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Genoveso MJ, Okuwaki M, Kato K, Nagata K, Kawaguchi A. Nuclear reorganization by NPM1-mediated phase separation triggered by adenovirus core protein VII. Microbiol Spectr 2024; 12:e0041624. [PMID: 39162498 PMCID: PMC11448090 DOI: 10.1128/spectrum.00416-24] [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: 04/12/2024] [Accepted: 07/18/2024] [Indexed: 08/21/2024] Open
Abstract
Recent evidence has revealed that the reorganization of nuclear domains is largely mediated by liquid-liquid phase separation (LLPS). During viral infection, numerous nuclear domains undergo significant changes through LLPS for and against the replication of the virus. However, the regulatory mechanism of LLPS in response to viral infection and its detailed functions in viral replication remain unclear. In this study, we found that the activity of the nucleolar protein NPM1, a remodeling factor for the chromatin-like structure of adenovirus DNA, to induce LLPS is required for deposition of adenovirus core protein VII in a subnuclear domain, the virus-induced post-replication (ViPR) body, in the late phases of infection. The interaction between NPM1 and protein VII was responsible for initiating LLPS. The inhibition of LLPS by 1,6-hexanediol treatment resulted in the dispersion of protein VII from the ViPR bodies. These findings suggest that protein VII accumulates in the ViPR bodies in concert with the LLPS formation of NPM1 triggered by protein VII. After photobleaching of EGFP-NPM1 in the ViPR bodies, EGFP-NPM1 showed a relatively fast recovery half-time, indicating the fluid-like properties of NPM1 in this compartment. Importantly, NPM1 depletion decreased the genome packaging in the viral capsids, possibly owing to the formation of a defective adenovirus core. This study highlights the dynamic interplay between viral pathogens and the host nucleus for the reorganization of membrane-less compartments that facilitate their replication. IMPORTANCE In this study, we explored how adenoviruses utilize a process known as liquid-liquid phase separation (LLPS) to enhance their replication. We focused on a cellular chromatin remodeling protein, NPM1, which plays a crucial role in nucleolar formation through LLPS. NPM1 facilitates LLPS by interacting with adenovirus protein VII, effectively accumulating protein VII into membrane-less compartments called virus-induced post-replication bodies. NPM1 functions as a molecular chaperone of protein VII to assemble viral chromatin by transferring protein VII to viral DNA. Remarkably, when NPM1 was depleted, this process was disrupted, decreasing viral genome packaging. These findings shed light on a critical aspect of virus-host interactions, illustrating how adenovirus utilizes NPM1-mediated LLPS activity. Our findings provide valuable insights into the dynamic interplay between viruses and the host nucleus.
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Affiliation(s)
- Michelle Jane Genoveso
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mitsuru Okuwaki
- Laboratory of Biochemistry, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Kohsuke Kato
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
- Center for Quantum and Information Life Sciences, University of Tsukuba, Tsukuba, Japan
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2
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Kelnhofer-Millevolte LE, Arnold EA, Nguyen DH, Avgousti DC. Controlling Much? Viral Control of Host Chromatin Dynamics. Annu Rev Virol 2024; 11:171-191. [PMID: 38684115 DOI: 10.1146/annurev-virology-100422-011616] [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: 05/02/2024]
Abstract
Viruses are exemplary molecular biologists and have been integral to scientific discovery for generations. It is therefore no surprise that nuclear replicating viruses have evolved to systematically take over host cell function through astoundingly specific nuclear and chromatin hijacking. In this review, we focus on nuclear replicating DNA viruses-herpesviruses and adenoviruses-as key examples of viral invasion in the nucleus. We concentrate on critical features of nuclear architecture, such as chromatin and the nucleolus, to illustrate the complexity of the virus-host battle for resources in the nucleus. We conclude with a discussion of the technological advances that have enabled the discoveries we describe and upcoming steps in this burgeoning field.
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Affiliation(s)
- Laurel E Kelnhofer-Millevolte
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
| | - Edward A Arnold
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Daniel H Nguyen
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA;
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA;
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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3
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Arnold EA, Kaai RJ, Leung K, Brinkley MR, Kelnhofer-Millevolte LE, Guo MS, Avgousti DC. Adenovirus protein VII binds the A-box of HMGB1 to repress interferon responses. PLoS Pathog 2023; 19:e1011633. [PMID: 37703278 PMCID: PMC10519595 DOI: 10.1371/journal.ppat.1011633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/25/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Viruses hijack host proteins to promote infection and dampen host defenses. Adenovirus encodes the multifunctional protein VII that serves both to compact viral genomes inside the virion and disrupt host chromatin. Protein VII binds the abundant nuclear protein high mobility group box 1 (HMGB1) and sequesters HMGB1 in chromatin. HMGB1 is an abundant host nuclear protein that can also be released from infected cells as an alarmin to amplify inflammatory responses. By sequestering HMGB1, protein VII prevents its release, thus inhibiting downstream inflammatory signaling. However, the consequences of this chromatin sequestration on host transcription are unknown. Here, we employ bacterial two-hybrid interaction assays and human cell culture to interrogate the mechanism of the protein VII-HMGB1 interaction. HMGB1 contains two DNA binding domains, the A- and B-boxes, that bend DNA to promote transcription factor binding while the C-terminal tail regulates this interaction. We demonstrate that protein VII interacts directly with the A-box of HMGB1, an interaction that is inhibited by the HMGB1 C-terminal tail. By cellular fractionation, we show that protein VII renders A-box containing constructs insoluble, thereby acting to prevent their release from cells. This sequestration is not dependent on HMGB1's ability to bind DNA but does require post-translational modifications on protein VII. Importantly, we demonstrate that protein VII inhibits expression of interferon β, in an HMGB1-dependent manner, but does not affect transcription of downstream interferon-stimulated genes. Together, our results demonstrate that protein VII specifically harnesses HMGB1 through its A-box domain to depress the innate immune response and promote infection.
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Affiliation(s)
- Edward A. Arnold
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Robin J. Kaai
- Molecular & Cellular Biology, Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Katie Leung
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Mia R. Brinkley
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | | | - Monica S. Guo
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Daphne C. Avgousti
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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4
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Wu S, Chen J, Teo BHD, Wee SYK, Wong MHM, Cui J, Chen J, Leong KP, Lu J. The axis of complement C1 and nucleolus in antinuclear autoimmunity. Front Immunol 2023; 14:1196544. [PMID: 37359557 PMCID: PMC10288996 DOI: 10.3389/fimmu.2023.1196544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Antinuclear autoantibodies (ANA) are heterogeneous self-reactive antibodies that target the chromatin network, the speckled, the nucleoli, and other nuclear regions. The immunological aberration for ANA production remains partially understood, but ANA are known to be pathogenic, especially, in systemic lupus erythematosus (SLE). Most SLE patients exhibit a highly polygenic disease involving multiple organs, but in rare complement C1q, C1r, or C1s deficiencies, the disease can become largely monogenic. Increasing evidence point to intrinsic autoimmunogenicity of the nuclei. Necrotic cells release fragmented chromatins as nucleosomes and the alarmin HMGB1 is associated with the nucleosomes to activate TLRs and confer anti-chromatin autoimmunogenecity. In speckled regions, the major ANA targets Sm/RNP and SSA/Ro contain snRNAs that confer autoimmunogenecity to Sm/RNP and SSA/Ro antigens. Recently, three GAR/RGG-containing alarmins have been identified in the nucleolus that helps explain its high autoimmunogenicity. Interestingly, C1q binds to the nucleoli exposed by necrotic cells to cause protease C1r and C1s activation. C1s cleaves HMGB1 to inactive its alarmin activity. C1 proteases also degrade many nucleolar autoantigens including nucleolin, a major GAR/RGG-containing autoantigen and alarmin. It appears that the different nuclear regions are intrinsically autoimmunogenic by containing autoantigens and alarmins. However, the extracellular complement C1 complex function to dampen nuclear autoimmunogenecity by degrading these nuclear proteins.
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Affiliation(s)
- Shan Wu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Junjie Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Heng Dennis Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Seng Yin Kelly Wee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Hui Millie Wong
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianzhou Cui
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jinmiao Chen
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Jinhua Lu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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5
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Arnold EA, Kaai RJ, Leung K, Brinkley MR, Kelnhofer-Millevolte LE, Guo MS, Avgousti DC. Adenovirus protein VII binds the A-box of HMGB1 to repress interferon responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537247. [PMID: 37131771 PMCID: PMC10153217 DOI: 10.1101/2023.04.17.537247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Viruses hijack host proteins to promote infection and dampen host defenses. Adenovirus encodes the multifunctional protein VII that serves both to compact viral genomes inside the virion and disrupt host chromatin. Protein VII binds the abundant nuclear protein high mobility group box 1 (HMGB1) and sequesters HMGB1 in chromatin. HMGB1 is an abundant host nuclear protein that can also be released from infected cells as an alarmin to amplify inflammatory responses. By sequestering HMGB1, protein VII prevents its release, thus inhibiting downstream inflammatory signaling. However, the consequences of this chromatin sequestration on host transcription are unknown. Here, we employ bacterial two-hybrid interaction assays and human cell biological systems to interrogate the mechanism of the protein VII-HMGB1 interaction. HMGB1 contains two DNA binding domains, the A- and B-boxes, that bend DNA to promote transcription factor binding while the C-terminal tail regulates this interaction. We demonstrate that protein VII interacts directly with the A-box of HMGB1, an interaction that is inhibited by the HMGB1 C-terminal tail. By cellular fractionation, we show that protein VII renders A-box containing constructs insoluble, thereby acting to prevent their release from cells. This sequestration is not dependent on HMGB1's ability to bind DNA but does require post-translational modifications on protein VII. Importantly, we demonstrate that protein VII inhibits expression of interferon β, in an HMGB1- dependent manner, but does not affect transcription of downstream interferon- stimulated genes. Together, our results demonstrate that protein VII specifically harnesses HMGB1 through its A-box domain to depress the innate immune response and promote infection.
