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Dickmander RJ, Lenarcic EM, Sears JD, Hale AE, Moorman NJ. RNA-targeted proteomics identifies YBX1 as critical for efficient HCMV mRNA translation. Proc Natl Acad Sci U S A 2025; 122:e2421155122. [PMID: 40035757 PMCID: PMC11912382 DOI: 10.1073/pnas.2421155122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 01/17/2025] [Indexed: 03/06/2025] Open
Abstract
Viruses have evolved unique strategies to circumvent host control of protein synthesis and enable viral protein synthesis in the face of the host response. Defining the factors that regulate viral messenger RNA (mRNA) translation is thus critical to understand how viruses replicate and cause disease. To identify factors that might regulate viral mRNA translation, we developed a technique for identifying proteins associated with a native RNA expressed from its endogenous promoter and genomic locus. This approach uses a guide RNA to target dCas13b fused to a biotin ligase domain to a specific RNA, where it covalently labels proteins in close proximity. Using this approach, we identified multiple proteins associated with transcripts encoding the human cytomegalovirus (HCMV) IE1 and IE2 proteins and found that several associated proteins positively or negatively regulate HCMV replication. We confirmed that one such protein, the cellular Y-box binding protein 1 (YBX1), binds to HCMV immediate early mRNAs and is required for efficient viral protein expression and virus replication. Ablating YBX1 expression reduced the association of HCMV immediate early mRNAs with polysomes, demonstrating a role for YBX1 as a positive regulator of viral RNA translation. These results provide a powerful tool for unraveling RNA-protein interactions that can be used in a wide range of biological processes and reveal a role for YBX1 as a critical regulator of HCMV immediate early gene expression.
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Affiliation(s)
- Rebekah J. Dickmander
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Erik M. Lenarcic
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - John D. Sears
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Andrew E. Hale
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nathaniel J. Moorman
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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2
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Giraldo-Ocampo S, Valiente-Echeverría F, Soto-Rifo R. Host RNA-Binding Proteins as Regulators of HIV-1 Replication. Viruses 2024; 17:43. [PMID: 39861832 PMCID: PMC11768693 DOI: 10.3390/v17010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Revised: 12/26/2024] [Accepted: 12/27/2024] [Indexed: 01/27/2025] Open
Abstract
RNA-binding proteins (RBPs) are cellular factors involved in every step of RNA metabolism. During HIV-1 infection, these proteins are key players in the fine-tuning of viral and host cellular and molecular pathways, including (but not limited to) viral entry, transcription, splicing, RNA modification, translation, decay, assembly, and packaging, as well as the modulation of the antiviral response. Targeted studies have been of paramount importance in identifying and understanding the role of RNA-binding proteins that bind to HIV-1 RNAs. However, novel approaches aimed at identifying all the proteins bound to specific RNAs (RBPome), such as RNA interactome capture, have also contributed to expanding our understanding of the HIV-1 replication cycle, allowing the identification of RBPs with functions not only in viral RNA metabolism but also in cellular metabolism. Strikingly, several of the RBPs found through interactome capture are not canonical RBPs, meaning that they do not have conventional RNA-binding domains and are therefore not readily predicted as being RBPs. Further studies on the different cellular targets of HIV-1, such as subtypes of T cells or myeloid cells, or on the context (active replication versus reactivation from latency) are needed to fully elucidate the host RBPome bound to the viral RNA, which will allow researchers and clinicians to discover new therapeutic targets during active replication and provirus reactivation from latency.
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Affiliation(s)
- Sebastian Giraldo-Ocampo
- Laboratory of Molecular and Cellular Virology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (S.G.-O.); (F.V.-E.)
- Center for HIV/AIDS Integral Research (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Millennium Institute in Immunology and Immunotherapy, Santiago 8380453, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (S.G.-O.); (F.V.-E.)
- Center for HIV/AIDS Integral Research (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Millennium Institute in Immunology and Immunotherapy, Santiago 8380453, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (S.G.-O.); (F.V.-E.)
