host genes affecting tombusvirus replication using yeast model host. One of those factors was Nsr1p (nucleolin), which is an abundant RNA-binding shuttle protein involved in rRNA maturation and ribosome assembly. We find that overexpression of Nsr1p in yeast or in Nicotiana benthamiana inhibited the accumulation of tombusvirus RNA by approximately 10-fold. Regulated overexpression of Nsr1p revealed that Nsr1p should be present at the beginning of viral replication for efficient inhibition, suggesting that Nsr1p inhibits an early step in the replication process. In vitro experiments revealed that Nsr1p binds preferably to the 3' UTR in the viral RNA. The purified recombinant Nsr1p inhibited the in vitro replication of the viral RNA in a yeast cell-free assay when preincubated with the viral RNA before the assay. These data support the model that Nsr1p/nucleolin inhibits tombusvirus replication by interfering with the recruitment of the viral RNA for replication.
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Affiliation(s)
- Yi Jiang
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
| | - Zhenghe Li
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
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Abstract
Viruses are intracellular pathogens that have to usurp some of the cellular machineries to provide an optimal environment for their own replication. An increasing number of reports reveal that many viruses induce modifications of nuclear substructures including nucleoli, whether they replicate or not in the nucleus of infected cells. Indeed, during infection of cells with various types of human viruses, nucleoli undergo important morphological modifications. A large number of viral components traffic to and from the nucleolus where they interact with different cellular and/or viral factors, numerous host nucleolar proteins are redistributed in other cell compartments or are modified and some cellular proteins are delocalised in the nucleolus of infected cells. Well‐documented studies have established that several of these nucleolar modifications play a role in some steps of the viral cycle, and also in fundamental cellular pathways. The nucleolus itself is the place where several essential steps of the viral cycle take place. In other cases, viruses divert host nucleolar proteins from their known functions in order to exert new unexpected role(s). Copyright © 2009 John Wiley & Sons, Ltd.
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Affiliation(s)
- Anna Greco
- Université de Lyon, Lyon F-69003, France.
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21
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Nucleolin – Characteristics of Protein and its Role in Biology of Cancers and Viral Infections. ACTA ACUST UNITED AC 2008. [DOI: 10.2478/v10052-008-0003-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cochrane AW, McNally MT, Mouland AJ. The retrovirus RNA trafficking granule: from birth to maturity. Retrovirology 2006; 3:18. [PMID: 16545126 PMCID: PMC1475878 DOI: 10.1186/1742-4690-3-18] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 03/17/2006] [Indexed: 11/10/2022] Open
Abstract
Post-transcriptional events in the life of an RNA including RNA processing, transport, translation and metabolism are characterized by the regulated assembly of multiple ribonucleoprotein (RNP) complexes. At each of these steps, there is the engagement and disengagement of RNA-binding proteins until the RNA reaches its final destination. For retroviral genomic RNA, the final destination is the capsid. Numerous studies have provided crucial information about these processes and serve as the basis for studies on the intracellular fate of retroviral RNA. Retroviral RNAs are like cellular mRNAs but their processing is more tightly regulated by multiple cis-acting sequences and the activities of many trans-acting proteins. This review describes the viral and cellular partners that retroviral RNA encounters during its maturation that begins in the nucleus, focusing on important events including splicing, 3' end-processing, RNA trafficking from the nucleus to the cytoplasm and finally, mechanisms that lead to its compartmentalization into progeny virions.
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Affiliation(s)
- Alan W Cochrane
- Department of Medical Genetics and Microbiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Mark T McNally
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital and McGill University, 3755 Côte-Ste-Catherine Road, H3T 1E2, Canada
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