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6
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Lee TA, Han H, Polash A, Cho SK, Lee JW, Ra EA, Lee E, Park A, Kang S, Choi JL, Kim JH, Lee JE, Min KW, Yang SW, Hafner M, Lee I, Yoon JH, Lee S, Park B. The nucleolus is the site for inflammatory RNA decay during infection. Nat Commun 2022; 13:5203. [PMID: 36057640 PMCID: PMC9440930 DOI: 10.1038/s41467-022-32856-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/16/2022] [Indexed: 11/12/2022] Open
Abstract
Inflammatory cytokines are key signaling molecules that can promote an immune response, thus their RNA turnover must be tightly controlled during infection. Most studies investigate the RNA decay pathways in the cytosol or nucleoplasm but never focused on the nucleolus. Although this organelle has well-studied roles in ribosome biogenesis and cellular stress sensing, the mechanism of RNA decay within the nucleolus is not completely understood. Here, we report that the nucleolus is an essential site of inflammatory pre-mRNA instability during infection. RNA-sequencing analysis reveals that not only do inflammatory genes have higher intronic read densities compared with non-inflammatory genes, but their pre-mRNAs are highly enriched in nucleoli during infection. Notably, nucleolin (NCL) acts as a guide factor for recruiting cytosine or uracil (C/U)-rich sequence-containing inflammatory pre-mRNAs and the Rrp6-exosome complex to the nucleolus through a physical interaction, thereby enabling targeted RNA delivery to Rrp6-exosomes and subsequent degradation. Consequently, Ncl depletion causes aberrant hyperinflammation, resulting in a severe lethality in response to LPS. Importantly, the dynamics of NCL post-translational modifications determine its functional activity in phases of LPS. This process represents a nucleolus-dependent pathway for maintaining inflammatory gene expression integrity and immunological homeostasis during infection. The nucleolus is the traditional site for ribosomal RNA biogenesis. Here, the authors find that the nucleolus is a site of inflammatory pre-mRNA turnover and elucidated how immune homeostasis can be maintained by controlling inflammatory gene expression.
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Affiliation(s)
- Taeyun A Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Heonjong Han
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Division of Tumor Immunology, Research Institute, National Cancer Center, Goyang, South Korea
| | - Ahsan Polash
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, MD, USA
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji Won Lee
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung, South Korea
| | - Eun A Ra
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Eunhye Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Areum Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Junhee L Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji Hyun Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji Eun Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea.,Samsung Genome Institute (SGI), Samsung Medical Center, Seoul, South Korea
| | - Kyung-Won Min
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung, South Korea.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, MD, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA.
| | - Sungwook Lee
- Division of Tumor Immunology, Research Institute, National Cancer Center, Goyang, South Korea.
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.
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7
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Vrazas V, Moustafa S, Makridakis M, Karakasiliotis I, Vlahou A, Mavromara P, Katsani KR. A Proteomic Approach to Study the Biological Role of Hepatitis C Virus Protein Core+1/ARFP. Viruses 2022; 14:v14081694. [PMID: 36016316 PMCID: PMC9518822 DOI: 10.3390/v14081694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis C virus is the major cause of chronic liver diseases and the only cytoplasmic RNA virus known to be oncogenic in humans. The viral genome gives rise to ten mature proteins and to additional proteins, which are the products of alternative translation initiation mechanisms. A protein-known as ARFP (alternative reading frame protein) or Core+1 protein-is synthesized by an open reading frame overlapping the HCV Core coding region in the (+1) frame of genotype 1a. Almost 20 years after its discovery, we still know little of the biological role of the ARFP/Core+1 protein. Here, our differential proteomic analysis of stable hepatoma cell lines expressing the Core+1/Long isoform of HCV-1a relates the expression of the Core+1/Long isoform with the progression of the pathology of HCV liver disease to cancer.
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Affiliation(s)
- Vasileios Vrazas
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
| | - Savvina Moustafa
- Clinical Immunology-Rheumatology Unit, 2nd Department of Medicine and Laboratory, Hippokration General Hospital of Athens, 11527 Athens, Greece;
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (A.V.); (M.M.)
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (A.V.); (M.M.)
| | - Penelope Mavromara
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
| | - Katerina R. Katsani
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
- Correspondence:
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8
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Hidalgo P, Pimentel A, Mojica-Santamaría D, von Stromberg K, Hofmann-Sieber H, Lona-Arrona C, Dobner T, González RA. Evidence That the Adenovirus Single-Stranded DNA Binding Protein Mediates the Assembly of Biomolecular Condensates to Form Viral Replication Compartments. Viruses 2021; 13:1778. [PMID: 34578359 PMCID: PMC8473285 DOI: 10.3390/v13091778] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
A common viral replication strategy is characterized by the assembly of intracellular compartments that concentrate factors needed for viral replication and simultaneously conceal the viral genome from host-defense mechanisms. Recently, various membrane-less virus-induced compartments and cellular organelles have been shown to represent biomolecular condensates (BMCs) that assemble through liquid-liquid phase separation (LLPS). In the present work, we analyze biophysical properties of intranuclear replication compartments (RCs) induced during human adenovirus (HAdV) infection. The viral ssDNA-binding protein (DBP) is a major component of RCs that contains intrinsically disordered and low complexity proline-rich regions, features shared with proteins that drive phase transitions. Using fluorescence recovery after photobleaching (FRAP) and time-lapse studies in living HAdV-infected cells, we show that DBP-positive RCs display properties of liquid BMCs, which can fuse and divide, and eventually form an intranuclear mesh with less fluid-like features. Moreover, the transient expression of DBP recapitulates the assembly and liquid-like properties of RCs in HAdV-infected cells. These results are of relevance as they indicate that DBP may be a scaffold protein for the assembly of HAdV-RCs and should contribute to future studies on the role of BMCs in virus-host cell interactions.
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Affiliation(s)
- Paloma Hidalgo
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Arturo Pimentel
- Laboratorio Nacional de Microscopía Avanzada (LNMA), Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca 62210, Mexico;
| | - Diana Mojica-Santamaría
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
| | - Konstantin von Stromberg
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Helga Hofmann-Sieber
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Christian Lona-Arrona
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Thomas Dobner
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (K.v.S.); (H.H.-S.); (T.D.)
| | - Ramón A. González
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.M.-S.); (C.L.-A.)
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9
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Dybas JM, Lum KK, Kulej K, Reyes ED, Lauman R, Charman M, Purman CE, Steinbock RT, Grams N, Price AM, Mendoza L, Garcia BA, Weitzman MD. Adenovirus Remodeling of the Host Proteome and Host Factors Associated with Viral Genomes. mSystems 2021; 6:e0046821. [PMID: 34463575 DOI: 10.1128/msystems.00468-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Viral infections are associated with extensive remodeling of the cellular proteome. Viruses encode gene products that manipulate host proteins to redirect cellular processes or subvert antiviral immune responses. Adenovirus (AdV) encodes proteins from the early E4 region which are necessary for productive infection. Some cellular antiviral proteins are known to be targeted by AdV E4 gene products, resulting in their degradation or mislocalization. However, the full repertoire of host proteome changes induced by viral E4 proteins has not been defined. To identify cellular proteins and processes manipulated by viral products, we developed a global, unbiased proteomics approach to analyze changes to the host proteome during infection with adenovirus serotype 5 (Ad5) virus. We used whole-cell proteomics to measure total protein abundances in the proteome during Ad5 infection. Since host antiviral proteins can antagonize viral infection by associating with viral genomes and inhibiting essential viral processes, we used Isolation of Proteins on Nascent DNA (iPOND) proteomics to identify proteins associated with viral genomes during infection with wild-type Ad5 or an E4 mutant virus. By integrating these proteomics data sets, we identified cellular factors that are degraded in an E4-dependent manner or are associated with the viral genome in the absence of E4 proteins. We further show that some identified proteins exert inhibitory effects on Ad5 infection. Our systems-level analysis reveals cellular processes that are manipulated during Ad5 infection and points to host factors counteracted by early viral proteins as they remodel the host proteome to promote efficient infection. IMPORTANCE Viral infections induce myriad changes to the host cell proteome. As viruses harness cellular processes and counteract host defenses, they impact abundance, post-translational modifications, interactions, or localization of cellular proteins. Elucidating the dynamic changes to the cellular proteome during viral replication is integral to understanding how virus-host interactions influence the outcome of infection. Adenovirus encodes early gene products from the E4 genomic region that are known to alter host response pathways and promote replication, but the full extent of proteome modifications they mediate is not known. We used an integrated proteomics approach to quantitate protein abundance and protein associations with viral DNA during virus infection. Systems-level analysis identifies cellular proteins and processes impacted in an E4-dependent manner, suggesting ways that adenovirus counteracts potentially inhibitory host defenses. This study provides a global view of adenovirus-mediated proteome remodeling, which can serve as a model to investigate virus-host interactions of DNA viruses.