- Center for HIV/AIDS Integral Research (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Millennium Institute in Immunology and Immunotherapy, Santiago 8380453, Chile
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3
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Smith S, Seth J, Midkiff A, Stahl R, Syu YC, Shkriabai N, Kvaratskhelia M, Musier-Forsyth K, Jain P, Green PL, Panfil AR. The Pleiotropic Effects of YBX1 on HTLV-1 Transcription. Int J Mol Sci 2023; 24:13119. [PMID: 37685922 PMCID: PMC10487795 DOI: 10.3390/ijms241713119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
HTLV-1 is an oncogenic human retrovirus and the etiologic agent of the highly aggressive ATL malignancy. Two viral genes, Tax and Hbz, are individually linked to oncogenic transformation and play an important role in the pathogenic process. Consequently, regulation of HTLV-1 gene expression is a central feature in the viral lifecycle and directly contributes to its pathogenic potential. Herein, we identified the cellular transcription factor YBX1 as a binding partner for HBZ. We found YBX1 activated transcription and enhanced Tax-mediated transcription from the viral 5' LTR promoter. Interestingly, YBX1 also interacted with Tax. shRNA-mediated loss of YBX1 decreased transcript and protein abundance of both Tax and HBZ in HTLV-1-transformed T-cell lines, as well as Tax association with the 5' LTR. Conversely, YBX1 transcriptional activation of the 5' LTR promoter was increased in the absence of HBZ. YBX1 was found to be associated with both the 5' and 3' LTRs in HTLV-1-transformed and ATL-derived T-cell lines. Together, these data suggest that YBX1 positively influences transcription from both the 5' and 3' promoter elements. YBX1 is able to interact with Tax and help recruit Tax to the 5' LTR. However, through interactions with HBZ, YBX1 transcriptional activation of the 5' LTR is repressed.
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Affiliation(s)
- Susan Smith
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Jaideep Seth
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Amanda Midkiff
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Rachel Stahl
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Yu-Ci Syu
- Center for Retrovirus Research, Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; (Y.-C.S.); (K.M.-F.)
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA; (N.S.); (M.K.)
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA; (N.S.); (M.K.)
| | - Karin Musier-Forsyth
- Center for Retrovirus Research, Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; (Y.-C.S.); (K.M.-F.)
| | - Pooja Jain
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA;
| | - Patrick L. Green
- Center for Retrovirus Research, Comprehensive Cancer Center and Solove Research Institute, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Amanda R. Panfil
- Center for Retrovirus Research, Comprehensive Cancer Center and Solove Research Institute, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
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4
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Diosa-Toro M, Kennedy DR, Chuo V, Popov VL, Pompon J, Garcia-Blanco MA. Y-Box Binding Protein 1 Interacts with Dengue Virus Nucleocapsid and Mediates Viral Assembly. mBio 2022; 13:e0019622. [PMID: 35189699 PMCID: PMC8903895 DOI: 10.1128/mbio.00196-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Infection with dengue virus (DENV) induces vast rearrangements of the endoplasmic reticulum, which allows the compartmentalization of viral RNA replication and particle assembly. Both processes occur in concert with viral and cellular proteins. Prior studies from our group suggest that the host RNA-binding protein (RBP) Y-box binding protein 1 (YBX1) is required for a late step in the DENV replication cycle. Here we report that YBX1 interacts with the viral nucleocapsid, distributes to DENV assembly sites and is required for efficient assembly of intracellular infectious virions and their secretion. Genetic ablation of YBX1 decreased the spatial proximity between capsid and envelope, increased the susceptibility of envelope to proteinase K mediated degradation, resulted in the formation of rough empty-looking particles, and decreased the secretion of viral particles. We propose a model wherein YBX1 enables the interaction between the viral nucleocapsid with the structural protein E, which is required for proper assembly of intracellular virus particles and their secretion. IMPORTANCE The global incidence of dengue virus (DENV) infections has steadily increased over the past decades representing an enormous challenge for public health. During infection, DENV viral RNA interacts with numerous host RNA binding proteins (RBPs) that aid viral replication and thus constitute potential molecular targets to curb infection. We recently reported that Y-box-binding protein 1 (YBX1) interacts with DENV RNA and is required at a late step of the replication cycle. Here we describe the molecular mechanism by which YBX1 mediates DENV infection. We show that YBX1 interacts with the viral nucleocapsid, distributes to DENV assembly sites and is required for efficient assembly of intracellular infectious virions. These results provide important insights into DENV assembly, revealing novel functions of host RBPs during viral infection and opening new avenues for antiviral intervention.
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Affiliation(s)
- Mayra Diosa-Toro
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Debbie R. Kennedy
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Vanessa Chuo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Vsevolod L. Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Julien Pompon
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Mariano A. Garcia-Blanco
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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5
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Evdokimova V. Y-box Binding Protein 1: Looking Back to the Future. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S5-S145. [PMID: 35501983 DOI: 10.1134/s0006297922140024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding protein 1 is a member of the cold shock domain (CSD) protein family and one of the most studied proteins associated with a large number of human diseases. This review aims to critically reassess the growing number of pathological functions ascribed to YB-1 in the past decades. The focus is given on the important role of YB-1 and related CSD proteins in the physiology of normal cells. The functional significance of these proteins is highlighted by their high evolutionary conservation from bacteria to men, where they are ubiquitously expressed and involved in coordinating all steps of mRNA biogenesis, including transcription, translation, storage, and degradation. Their activities are especially important under conditions requiring rapid change in the gene expression programs, such as early embryonic development, differentiation, stress, and adaptation to new environments. Therefore, to define a precise role of YB-1 in tumorigenic transformation and in other pathological conditions, it is important to understand its basic properties and functions in normal cells, and how they are interrupted in complex diseases including cancer.
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6
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Knoener R, Evans E, Becker JT, Scalf M, Benner B, Sherer NM, Smith LM. Identification of host proteins differentially associated with HIV-1 RNA splice variants. eLife 2021; 10:e62470. [PMID: 33629952 PMCID: PMC7906601 DOI: 10.7554/elife.62470] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
HIV-1 generates unspliced (US), partially spliced (PS), and completely spliced (CS) classes of RNAs, each playing distinct roles in viral replication. Elucidating their host protein 'interactomes' is crucial to understanding virus-host interplay. Here, we present HyPR-MSSV for isolation of US, PS, and CS transcripts from a single population of infected CD4+ T-cells and mass spectrometric identification of their in vivo protein interactomes. Analysis revealed 212 proteins differentially associated with the unique RNA classes, including preferential association of regulators of RNA stability with US and PS transcripts and, unexpectedly, mitochondria-linked proteins with US transcripts. Remarkably, >80 of these factors screened by siRNA knockdown impacted HIV-1 gene expression. Fluorescence microscopy confirmed several to co-localize with HIV-1 US RNA and exhibit changes in abundance and/or localization over the course of infection. This study validates HyPR-MSSV for discovery of viral splice variant protein interactomes and provides an unprecedented resource of factors and pathways likely important to HIV-1 replication.
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Affiliation(s)
- Rachel Knoener
- Department of Chemistry, University of WisconsinMadisonUnited States
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Edward Evans
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Jordan T Becker
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Mark Scalf
- Department of Chemistry, University of WisconsinMadisonUnited States
| | - Bayleigh Benner
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Lloyd M Smith
- Department of Chemistry, University of WisconsinMadisonUnited States
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7
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Sangermano F, Delicato A, Calabrò V. Y box binding protein 1 (YB-1) oncoprotein at the hub of DNA proliferation, damage and cancer progression. Biochimie 2020; 179:205-216. [PMID: 33058958 DOI: 10.1016/j.biochi.2020.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022]
Abstract
The Y Box binding protein 1 (YB-1) belongs to the highly conserved Cold Shock Domain protein family and is a major component of messenger ribonucleoprotein particles (mRNPs) in various organisms and cells. Cold Shock proteins are multifunctional nucleic acids binding proteins involved in a variety of cellular functions. Biological activities of YB-1 range from the regulation of transcription, splicing and translation, to the orchestration of exosomal RNA content. The role of YB-1 in malignant cell transformation and fate transition is the subject of intensive investigation. Besides, emerging evidence indicates that YB-1 participates in several DNA damage repair pathways as a non-canonical DNA repair factor thus pointing out that the protein can allow cancer cells to evade conventional anticancer therapies and avoid cell death. Here, we will attempt to collect and summarize the current knowledge on this subject and provide the basis for further lines of inquiry.