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Affiliation(s)
- Joseph M Dybas
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Krystal K Lum
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Katarzyna Kulej
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emigdio D Reyes
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Richard Lauman
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Matthew Charman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Caitlin E Purman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Robert T Steinbock
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nicholas Grams
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Alexander M Price
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lydia Mendoza
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Matthew D Weitzman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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10
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Iarovaia OV, Ioudinkova ES, Velichko AK, Razin SV. Manipulation of Cellular Processes via Nucleolus Hijaking in the Course of Viral Infection in Mammals. Cells 2021; 10:cells10071597. [PMID: 34202380 PMCID: PMC8303250 DOI: 10.3390/cells10071597] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/16/2022] Open
Abstract
Due to their exceptional simplicity of organization, viruses rely on the resources, molecular mechanisms, macromolecular complexes, regulatory pathways, and functional compartments of the host cell for an effective infection process. The nucleolus plays an important role in the process of interaction between the virus and the infected cell. The interactions of viral proteins and nucleic acids with the nucleolus during the infection process are universal phenomena and have been described for almost all taxonomic groups. During infection, proteins of the nucleolus in association with viral components can be directly used for the processes of replication and transcription of viral nucleic acids and the assembly and transport of viral particles. In the course of a viral infection, the usurpation of the nucleolus functions occurs and the usurpation is accompanied by profound changes in ribosome biogenesis. Recent studies have demonstrated that the nucleolus is a multifunctional and dynamic compartment. In addition to the biogenesis of ribosomes, it is involved in regulating the cell cycle and apoptosis, responding to cellular stress, repairing DNA, and transcribing RNA polymerase II-dependent genes. A viral infection can be accompanied by targeted transport of viral proteins to the nucleolus, massive release of resident proteins of the nucleolus into the nucleoplasm and cytoplasm, the movement of non-nucleolar proteins into the nucleolar compartment, and the temporary localization of viral nucleic acids in the nucleolus. The interaction of viral and nucleolar proteins interferes with canonical and non-canonical functions of the nucleolus and results in a change in the physiology of the host cell: cell cycle arrest, intensification or arrest of ribosome biogenesis, induction or inhibition of apoptosis, and the modification of signaling cascades involved in the stress response. The nucleolus is, therefore, an important target during viral infection. In this review, we discuss the functional impact of viral proteins and nucleic acid interaction with the nucleolus during infection.
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11
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Kobiita A, Godbersen S, Araldi E, Ghoshdastider U, Schmid MW, Spinas G, Moch H, Stoffel M. The Diabetes Gene JAZF1 Is Essential for the Homeostatic Control of Ribosome Biogenesis and Function in Metabolic Stress. Cell Rep 2021; 32:107846. [PMID: 32640216 DOI: 10.1016/j.celrep.2020.107846] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/23/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
The ability of pancreatic β-cells to respond to increased demands for insulin during metabolic stress critically depends on proper ribosome homeostasis and function. Excessive and long-lasting stimulation of insulin secretion can elicit endoplasmic reticulum (ER) stress, unfolded protein response, and β-cell apoptosis. Here we show that the diabetes susceptibility gene JAZF1 is a key transcriptional regulator of ribosome biogenesis, global protein, and insulin translation. JAZF1 is excluded from the nucleus, and its expression levels are reduced upon metabolic stress and in diabetes. Genetic deletion of Jazf1 results in global impairment of protein synthesis that is mediated by defects in ribosomal protein synthesis, ribosomal RNA processing, and aminoacyl-synthetase expression, thereby inducing ER stress and increasing β-cell susceptibility to apoptosis. Importantly, JAZF1 function and its pleiotropic actions are impaired in islets of murine T2D and in human islets exposed to metabolic stress. Our study identifies JAZF1 as a central mediator of metabolic stress in β-cells.
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Affiliation(s)
- Ahmad Kobiita
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, HPL H36, 8093 Zürich, Switzerland
| | - Svenja Godbersen
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, HPL H36, 8093 Zürich, Switzerland
| | - Elisa Araldi
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, HPL H36, 8093 Zürich, Switzerland
| | - Umesh Ghoshdastider
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, HPL H36, 8093 Zürich, Switzerland
| | - Marc W Schmid
- MWSchmid GmbH, Möhrlistrasse 25, 8006 Zurich, Switzerland
| | - Giatgen Spinas
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Universitäts-Spital Zürich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Schmelzbergstrasse 12, 8091 Zürich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, HPL H36, 8093 Zürich, Switzerland; Medical Faculty, University of Zurich, Zurich, Switzerland.
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12
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Kulanayake S, Tikoo SK. Adenovirus Core Proteins: Structure and Function. Viruses 2021; 13:v13030388. [PMID: 33671079 PMCID: PMC7998265 DOI: 10.3390/v13030388] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023] Open
Abstract
Adenoviruses have served as a model for investigating viral-cell interactions and discovering different cellular processes, such as RNA splicing and DNA replication. In addition, the development and evaluation of adenoviruses as the viral vectors for vaccination and gene therapy has led to detailed investigations about adenovirus biology, including the structure and function of the adenovirus encoded proteins. While the determination of the structure and function of the viral capsid proteins in adenovirus biology has been the subject of numerous reports, the last few years have seen increased interest in elucidating the structure and function of the adenovirus core proteins. Here, we provide a review of research about the structure and function of the adenovirus core proteins in adenovirus biology.
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Affiliation(s)
- Shermila Kulanayake
- Vaccine and Infectious Disease Organization-International Vaccine Center (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N5E3, Canada;
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N5E3, Canada
| | - Suresh K. Tikoo
- Vaccine and Infectious Disease Organization-International Vaccine Center (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N5E3, Canada;
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N5E3, Canada
- Correspondence:
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13
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Zhao X, Tikoo SK. Nuclear and Nucleolar Localization of Bovine Adenovirus-3 Protein V. Front Microbiol 2021; 11:579593. [PMID: 33488533 PMCID: PMC7815533 DOI: 10.3389/fmicb.2020.579593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/03/2020] [Indexed: 02/01/2023] Open
Abstract
The L2 region of bovine adenovirus-3 (BAdV-3) encodes a Mastadenovirus genus-specific protein, designated as pV, which is important for the production of progeny viruses. Here, we demonstrate that BAdV-3 pV, expressed as 55 kDa protein, localizes to the nucleus and specifically targets nucleolus of the infected cells. Analysis of deletion mutants of pV suggested that amino acids 81–120, 190–210, and 380–389 act as multiple nuclear localization signals (NLS), which also appear to serve as the binding sites for importin α-3 protein, a member of the importin α/β nuclear import receptor pathway. Moreover, pV amino acids 21–50 and 380–389 appear to act as nucleolar localization signals (NoLs). Interestingly, amino acids 380–389 appear to act both as NLS and as NoLS. The presence of NoLS is essential for the production of infectious progeny virions, as deletion of both NoLs are lethal for the production of infectious BAdV-3. Analysis of mutant BAV.pVd1d3 (isolated in pV completing CRL cells) containing deletion/mutation of both NoLS in non-complementing CRL cells not only revealed the altered intracellular localization of mutant pV but also reduced the expression of some late proteins. However, it does not appear to affect the incorporation of viral proteins, including mutant pV, in BAV.pVd1d3 virions. Further analysis of CsCl purified BAV.pVd1d3 suggested the presence of thermo-labile virions with disrupted capsids, which appear to affect the infectivity of the progeny virions. Our results suggest that pV contains overlapping and non-overlapping NoLS/NLS. Moreover, the presence of both NoLS appear essential for the production of stable and infectious progeny BAV.pVd1d3 virions.
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Affiliation(s)
- Xin Zhao
- VIDO-InterVac, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Suresh K Tikoo
- VIDO-InterVac, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.,Vaccinology and Imuunothepapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
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14
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Abstract
The nucleolus is the most prominent nuclear body and serves a fundamentally important biological role as a site of ribonucleoprotein particle assembly, primarily dedicated to ribosome biogenesis. Despite being one of the first intracellular structures visualized historically, the biophysical rules governing its assembly and function are only starting to become clear. Recent studies have provided increasing support for the concept that the nucleolus represents a multilayered biomolecular condensate, whose formation by liquid-liquid phase separation (LLPS) facilitates the initial steps of ribosome biogenesis and other functions. Here, we review these biophysical insights in the context of the molecular and cell biology of the nucleolus. We discuss how nucleolar function is linked to its organization as a multiphase condensate and how dysregulation of this organization could provide insights into still poorly understood aspects of nucleolus-associated diseases, including cancer, ribosomopathies and neurodegeneration as well as ageing. We suggest that the LLPS model provides the starting point for a unifying quantitative framework for the assembly, structural maintenance and function of the nucleolus, with implications for gene regulation and ribonucleoprotein particle assembly throughout the nucleus. The LLPS concept is also likely useful in designing new therapeutic strategies to target nucleolar dysfunction.
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15
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Goto C, Hashizume S, Fukao Y, Hara-Nishimura I, Tamura K. Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction. Nucleus 2020; 10:81-92. [PMID: 30961429 PMCID: PMC6527390 DOI: 10.1080/19491034.2019.1603093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In eukaryotes, the nucleus plays key roles in fundamental cellular processes, including DNA replication, chromatin maintenance, transcription, and translation. To better understand the functional diversity of nuclei, we developed a method for the comprehensive extraction of the nuclear proteome from Arabidopsis. We used a buffer with a high sucrose concentration to purify nuclei and then conducted solubility-based fractionation to increase proteome coverage. We identified 1539 proteins and two novel nuclear envelope (NE) proteins in the nuclear fraction of Arabidopsis cultured cells. The localization of 25 proteins was determined by GFP fusion analyses; 23 of these proteins were localized either in the nucleus or the NE-associated endoplasmic reticulum. This result was indicative of the high quality of the proteome. These findings will be useful for clarifying novel nuclear functions in plants.
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Affiliation(s)
- Chieko Goto
- a Graduate School of Agricultural and Life Sciences , University of Tokyo , Tokyo , Japan
| | - Shoko Hashizume
- b Department of Botany , Graduate School of Science, Kyoto University , Kyoto , Japan
| | - Yoichiro Fukao
- c Department of Bioinformatics , College of Life Sciences, Ritsumeikan University , Shiga , Japan
| | | | - Kentaro Tamura
- e Department of Environmental and Life Sciences , University of Shizuoka , Shizuoka , Japan
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16
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Civra A, Colzani M, Cagno V, Francese R, Leoni V, Aldini G, Lembo D, Poli G. Modulation of cell proteome by 25-hydroxycholesterol and 27-hydroxycholesterol: A link between cholesterol metabolism and antiviral defense. Free Radic Biol Med 2020; 149:30-36. [PMID: 31525455 PMCID: PMC7126780 DOI: 10.1016/j.freeradbiomed.2019.08.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/19/2019] [Accepted: 08/30/2019] [Indexed: 12/11/2022]
Abstract
Physiological cholesterol metabolism implies the generation of a series of oxidized derivatives, whose oxysterols are by far the most investigated ones for their potential multifaceted involvement in human pathophysiology. In this regard, noteworthy is the broad antiviral activity displayed by defined side chain oxysterols, in particular 25-hydroxycholesterol (25HC) and 27-hydroxycholesterol (27HC). Although their antiviral mechanism(s) may vary depending on virus/host interaction, these oxysterols share the common feature to hamper viral replication by interacting with cellular proteins. Here reported is the first analysis of the modulation of a cell proteome by these two oxysterols, that, besides yielding additional clues about their potential involvement in the regulation of sterol metabolism, provides novelinsights about the mechanism underlying the inhibition of virus entry and trafficking within infected cells. We show here that both 25HC and 27HC can down-regulate the junction adhesion molecule-A (JAM-A) and the cation independent isoform of mannose-6-phosphate receptor (MPRci), two crucial molecules for the replication of all those viruses that exploit adhesion molecules and the endosomal pathway to enter and diffuse within target cells.