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Affiliation(s)
- Felicia Sangermano
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Napoli, Italy.
| | - Antonella Delicato
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Viola Calabrò
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Napoli, Italy
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8
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Kong W, Rivera-Serrano EE, Neidleman JA, Zhu J. HIV-1 Replication Benefits from the RNA Epitranscriptomic Code. J Mol Biol 2019; 431:5032-5038. [PMID: 31626810 DOI: 10.1016/j.jmb.2019.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/22/2019] [Accepted: 09/27/2019] [Indexed: 12/27/2022]
Abstract
The effects of RNA methylation on HIV-1 replication remain largely unknown. Recent studies have discovered new insights into the effect of 2'-O-methylation and 5-methylcytidine marks on the HIV-1 RNA genome. As so far, HIV-1 benefits from diverse RNA methylations through distinct mechanisms. In this review, we summarize the recent advances in this emerging field and discuss the role of RNA methylation writers and readers in HIV-1 infection, which may help to find alternative strategies to control HIV-1 infection.
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Affiliation(s)
- Weili Kong
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA; Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, 94158, USA.
| | - Efraín E Rivera-Serrano
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Jason A Neidleman
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, 94158, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
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9
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He J, Xie TL, Li X, Yu Y, Zhan ZP, Weng SP, Guo CJ, He JG. Molecular cloning of Y-Box binding protein-1 from mandarin fish and its roles in stress-response and antiviral immunity. FISH & SHELLFISH IMMUNOLOGY 2019; 93:406-415. [PMID: 31369857 DOI: 10.1016/j.fsi.2019.07.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/14/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Mandarin fish (Siniperca chuatsi) is a universally farmed fish species in China and has a large farming scale and economic value. With the high-density cultural mode in mandarin fish, viral diseases, such as infectious spleen and kidney necrosis virus (ISKNV) and Siniperca chuatsi rhabdovirus (SCRV), have increased loss, which has seriously restricted the development of aquaculture. Y-Box binding protein 1 (YB-1) is a member of cold shock protein family that regulates multiple cellular processes. The roles of mammalian YB-1 protein in environmental stress and innate immunity have been studied well, but its roles in teleost fishes remain unknown. In the present study, the characteristic of S. chuatsi YB-1 (scYB-1) and its roles in cold stress and virus infection were investigated. The scYB-1 obtained an 1541 bp cDNA that contains a 903 bp open reading frame encoding a protein of 300 amino acids. Tissue distribution results showed that the scYB-1 is a ubiquitously expressed gene found among tissues from mandarin fish. Overexpression of scYB-1 can increase the expression levels of cold shock-responsive genes, such as scHsc70a, scHsc70b, and scp53. Furthermore, the role of scYB-1 in innate immunity was also investigated in mandarin fish fry (MFF-1) cells. The expression level of scYB-1 was significant change in response to poly (I:C), poly (dG:dC), PMA, ISKNV, or SCRV stimulation. The overexpression of scYB-1 can significantly increase the expression levels of NF-κB-responsive genes, including scIL-8, scTNF-α, and scIFN-h. The NF-κB-luciferase report assay results showed that the relative expression of luciferin was significantly increased in the cells overexpressed with scYB-1 compared with those in cells overexpressed with control plasmid. These results indicate that scYB-1 can induce the NF-κB signaling pathway in MFF-1 cells. Overexpressed scYB-1 can downregulate the expression of ISKNV viral major capsid protein (mcp) gene but upregulates the expression of SCRV mcp gene. Moreover, knockdown of scYB-1 using siRNA can upregulate the expression of ISKNV mcp gene but downregulates the expression of SCRV mcp gene. These results indicate that scYB-1 suppresses ISKNV infection while enhancing SCRV infection. The above observations suggest that scYB-1 is involved in cold stress and virus infection. Our study will provide an insight into the roles of teleost fish YB-1 protein in stress response and innate immunity.
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Affiliation(s)
- Jian He
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China
| | - Tao-Lin Xie
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China
| | - Xiao Li
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China
| | - Yang Yu
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China
| | - Zhi-Peng Zhan
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, PR China
| | - Shao-Ping Weng
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, PR China
| | - Chang-Jun Guo
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, PR China.
| | - Jian-Guo He
- State Key Laboratory for Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, No.132 Waihuan Dong Road, Higher Education Mega Center, Guangzhou, Guangdong, 510006, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, PR China
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10
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IL-27 posttranslationally regulates Y-box binding protein-1 to inhibit HIV-1 replication in human CD4+ T cells. AIDS 2019; 33:1819-1830. [PMID: 31274540 PMCID: PMC6731144 DOI: 10.1097/qad.0000000000002288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
IL-27 is known as an antiviral cytokine that inhibits HIV, hepatitis C virus, and other viruses. We have previously demonstrated that, IL-27 posttreatment after HIV-infection inhibits viral replication in primary CD4+ T cells.