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Affiliation(s)
- Andrea Civra
- Department of Clinical and Biological Sciences, University of Torino at San Luigi Hospital, Orbassano, Torino, Italy.
| | - Mara Colzani
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy.
| | - Valeria Cagno
- Department of Molecular Microbiology, University of Geneva, Geneva, Switzerland.
| | - Rachele Francese
- Department of Clinical and Biological Sciences, University of Torino at San Luigi Hospital, Orbassano, Torino, Italy.
| | - Valerio Leoni
- Department of Laboratory Medicine, University of Milano-Bicocca, School of Medicine, Hospital of Desio, Milano, Italy.
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy.
| | - David Lembo
- Department of Clinical and Biological Sciences, University of Torino at San Luigi Hospital, Orbassano, Torino, Italy.
| | - Giuseppe Poli
- Department of Clinical and Biological Sciences, University of Torino at San Luigi Hospital, Orbassano, Torino, Italy.
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17
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Zhao H, Punga T, Pettersson U. Adenovirus in the omics era - a multipronged strategy. FEBS Lett 2020; 594:1879-1890. [PMID: 31811727 DOI: 10.1002/1873-3468.13710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 01/15/2023]
Abstract
Human adenoviruses (HAdVs) are common pathogens associated with a wide variety of respiratory, ocular, and gastrointestinal diseases. To achieve its effective lytic mode of replication, HAdVs have to reprogram host-cell gene expression and fine-tune viral gene expression in a temporal manner. In two decades, omics revolution has advanced our knowledge about the HAdV and host-cell interplay at the RNA and protein levels. This review summarizes the current knowledge from large-scale datasets on how HAdV infections adjust coding and noncoding RNA expression, as well as how they reprogram host-cell proteome during the lytic course of infection.
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Affiliation(s)
- Hongxing Zhao
- Beijer Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
| | - Ulf Pettersson
- Beijer Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
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18
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Charman M, Herrmann C, Weitzman MD. Viral and cellular interactions during adenovirus DNA replication. FEBS Lett 2019; 593:3531-3550. [PMID: 31764999 DOI: 10.1002/1873-3468.13695] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/30/2022]
Abstract
Adenoviruses represent ubiquitous and clinically significant human pathogens, gene-delivery vectors, and oncolytic agents. The study of adenovirus-infected cells has long been used as an excellent model to investigate fundamental aspects of both DNA virus infection and cellular biology. While many key details supporting a well-established model of adenovirus replication have been elucidated over a period spanning several decades, more recent findings suggest that we have only started to appreciate the complex interplay between viral genome replication and cellular processes. Here, we present a concise overview of adenovirus DNA replication, including the biochemical process of replication, the spatial organization of replication within the host cell nucleus, and insights into the complex plethora of virus-host interactions that influence viral genome replication. Finally, we identify emerging areas of research relating to the replication of adenovirus genomes.
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Affiliation(s)
- Matthew Charman
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christin Herrmann
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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19
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Pied N, Wodrich H. Imaging the adenovirus infection cycle. FEBS Lett 2019; 593:3419-3448. [PMID: 31758703 DOI: 10.1002/1873-3468.13690] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022]
Abstract
Incoming adenoviruses seize control of cytosolic transport mechanisms to relocate their genome from the cell periphery to specialized sites in the nucleoplasm. The nucleus is the site for viral gene expression, genome replication, and the production of progeny for the next round of infection. By taking control of the cell, adenoviruses also suppress cell-autonomous immunity responses. To succeed in their production cycle, adenoviruses rely on well-coordinated steps, facilitated by interactions between viral proteins and cellular factors. Interactions between virus and host can impose remarkable morphological changes in the infected cell. Imaging adenoviruses has tremendously influenced how we delineate individual steps in the viral life cycle, because it allowed the development of specific optical markers to label these morphological changes in space and time. As technology advances, innovative imaging techniques and novel tools for specimen labeling keep uncovering previously unseen facets of adenovirus biology emphasizing why imaging adenoviruses is as attractive today as it was in the past. This review will summarize past achievements and present developments in adenovirus imaging centered on fluorescence microscopy approaches.
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Affiliation(s)
- Noémie Pied
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
| | - Harald Wodrich
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
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20
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Hidalgo P, Gonzalez RA. Formation of adenovirus DNA replication compartments. FEBS Lett 2019; 593:3518-3530. [PMID: 31710378 DOI: 10.1002/1873-3468.13672] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/23/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Adenoviruses induce an extensive reorganization of the host cell nucleus during replication. Such a process results in the assembly of viral and cellular macromolecules into nuclear structures called adenovirus replication compartments (AdRCs), which function as platforms for viral DNA replication and gene expression. AdRCs co-opt host proteins and cellular pathways that restrict viral replication, suggesting that the mechanisms that control AdRC formation and function are essential for viral replication and lay at the basis of virus-host interactions. Here, we review the hallmarks of AdRCs and recent progress in our understanding of the formation, composition, and function of AdRCs. Furthermore, we discuss how AdRCs facilitate the interplay between viral and cellular machineries and hijack cellular functions to promote viral genome replication and expression.
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Affiliation(s)
- Paloma Hidalgo
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón A Gonzalez
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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21
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Azkanaz M, Rodríguez López A, de Boer B, Huiting W, Angrand PO, Vellenga E, Kampinga HH, Bergink S, Martens JH, Schuringa JJ, van den Boom V. Protein quality control in the nucleolus safeguards recovery of epigenetic regulators after heat shock. eLife 2019; 8:45205. [PMID: 31199242 PMCID: PMC6570483 DOI: 10.7554/elife.45205] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/21/2019] [Indexed: 12/19/2022] Open
Abstract
Maintenance of epigenetic modifiers is of utmost importance to preserve the epigenome and consequently appropriate cellular functioning. Here, we analyzed Polycomb group protein (PcG) complex integrity in response to heat shock (HS). Upon HS, various Polycomb Repressive Complex (PRC)1 and PRC2 subunits, including CBX proteins, but also other chromatin regulators, are found to accumulate in the nucleolus. In parallel, binding of PRC1/2 to target genes is strongly reduced, coinciding with a dramatic loss of H2AK119ub and H3K27me3 marks. Nucleolar-accumulated CBX proteins are immobile, but remarkably both CBX protein accumulation and loss of PRC1/2 epigenetic marks are reversible. This post-heat shock recovery of pan-nuclear CBX protein localization and reinstallation of epigenetic marks is HSP70 dependent. Our findings demonstrate that the nucleolus is an essential protein quality control center, which is indispensable for recovery of epigenetic regulators and maintenance of the epigenome after heat shock.
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Affiliation(s)
- Maria Azkanaz
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aida Rodríguez López
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bauke de Boer
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Wouter Huiting
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Edo Vellenga
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Harm H Kampinga
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Steven Bergink
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Joost Ha Martens
- Department of Molecular Biology, Faculty of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Vincent van den Boom
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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22
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Badr KR, Parente‐Rocha JA, Baeza LC, Ficcadori FS, Souza M, Soares CM, Guissoni ACP, Almeida TN, Cardoso DD. Quantitative proteomic analysis of A549 cells infected with human adenovirus type 2. J Med Virol 2019; 91:1239-1249. [DOI: 10.1002/jmv.25439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Kareem R. Badr
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Juliana A. Parente‐Rocha
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Lilian C. Baeza
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Fabiola S. Ficcadori
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Menira Souza
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Célia M. Soares
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Ana Carla P. Guissoni
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Tâmera N. Almeida
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Divina D. Cardoso
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
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23
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Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection. BMC Microbiol 2019; 19:15. [PMID: 30642258 PMCID: PMC6332865 DOI: 10.1186/s12866-018-1375-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/16/2018] [Indexed: 12/27/2022] Open
Abstract
Background Human adenovirus (Ad) infection leads to the changes of host cell gene expression and biosynthetic processes. Transcriptomics in adenovirus type 2 (Ad2)-infected lung fibroblasts (IMR-90) cells has previously been studied using RNA sequencing. However, this study included only two time points (12 and 24 hpi) using constrained 76 bp long sequencing reads. Therefore, a more detailed study of transcription at different phases of infection using an up-graded sequencing technique is recalled. Furthermore, the correlation between transcription and protein expression needs to be addressed. Results In total, 3556 unique cellular genes were identified as differentially expressed at the transcriptional level with more than 2-fold changes in Ad2-infected cells as compared to non-infected cells by using paired-end sequencing. Based on the kinetics of the gene expression changes at different times after infection, these RNAs fell into 20 clusters. Among them, cellular genes involved in immune response were highly up-regulated in the early phase before becoming down-regulated in the late phase. Comparison of differentially expressed genes at transcriptional and posttranscriptional levels revealed low correlation. Particularly genes involved in cellular immune pathways showed a negative correlation. Here, we highlight the genes which expose inconsistent expression profiles with an emphasis on key factors in cellular immune pathways including NFκB, JAK/STAT, caspases and MAVS. Different from their transcriptional profiles with up- and down-regulation in the early and late phase, respectively, these proteins were up-regulated in the early phase and were sustained in the late phase. A surprising finding was that the target genes of the sustained activators failed to show response. Conclusion There were features common to genes which play important roles in cellular immune pathways. Their expression was stimulated at both RNA and protein levels during the early phase. In the late phase however, their transcription was suppressed while protein levels remained stable. These results indicate that Ad2 and the host cell use different strategies to regulate cellular immune pathways. A control mechanism at the post-translational level must thus exist which is under the control of Ad2. Electronic supplementary material The online version of this article (10.1186/s12866-018-1375-5) contains supplementary material, which is available to authorized users.
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24
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Valdés A, Zhao H, Pettersson U, Lind SB. Time-resolved proteomics of adenovirus infected cells. PLoS One 2018; 13:e0204522. [PMID: 30252905 PMCID: PMC6155545 DOI: 10.1371/journal.pone.0204522] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
Viral infections cause large problems in the world and deeper understanding of the disease mechanisms is needed. Here we present an analytical strategy to investigate the host cell protein changes during human adenovirus type 2 (HAdV-C2 or Ad2) infection of lung fibroblasts by stable isotope labelling of amino acids in cell culture (SILAC) and nanoLC-MS/MS. This work focuses on early phase of infection (6 and 12 h post-infection (hpi)) but the data is combined with previously published late phase (24 and 36 hpi) proteomics data to produce a time series covering the complete infection. As many as 2169 proteins were quantitatively monitored from 6 to 36 hpi, while some proteins were time-specific. After applying different filter criteria, 2027 and 2150 proteins were quantified at 6 and 12 hpi and among them, 431 and 544 were significantly altered at the two time points. Pathway analysis showed that the De novo purine and pyrimidine biosynthesis, Glycolysis and Cytoskeletal regulation by Rho GTPase pathways were activated early during infection while inactivation of the Integrin signalling pathway started between 6 and 12 hpi. Moreover, upstream regulator analysis predicted MYC to be activated with time of infection and protein and RNA data for genes controlled by this transcription factor showed good correlation, which validated the use of protein data for this prediction. Among the identified phosphorylation sites, a group related to glycolysis and cytoskeletal reorganization were up-regulated during infection. The results show specific aspects on how the host cell proteins, the final products in the genetic information flow, are influenced by Ad2 infection, which would be overlooked if only knowledge derived from mRNA data is considered.
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Affiliation(s)
- Alberto Valdés
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Hongxing Zhao
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Ulf Pettersson
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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25
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González-Morales A, Zabaleta A, Guruceaga E, Alonso MM, García-Moure M, Fernández-Irigoyen J, Santamaría E. Spatial and temporal proteome dynamics of glioma cells during oncolytic adenovirus Delta-24-RGD infection. Oncotarget 2018; 9:31045-31065. [PMID: 30123426 PMCID: PMC6089549 DOI: 10.18632/oncotarget.25774] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/22/2018] [Indexed: 11/25/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive type of malignant glioma. Oncolytic adenoviruses are being modified to exploit the aberrant expression of proteins in tumor cells to increase the antiglioma efficacy. E1A mutant adenovirus Delta-24-RGD (DNX-2401) has shown a favorable toxicity profile and remarkable efficacy in a first-in-human phase I clinical trial. However, the comprehensive modulation of glioma metabolism in response to Delta-24-RGD infection is poorly understood. Integrating mass spectrometry based-quantitative proteomics, physical and functional interaction data, and biochemical approaches, we conducted a cell-wide study of cytosolic, nuclear, and secreted glioma proteomes throughout the early time course of Delta-24-RGD infection. In addition to the severe proteostasis impairment detected during the first hours post-infection (hpi), Delta-24-RGD induces a transient inhibition of signal transducer and activator of transcription 3 (STAT3), and transcription factor AP-1 (c-JUN) between 3 and 10hpi, increasing the nuclear factor kappa B (NF-κB) activity at 6hpi. Furthermore, Delta-24-RGD specifically modulates the activation dynamics of protein kinase C (PKC), extracellular signal-regulated kinase 1/2 (ERK1/2), and p38 mitogen-activated protein kinase (p38 MAPK) pathways early in infection. At extracellular level, Delta-24-RGD triggers a time -dependent dynamic production of multitasking cytokines, and chemotactic factors, suggesting potential pleiotropic effects on the immune system reactivation. Taken together, these data help us to understand the mechanisms used by Delta-24-RGD to exploit glioma proteome organization. Further mining of this proteomic resource may enable design and engineering complementary adenoviral based-vectors to increase the specificity and potency against glioma.
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Affiliation(s)
- Andrea González-Morales
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain
| | - Aintzane Zabaleta
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Oncohematology Area, University Hospital of Navarra, Center for Applied Medical Research, CIBERONC, Pamplona, Spain
| | - Elizabeth Guruceaga
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Marta M Alonso
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Program in Solid Tumors and Biomarkers, Foundation for the Applied Medical Research, Pamplona, Spain.,Department of Pediatrics, University Hospital of Navarra, Pamplona, Spain
| | - Marc García-Moure
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Program in Solid Tumors and Biomarkers, Foundation for the Applied Medical Research, Pamplona, Spain.,Department of Pediatrics, University Hospital of Navarra, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain
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26
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Guissoni ACP, Soares CMA, Badr KR, Ficcadori FS, Parente AFA, Parente JA, Baeza LC, Souza M, Cardoso DDDDP. Proteomic analysis of A-549 cells infected with human adenovirus 40 by LC-MS. Virus Genes 2018; 54:351-360. [PMID: 29546667 DOI: 10.1007/s11262-018-1554-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
Abstract
Human Adenoviruses (HAdVs) are etiological agents of different syndromes such as gastroenteritis, cystitis, ocular, and respiratory diseases, and infection by these viruses may cause alterations in cellular homeostasis. The objective of the study was the proteomic analysis of A-549 cells infected with HAdV-40 using LC-MS. At 30 h of infection, the quantitative analysis revealed 336 differentially expressed proteins. From them, 206 were induced (up-regulated) and 130 were suppressed (down-regulated). The majority of up-regulated proteins were related to energy, cellular organization, stress response, and apoptosis pathways. It was observed alteration of cell metabolism with increase of the glycolytic pathway, β-oxidation, and respiratory chain. Also, the results suggest cytoskeleton reorganization and apoptosis induction. The data can improve knowledge about the replication of HAdV-40 in cell culture considering the proteins related to distinct metabolic pathways induced by viral infection in A-549 cells.
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Affiliation(s)
- Ana Carla Peixoto Guissoni
- Human Virology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goias, Rua 235, S/N, Sala 418, Setor Universitário, Goiania, Goias, 74605050, Brazil
| | - Célia Maria Almeida Soares
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Goias, Goiania, Goias, Brazil
| | - Kareem R Badr
- Human Virology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goias, Rua 235, S/N, Sala 418, Setor Universitário, Goiania, Goias, 74605050, Brazil
| | - Fabiola Sousa Ficcadori
- Human Virology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goias, Rua 235, S/N, Sala 418, Setor Universitário, Goiania, Goias, 74605050, Brazil
| | - Ana Flávia Alves Parente
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Goias, Goiania, Goias, Brazil
| | - Juliana Alves Parente
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Goias, Goiania, Goias, Brazil
| | - Lilian Cristina Baeza
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Goias, Goiania, Goias, Brazil
| | - Menira Souza
- Human Virology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goias, Rua 235, S/N, Sala 418, Setor Universitário, Goiania, Goias, 74605050, Brazil
| | - Divina das Dores de Paula Cardoso
- Human Virology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goias, Rua 235, S/N, Sala 418, Setor Universitário, Goiania, Goias, 74605050, Brazil.
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27
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Fernández-Ponce C, Durán-Ruiz MC, Narbona-Sánchez I, Muñoz-Miranda JP, Arbulo-Echevarria MM, Serna-Sanz A, Baumann C, Litrán R, Aguado E, Bloch W, García-Cozar F. Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells. Front Microbiol 2018; 8:2595. [PMID: 29354102 PMCID: PMC5758585 DOI: 10.3389/fmicb.2017.02595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4+ T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4+ T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4+ T cells.
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Affiliation(s)
- Cecilia Fernández-Ponce
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Maria C Durán-Ruiz
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Isaac Narbona-Sánchez
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Juan P Muñoz-Miranda
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Mikel M Arbulo-Echevarria
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | | | | | - Rocío Litrán
- Department of Condensed Matter Physics, University of Cádiz, Puerto Real, Spain
| | - Enrique Aguado
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Cologne, Germany
| | - Francisco García-Cozar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
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28
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Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD. Identifying Host Factors Associated with DNA Replicated During Virus Infection. Mol Cell Proteomics 2017; 16:2079-2097. [PMID: 28972080 DOI: 10.1074/mcp.m117.067116] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/14/2017] [Indexed: 01/22/2023] Open
Abstract
Viral DNA genomes replicating in cells encounter a myriad of host factors that facilitate or hinder viral replication. Viral proteins expressed early during infection modulate host factors interacting with viral genomes, recruiting proteins to promote viral replication, and limiting access to antiviral repressors. Although some host factors manipulated by viruses have been identified, we have limited knowledge of pathways exploited during infection and how these differ between viruses. To identify cellular processes manipulated during viral replication, we defined proteomes associated with viral genomes during infection with adenovirus, herpes simplex virus and vaccinia virus. We compared enrichment of host factors between virus proteomes and confirmed association with viral genomes and replication compartments. Using adenovirus as an illustrative example, we uncovered host factors deactivated by early viral proteins, and identified a subgroup of nucleolar proteins that aid virus replication. Our data sets provide valuable resources of virus-host interactions that affect proteins on viral genomes.
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Affiliation(s)
- Emigdio D Reyes
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katarzyna Kulej
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Neha J Pancholi
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,¶Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lisa N Akhtar
- ‖Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daphne C Avgousti
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Eui Tae Kim
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daniel K Bricker
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lynn A Spruce
- **Protein and Proteomics Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah A Koniski
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Steven H Seeholzer
- **Protein and Proteomics Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stuart N Isaacs
- ‡‡Division of Infectious Diseases, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Benjamin A Garcia
- §§Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; .,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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29
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Blank MF, Chen S, Poetz F, Schnölzer M, Voit R, Grummt I. SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription. Nucleic Acids Res 2017; 45:2675-2686. [PMID: 28426094 PMCID: PMC5389538 DOI: 10.1093/nar/gkx053] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/20/2017] [Indexed: 01/08/2023] Open
Abstract
SIRT7 is an NAD+-dependent protein deacetylase that regulates cell growth and proliferation. Previous studies have shown that SIRT7 is required for RNA polymerase I (Pol I) transcription and pre-rRNA processing. Here, we took a proteomic approach to identify novel molecular targets and characterize the role of SIRT7 in non-nucleolar processes. We show that SIRT7 interacts with numerous proteins involved in transcriptional regulation and RNA metabolism, the majority of interactions requiring ongoing transcription. In addition to its role in Pol I transcription, we found that SIRT7 also regulates transcription of snoRNAs and mRNAs. Mechanistically, SIRT7 promotes the release of P-TEFb from the inactive 7SK snRNP complex and deacetylates CDK9, a subunit of the elongation factor P-TEFb, which activates transcription by phosphorylating serine 2 within the C-terminal domain (CTD) of Pol II. SIRT7 counteracts GCN5-directed acetylation of lysine 48 within the catalytic domain of CDK9, deacetylation promoting CTD phosphorylation and transcription elongation.
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Affiliation(s)
- Maximilian F Blank
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Sifan Chen
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Fabian Poetz
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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30
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Vidotto A, Morais ATS, Ribeiro MR, Pacca CC, Terzian ACB, Gil LHVG, Mohana-Borges R, Gallay P, Nogueira ML. Systems Biology Reveals NS4B-Cyclophilin A Interaction: A New Target to Inhibit YFV Replication. J Proteome Res 2017; 16:1542-1555. [PMID: 28317380 DOI: 10.1021/acs.jproteome.6b00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 proteins confirmed using Scaffold 3 Software. Cyclophilin A (CypA), a protein that has been shown to be necessary for the positive regulation of flavivirus replication, was identified as a possible NS4B partner. 59 proteins were found to be significantly increased when compared with a negative control, and CypA exhibited the greatest difference, with a 22-fold change. Fisher's exact test was significant for 58 proteins, and the p value of CypA was the most significant (0.000000019). The Ingenuity Systems software identified 16 pathways, and this analysis indicated sirolimus, an mTOR pathway inhibitor, as a potential inhibitor of CypA. Immunofluorescence and viral plaque assays showed a significant reduction in YFV replication using sirolimus and cyclosporine A (CsA) as inhibitors. Furthermore, YFV replication was strongly inhibited in cells treated with both inhibitors using reporter BHK-21-rep-YFV17D-LucNeoIres cells. Taken together, these data suggest that CypA-NS4B interaction regulates YFV replication. Finally, we present the first evidence that YFV inhibition may depend on NS4B-CypA interaction.
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Affiliation(s)
- Alessandra Vidotto
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana T S Morais
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Milene R Ribeiro
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Carolina C Pacca
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana C B Terzian
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Laura H V G Gil
- Departamento de Virologia, Centro de Pesquisa Aggeu Magalhães , Fundação Oswaldo Cruz (FIOCRUZ) - Recife, Pernambuco 50740-465, Brazil
| | - Ronaldo Mohana-Borges
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro - UFRJ , Rio de Janeiro RJ 21941-902, Brazil
| | - Philippe Gallay
- Department of Immunology & Microbial Science, The Scripps Research Institute - La Jolla , San Diego, California 92037, United States
| | - Mauricio L Nogueira
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
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31
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Herrmann C, Avgousti DC, Weitzman MD. Differential Salt Fractionation of Nuclei to Analyze Chromatin-associated Proteins from Cultured Mammalian Cells. Bio Protoc 2017; 7:e2175. [PMID: 28845440 DOI: 10.21769/bioprotoc.2175] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Nucleosomes are the core units of cellular chromatin and are comprised of 147 base pairs (bp) of DNA wrapped around an octamer of histone proteins. Proteins such as chromatin remodelers, transcription factors, and DNA repair proteins interact dynamically with chromatin to regulate access to DNA, control gene transcription, and maintain genome integrity. The extent of association with chromatin changes rapidly in response to stresses, such as immune activation, oxidative stress, or viral infection, resulting in downstream effects on chromatin conformation and transcription of target genes. To elucidate changes in the composition of proteins associated with chromatin under different conditions, we adapted existing protocols to isolate nuclei and fractionate cellular chromatin using a gradient of salt concentrations. The presence of specific proteins in different salt fractions can be assessed by Western blotting or mass spectrometry, providing insight into the degree to which they are associated with chromatin.
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Affiliation(s)
- Christin Herrmann
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, USA.,Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, USA
| | - Daphne C Avgousti
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Matthew D Weitzman
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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32
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Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB. Posttranscriptional Regulation in Adenovirus Infected Cells. J Proteome Res 2016; 16:872-888. [PMID: 27959563 DOI: 10.1021/acs.jproteome.6b00834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A deeper understanding of how viruses reprogram their hosts for production of progeny is needed to combat infections. Most knowledge on the regulation of cellular gene expression during adenovirus infection is derived from mRNA studies. Here, we investigated the changes in protein expression during the late phase of adenovirus type 2 (Ad2) infection of the IMR-90 cell line by stable isotope labeling in cell culture with subsequent liquid chromatography-high resolution tandem mass spectrometric analysis. Two biological replicates of samples collected at 24 and 36 h post-infection (hpi) were investigated using swapped labeling. In total, 2648 and 2394 proteins were quantified at 24 and 36 hpi, respectively. Among them, 659 and 645 were deregulated >1.6-fold at the two time points. The protein expression was compared with RNA expression using cDNA sequencing data. The correlation was surprisingly low (r = 0.3), and several examples of posttranscriptional regulation were observed; e.g., proteins related to carbohydrate metabolism were up-regulated at the protein level but unchanged at the RNA level, whereas histone proteins were down-regulated at the protein level but up-regulated at the RNA level. The deregulation of cellular gene expression by adenovirus is mediated at multiple levels and more complex than hitherto believed.
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Affiliation(s)
- Hongxing Zhao
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory , 751 85 Uppsala, Sweden
| | - Anne Konzer
- Department of Chemistry-BMC, Science for Life Laboratory, Analytical Chemistry, Box 599, Uppsala University , 751 24 Uppsala, Sweden
| | - Jia Mi
- Department of Chemistry-BMC, Science for Life Laboratory, Analytical Chemistry, Box 599, Uppsala University , 751 24 Uppsala, Sweden
| | - Moashan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, LaTrobe University , Melbourne, Victoria 3086, Australia
| | - Ulf Pettersson
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory , 751 85 Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Science for Life Laboratory, Analytical Chemistry, Box 599, Uppsala University , 751 24 Uppsala, Sweden
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Automatic detection and measurement of viral replication compartments by ellipse adjustment. Sci Rep 2016; 6:36505. [PMID: 27819325 PMCID: PMC5098162 DOI: 10.1038/srep36505] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 10/13/2016] [Indexed: 01/03/2023] Open
Abstract
Viruses employ a variety of strategies to hijack cellular activities through the orchestrated recruitment of macromolecules to specific virus-induced cellular micro-environments. Adenoviruses (Ad) and other DNA viruses induce extensive reorganization of the cell nucleus and formation of nuclear Replication Compartments (RCs), where the viral genome is replicated and expressed. In this work an automatic algorithm designed for detection and segmentation of RCs using ellipses is presented. Unlike algorithms available in the literature, this approach is deterministic, automatic, and can adjust multiple RCs using ellipses. The proposed algorithm is non iterative, computationally efficient and is invariant to affine transformations. The method was validated over both synthetic images and more than 400 real images of Ad-infected cells at various timepoints of the viral replication cycle obtaining relevant information about the biogenesis of adenoviral RCs. As proof of concept the algorithm was then used to quantitatively compare RCs in cells infected with the adenovirus wild type or an adenovirus mutant that is null for expression of a viral protein that is known to affect activities associated with RCs that result in deficient viral progeny production.
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Komatsu T, Robinson DR, Hisaoka M, Ueshima S, Okuwaki M, Nagata K, Wodrich H. Tracking adenovirus genomes identifies morphologically distinct late DNA replication compartments. Traffic 2016; 17:1168-1180. [PMID: 27492875 DOI: 10.1111/tra.12429] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/02/2016] [Accepted: 08/02/2016] [Indexed: 02/01/2023]
Abstract
In adenoviral virions, the genome is organized into a chromatin-like structure by viral basic core proteins. Consequently viral DNAs must be replicated, chromatinized and packed into progeny virions in infected cells. Although viral DNA replication centers can be visualized by virtue of viral and cellular factors, the spatiotemporal regulation of viral genomes during subsequent steps remains to be elucidated. In this study, we used imaging analyses to examine the fate of adenoviral genomes and to track newly replicated viral DNA as well as replication-related factors. We show de novo formation of a subnuclear domain, which we termed Virus-induced Post-Replication (ViPR) body, that emerges concomitantly with or immediately after disintegration of initial replication centers. Using a nucleoside analogue, we show that viral genomes continue being synthesized in morphologically distinct replication compartments at the periphery of ViPR bodies and are then transported inward. In addition, we identified a nucleolar protein Mybbp1a as a molecular marker for ViPR bodies, which specifically associated with viral core protein VII. In conclusion, our work demonstrates the formation of previously uncharacterized viral DNA replication compartments specific for late phases of infection that produce progeny viral genomes accumulating in ViPR bodies.
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Affiliation(s)
- Tetsuro Komatsu
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France.,Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Derrick R Robinson
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Miharu Hisaoka
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shuhei Ueshima
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mitsuru Okuwaki
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France.
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Nicolas E, Parisot P, Pinto-Monteiro C, de Walque R, De Vleeschouwer C, Lafontaine DLJ. Involvement of human ribosomal proteins in nucleolar structure and p53-dependent nucleolar stress. Nat Commun 2016; 7:11390. [PMID: 27265389 PMCID: PMC4897761 DOI: 10.1038/ncomms11390] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 03/21/2016] [Indexed: 02/07/2023] Open
Abstract
The nucleolus is a potent disease biomarker and a target in cancer therapy. Ribosome biogenesis is initiated in the nucleolus where most ribosomal (r-) proteins assemble onto precursor rRNAs. Here we systematically investigate how depletion of each of the 80 human r-proteins affects nucleolar structure, pre-rRNA processing, mature rRNA accumulation and p53 steady-state level. We developed an image-processing programme for qualitative and quantitative discrimination of normal from altered nucleolar morphology. Remarkably, we find that uL5 (formerly RPL11) and uL18 (RPL5) are the strongest contributors to nucleolar integrity. Together with the 5S rRNA, they form the late-assembling central protuberance on mature 60S subunits, and act as an Hdm2 trap and p53 stabilizer. Other major contributors to p53 homeostasis are also strictly late-assembling large subunit r-proteins essential to nucleolar structure. The identification of the r-proteins that specifically contribute to maintaining nucleolar structure and p53 steady-state level provides insights into fundamental aspects of cell and cancer biology. The nucleolus is a specialized functional domain of the nucleus where ribosome biogenesis is initiated and also implicated in a p53-dependent anti-tumor surveillance. Here the authors use a quantitative imaging approach to detail the role of each ribosomal protein on the structural integrity of the nucleolus and p53 homeostasis.
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Affiliation(s)
- Emilien Nicolas
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium.,Center for Microscopy and Molecular Imaging, B-6041 Charleroi-Gosselies, Belgium
| | - Pascaline Parisot
- ICTEAM-ELEN, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Celina Pinto-Monteiro
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Roxane de Walque
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | | | - Denis L J Lafontaine
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium.,Center for Microscopy and Molecular Imaging, B-6041 Charleroi-Gosselies, Belgium
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Ma TH, Lee LW, Lee CC, Yi YH, Chan SP, Tan BCM, Lo SJ. Genetic control of nucleolar size: An evolutionary perspective. Nucleus 2016; 7:112-20. [PMID: 27003693 DOI: 10.1080/19491034.2016.1166322] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Exploiting a C. elegans mutant (ncl-1) exhibiting nucleolar abnormalities, we recently identified the let-7/ncl-1/fib-1 genetic cascade underlying proper rRNA abundance and nucleolar size. These 3 factors, let-7 (a miRNA), NCL-1 (a member of the TRIM-NHL family), and fibrillarin (a nucleolar methyltransferase), are evolutionarily conserved across metazoans. In this article, we provide several lines of bioinformatic evidence showing that human and Drosophila homologues of C. elegans NCL-1, TRIM-71 and Brat, respectively, likely act as translational suppressors of fibrillarin. Moreover, since their 3'-UTRs contain putative target sites, they may also be under the control of the let-7 miRNA. We hypothesize that let-7, TRIM and fibrillarin contribute activities in concert, and constitute a conserved network controlling nucleolar size in eukaryotes. We provide an in-depth literature review of various molecular pathways, including the let-7/ncl-1/fib-1 genetic cascade, implicated in the regulation of nucleolar size.
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Affiliation(s)
- Tian-Hsiang Ma
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Li-Wei Lee
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Chi-Chang Lee
- d Institute of Chemistry , Academia Sinica , Taipei , Taiwan
| | - Yung-Hsiang Yi
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Shih-Peng Chan
- e Graduate Institute of Microbiology , College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Bertrand Chin-Ming Tan
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Szecheng J Lo
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
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37
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Källsten M, Bergquist J, Zhao H, Konzer A, Lind SB. A comparative study of phosphopeptide-selective techniques for a sub-proteome of a complex biological sample. Anal Bioanal Chem 2016; 408:2347-56. [DOI: 10.1007/s00216-016-9333-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/18/2015] [Accepted: 01/13/2016] [Indexed: 11/24/2022]
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Morphological, Biochemical, and Functional Study of Viral Replication Compartments Isolated from Adenovirus-Infected Cells. J Virol 2016; 90:3411-27. [PMID: 26764008 DOI: 10.1128/jvi.00033-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 01/11/2016] [Indexed: 01/09/2023] Open
Abstract
UNLABELLED Adenovirus (Ad) replication compartments (RC) are nuclear microenvironments where the viral genome is replicated and a coordinated program of late gene expression is established. These virus-induced nuclear sites seem to behave as central hubs for the regulation of virus-host cell interactions, since proteins that promote efficient viral replication as well as factors that participate in the antiviral response are coopted and concentrated there. To gain further insight into the activities of viral RC, here we report, for the first time, the morphology, composition, and activities of RC isolated from Ad-infected cells. Morphological analyses of isolated RC particles by superresolution microscopy showed that they were indistinguishable from RC within infected cells and that they displayed a dynamic compartmentalization. Furthermore, the RC-containing fractions (RCf) proved to be functional, as they directed de novo synthesis of viral DNA and RNA as well as RNA splicing, activities that are associated with RC in vivo. A detailed analysis of the production of viral late mRNA from RCf at different times postinfection revealed that viral mRNA splicing occurs in RC and that the synthesis, posttranscriptional processing, and release from RC to the nucleoplasm of individual viral late transcripts are spatiotemporally separate events. The results presented here demonstrate that RCf are a powerful system for detailed study into RC structure, composition, and activities and, as a result, the determination of the molecular mechanisms that induce the formation of these viral sites of adenoviruses and other nuclear-replicating viruses. IMPORTANCE RC may represent molecular hubs where many aspects of virus-host cell interaction are controlled. Here, we show by superresolution microscopy that RCf have morphologies similar to those of RC within Ad-infected cells and that they appear to be compartmentalized, as nucleolin and DBP display different localization in the periphery of these viral sites. RCf proved to be functional, as they direct de novo synthesis of viral DNA and mRNA, allowing the detailed study of the regulation of viral genome replication and expression. Furthermore, we show that the synthesis and splicing of individual viral late mRNA occurs in RC and that they are subject to different temporal patterns of regulation, from their synthesis to their splicing and release from RC to the nucleoplasm. Hence, RCf represent a novel system to study molecular mechanisms that are orchestrated in viral RC to take control of the infected cell and promote an efficient viral replication cycle.
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39
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Rawlinson SM, Moseley GW. The nucleolar interface of
RNA
viruses. Cell Microbiol 2015; 17:1108-20. [DOI: 10.1111/cmi.12465] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Stephen M. Rawlinson
- Viral Pathogenesis Laboratory Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute The University of Melbourne Melbourne Australia
| | - Gregory W. Moseley
- Viral Pathogenesis Laboratory Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute The University of Melbourne Melbourne Australia
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40
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Munday DC, Howell G, Barr JN, Hiscox JA. Proteomic analysis of mitochondria in respiratory epithelial cells infected with human respiratory syncytial virus and functional implications for virus and cell biology. ACTA ACUST UNITED AC 2014; 67:300-18. [PMID: 25533920 DOI: 10.1111/jphp.12349] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/12/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this study was to quantitatively characterise the mitochondrial proteome of airway epithelial cells infected with human respiratory syncytial virus (HRSV), a major cause of paediatric illness. METHODS Quantitative proteomics, underpinned by stable isotope labelling with amino acids in cell culture, coupled to LC-MS/MS, was applied to mitochondrial fractions prepared from HRSV-infected and mock-infected cells 12 and 24 h post-infection. Datasets were analysed using ingenuity pathway analysis, and the results were validated and characterised using bioimaging, targeted inhibition and gene depletion. KEY FINDINGS The data quantitatively indicated that antiviral signalling proteins converged on mitochondria during HRSV infection. The mitochondrial receptor protein Tom70 was found to act in an antiviral manner, while its chaperone, Hsp90, was confirmed to be a positive viral factor. Proteins associated with different organelles were also co-enriched in the mitochondrial fractions from HRSV-infected cells, suggesting that alterations in organelle dynamics and membrane associations occur during virus infection. CONCLUSIONS Protein and pathway-specific alterations occur to the mitochondrial proteome in a spatial and temporal manner during HRSV infection, suggesting that this organelle may have altered functions. These could be targeted as part of potential therapeutic strategies to disrupt virus biology.
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Affiliation(s)
- Diane C Munday
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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41
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Kleinman CL, Doria M, Orecchini E, Giuliani E, Galardi S, De Jay N, Michienzi A. HIV-1 infection causes a down-regulation of genes involved in ribosome biogenesis. PLoS One 2014; 9:e113908. [PMID: 25462981 PMCID: PMC4252078 DOI: 10.1371/journal.pone.0113908] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/28/2014] [Indexed: 01/04/2023] Open
Abstract
HIV-1 preferentially infects CD4+ T cells, causing fundamental changes that eventually lead to the release of new viral particles and cell death. To investigate in detail alterations in the transcriptome of the CD4+ T cells upon viral infection, we sequenced polyadenylated RNA isolated from Jurkat cells infected or not with HIV-1. We found a marked global alteration of gene expression following infection, with an overall trend toward induction of genes, indicating widespread modification of the host biology. Annotation and pathway analysis of the most deregulated genes showed that viral infection produces a down-regulation of genes associated with the nucleolus, in particular those implicated in regulating the different steps of ribosome biogenesis, such as ribosomal RNA (rRNA) transcription, pre-rRNA processing, and ribosome maturation. The impact of HIV-1 infection on genes involved in ribosome biogenesis was further validated in primary CD4+ T cells. Moreover, we provided evidence by Northern Blot experiments, that host pre-rRNA processing in Jurkat cells might be perturbed during HIV-1 infection, thus strengthening the hypothesis of a crosstalk between nucleolar functions and viral pathogenesis.
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Affiliation(s)
- Claudia L. Kleinman
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital and Department of Human Genetics, McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec, H3T 1E2, Canada
| | - Margherita Doria
- Laboratory of Immunoinfectivology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elisa Orecchini
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Erica Giuliani
- Laboratory of Immunoinfectivology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Nicolas De Jay
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital and Department of Human Genetics, McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec, H3T 1E2, Canada
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
- * E-mail:
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Zaas AK, Garner BH, Tsalik EL, Burke T, Woods CW, Ginsburg GS. The current epidemiology and clinical decisions surrounding acute respiratory infections. Trends Mol Med 2014; 20:579-88. [PMID: 25201713 DOI: 10.1016/j.molmed.2014.08.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 12/15/2022]
Abstract
Acute respiratory infection (ARI) is a common diagnosis in outpatient and emergent care settings. Currently available diagnostics are limited, creating uncertainty in the use of antibacterial, antiviral, or supportive care. Up to 72% of ambulatory care patients with ARI are treated with an antibacterial, despite only a small fraction actually needing one. Antibiotic overuse is not restricted to ambulatory care: ARI accounts for approximately 5 million emergency department (ED) visits annually in the USA, where 52-61% of such patients receive antibiotics. Thus, an accurate test for the presence or absence of viral or bacterial infection is needed. In this review, we focus on recent research showing that the host-response (genomic, proteomic, or miRNA) can accomplish this task.
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Affiliation(s)
- Aimee K Zaas
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
| | - Bronwen H Garner
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Thomas Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
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Diesch J, Hannan RD, Sanij E. Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease. Cell Biosci 2014; 4:43. [PMID: 25949792 PMCID: PMC4422213 DOI: 10.1186/2045-3701-4-43] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 07/27/2014] [Indexed: 01/05/2023] Open
Abstract
Ribosomal RNA (rRNA) gene (rDNA) transcription by RNA Polymerase I (Pol I) drives cell growth and underlies nucleolar structure and function, indirectly coordinating many fundamental cellular processes. The importance of keeping rDNA transcription under tight control is reflected by the fact that deranged Pol I transcription is a feature of cancer and other human disorders. In this review, we discuss multiple aspects of rDNA function including the relationship between Pol I transcription and proliferative capacity, the role of Pol I transcription in mediating nucleolar structure and integrity, and rDNA/nucleolar interactions with the genome and their influence on heterochromatin and global genome stability. Furthermore, we discuss how perturbations in the structure of the rDNA loci might contribute to human disease, in some cases independent of effects on ribosome biogenesis.
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Affiliation(s)
- Jeannine Diesch
- Growth Control Laboratory, Research Division, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross D Hannan
- Growth Control Laboratory, Research Division, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia ; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia ; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia ; Division of Cancer Medicine, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elaine Sanij
- Growth Control Laboratory, Research Division, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia ; Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
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Greco TM, Diner BA, Cristea IM. The Impact of Mass Spectrometry-Based Proteomics on Fundamental Discoveries in Virology. Annu Rev Virol 2014; 1:581-604. [PMID: 26958735 DOI: 10.1146/annurev-virology-031413-085527] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In recent years, mass spectrometry has emerged as a core component of fundamental discoveries in virology. As a consequence of their coevolution, viruses and host cells have established complex, dynamic interactions that function either in promoting virus replication and dissemination or in host defense against invading pathogens. Thus, viral infection triggers an impressive range of proteome changes. Alterations in protein abundances, interactions, posttranslational modifications, subcellular localizations, and secretion are temporally regulated during the progression of an infection. Consequently, understanding viral infection at the molecular level requires versatile approaches that afford both breadth and depth of analysis. Mass spectrometry is uniquely positioned to bridge this experimental dichotomy. Its application to both unbiased systems analyses and targeted, hypothesis-driven studies has accelerated discoveries in viral pathogenesis and host defense. Here, we review the contributions of mass spectrometry-based proteomic approaches to understanding viral morphogenesis, replication, and assembly and to characterizing host responses to infection.
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Affiliation(s)
- Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
| | - Benjamin A Diner
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
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45
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The nucleolus—guardian of cellular homeostasis and genome integrity. Chromosoma 2014; 122:487-97. [PMID: 24022641 DOI: 10.1007/s00412-013-0430-0] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/05/2013] [Indexed: 01/25/2023]
Abstract
All organisms sense and respond to conditions that stress their homeostasis by downregulating the synthesis of rRNA and ribosome biogenesis, thus designating the nucleolus as the central hub in coordinating the cellular stress response. One of the most intriguing roles of the nucleolus, long regarded as a mere ribosome-producing factory, is its participation in monitoring cellular stress signals and transmitting them to the RNA polymerase I (Pol I) transcription machinery. As rRNA synthesis is a most energy-consuming process, switching off transcription of rRNA genes is an effective way of saving the energy required to maintain cellular homeostasis during acute stress. The Pol I transcription machinery is the key convergence point that collects and integrates a vast array of information from cellular signaling cascades to regulate ribosome production which, in turn, guides cell growth and proliferation. This review focuses on the mechanisms that link cell physiology to rDNA silencing, a prerequisite for nucleolar integrity and cell survival.
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46
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Dillinger S, Garea AV, Deutzmann R, Németh A. Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry. Methods Mol Biol 2014; 1094:277-93. [PMID: 24162996 DOI: 10.1007/978-1-62703-706-8_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin is unevenly distributed within the eukaryote nucleus and it contributes to the formation of morphologically and functionally distinct substructures, called chromatin domains and nuclear bodies. Here we describe an approach to assess specific chromatin features, the histone posttranslational modifications (PTMs), of the largest nuclear sub-compartment, the nucleolus. In this chapter, methods for the isolation of nucleolus-associated chromatin from native or formaldehyde-fixed cells and the effect of experimental procedures on the outcome of mass spectrometry analysis of histone PTMs are compared.
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Affiliation(s)
- Stefan Dillinger
- Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany
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Lee YJ, Wei HM, Chen LY, Li C. Localization of SERBP1 in stress granules and nucleoli. FEBS J 2013; 281:352-64. [DOI: 10.1111/febs.12606] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 11/06/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Yu-Jen Lee
- Institute of Biochemistry and Biotechnology; Chung Shan Medical University; Taichung Taiwan
| | - Hung-Ming Wei
- Department of Biomedical Sciences; Chung Shan Medical University; Taichung Taiwan
| | - Ling-Yun Chen
- Institute of Biochemistry and Biotechnology; Chung Shan Medical University; Taichung Taiwan
| | - Chuan Li
- Department of Biomedical Sciences; Chung Shan Medical University; Taichung Taiwan
- Department of Medical Research; Chung Shan Medical University Hospital; Taichung Taiwan
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Wu X, Wang S, Yu Y, Zhang J, Sun Z, Yan Y, Zhou J. Subcellular proteomic analysis of human host cells infected with H3N2 swine influenza virus. Proteomics 2013; 13:3309-26. [PMID: 24115376 DOI: 10.1002/pmic.201300180] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/25/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022]
Abstract
Cross-species transmissions of swine influenza viruses (SIVs) raise great public health concerns. In this study, subcellular proteomic profiles of human A549 cells inoculated with H3N2 subtype SIV were used to characterize dynamic cellular responses to infection. By 2DE and MS, 27 differentially expressed (13 upregulated, 14 downregulated) cytoplasmic proteins and 20 differentially expressed (13 upregulated, 7 downregulated) nuclear proteins were identified. Gene ontology analysis suggested that these differentially expressed proteins were mainly involved in cell death, stress response, lipid metabolism, cell signaling, and RNA PTMs. Moreover, 25 corresponding genes of the differentially expressed proteins were quantitated by real time RT-PCR to examine the transcriptional profiles between mock- and virus-infected A549 cells. Western blot analysis confirmed that changes in abundance of identified cellular proteins heterogeneous nuclear ribonucleoprotein (hnRNP) U, hnRNP C, ALDH1A1, tryptophanyl-tRNA synthetase, IFI35, and HSPB1 in H3N2 SIV-infected cells were consistent with results of 2DE analysis. By confocal microscopy, nucleus-to-cytoplasm translocation of hnRNP C and colocalization between the viral nonstructural protein 1 and hnRNP C as well as N-myc (and STAT) interactor were observed upon infection. Ingenuity Pathway Analysis revealed that cellular proteins altered during infection were grouped mainly into NFκB and interferon signaling networks. Collectively, these identified subcellular constituents provide an important framework for understanding host/SIV interactions and underlying mechanisms of SIV cross-species infection and pathogenesis.
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Affiliation(s)
- Xiaopeng Wu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, P. R. China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou, P. R. China
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49
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Hein N, Hannan KM, George AJ, Sanij E, Hannan RD. The nucleolus: an emerging target for cancer therapy. Trends Mol Med 2013; 19:643-54. [PMID: 23953479 DOI: 10.1016/j.molmed.2013.07.005] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 02/07/2023]
Abstract
For over 100 years, pathologists have utilised an increase in size and number of nucleoli, the subnuclear site of ribosome synthesis, as a marker of aggressive tumours. Despite this, the contribution of the nucleolus and ribosomal RNA synthesis to cancer has been largely overlooked. This concept has recently changed with the demonstration that the nucleolus indirectly controls numerous other cellular functions, in particular, the cellular activity of the critical tumour suppressor protein, p53. Moreover, selective inhibition of ribosomal gene transcription in the nucleolus has been shown to be an effective therapeutic strategy to promote cancer-specific activation of p53. This article reviews the largely untapped potential of the nucleolus and ribosomal gene transcription as exciting new targets for cancer therapy.
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Affiliation(s)
- Nadine Hein
- Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, 3002, Victoria, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Victoria, Australia
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Tafforeau L, Zorbas C, Langhendries JL, Mullineux ST, Stamatopoulou V, Mullier R, Wacheul L, Lafontaine D. The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors. Mol Cell 2013; 51:539-51. [DOI: 10.1016/j.molcel.2013.08.011] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/06/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
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