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11
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Jung YM, Yu KL, Park SH, Lee SD, Kim MJ, You JC. Investigation of function and regulation of the YB-1 cellular factor in HIV replication. BMB Rep 2018; 51:290-295. [PMID: 29429449 PMCID: PMC6033064 DOI: 10.5483/bmbrep.2018.51.6.231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Indexed: 12/21/2022] Open
Abstract
Y-box binding protein 1 (YB-1) is a member of the cold-shock domain (CSD) protein superfamily. It participates in a wide variety of cellular events, including transcription, RNA splicing, translation, DNA repair, drug resistance, and stress responses. We investigated putative functions of YB-1 in HIV-1 replication. Functional studies using overexpression or knockdown of YB-1 in conjunction with transfection of proviral DNA showed that YB-1 enhances virus production. We found YB-1 regulates HIV-1 production by stimulating viral transcription using HIV-1 LTR sequence U3RU5 with Luciferase assay. We also identified a specific region from amino acids 1 to 324 of YB-1 as necessary for the participation of the protein in the production of virions.
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Affiliation(s)
- Yu-Mi Jung
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Kyung-Lee Yu
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seong-Hyun Park
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seong-Deok Lee
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | | | - Ji-Chang You
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591; Avixgen Inc., Seoul 06649, Korea
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Weydert C, van Heertum B, Dirix L, De Houwer S, De Wit F, Mast J, Husson SJ, Busschots K, König R, Gijsbers R, De Rijck J, Debyser Z. Y-box-binding protein 1 supports the early and late steps of HIV replication. PLoS One 2018; 13:e0200080. [PMID: 29995936 PMCID: PMC6040738 DOI: 10.1371/journal.pone.0200080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 06/19/2018] [Indexed: 12/31/2022] Open
Abstract
The human immunodeficiency virus (HIV) depends on cellular proteins, so-called cofactors, to complete its replication cycle. In search for new therapeutic targets we identified the DNA and RNA binding protein Y-box-binding Protein 1 (YB-1) as a cofactor supporting early and late steps of HIV replication. YB-1 depletion resulted in a 10-fold decrease in HIV-1 replication in different cell lines. Dissection of the replication defects revealed that knockdown of YB-1 is associated with a 2- to 5-fold decrease in virion production due to interference with the viral RNA metabolism. Using single-round virus infection experiments we demonstrated that early HIV-1 replication also depends on the cellular YB-1 levels. More precisely, using quantitative PCR and an in vivo nuclear import assay with fluorescently labeled viral particles, we showed that YB-1 knockdown leads to a block between reverse transcription and nuclear import of HIV-1. Interaction studies revealed that YB-1 associates with integrase, although a direct interaction with HIV integrase could not be unambiguously proven. In conclusion, our results indicate that YB-1 affects multiple stages of HIV replication. Future research on the interaction between YB-1 and the virus will reveal whether this protein qualifies as a new antiviral target.
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Affiliation(s)
- Caroline Weydert
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Bart van Heertum
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Lieve Dirix
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Belgium
| | - Stéphanie De Houwer
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Flore De Wit
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan Mast
- Veterinary and Agrochemical Research Centre, VAR-CODA-CERVA, Brussels, Belgium
| | - Steven J. Husson
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, 3000 Leuven, Belgium
- Systemic Physiological & Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, 2000 Antwerp, Belgium
| | - Katrien Busschots
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Renate König
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Rik Gijsbers
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan De Rijck
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- * E-mail:
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13
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Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Sci Rep 2017; 7:16965. [PMID: 29208937 PMCID: PMC5717263 DOI: 10.1038/s41598-017-16793-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/17/2017] [Indexed: 02/05/2023] Open
Abstract
HIV-1 replication requires myriad interactions between cellular proteins and the viral unspliced RNA. These interactions are important in archetypal RNA processes such as transcription and translation as well as for more specialized functions including alternative splicing and packaging of unspliced genomic RNA into virions. We present here a hybridization capture strategy for purification of unspliced full-length HIV RNA-protein complexes preserved in vivo by formaldehyde crosslinking, and coupled with mass spectrometry to identify HIV RNA-protein interactors in HIV-1 infected cells. One hundred eighty-nine proteins were identified to interact with unspliced HIV RNA including Rev and Gag/Gag-Pol, 24 host proteins previously shown to bind segments of HIV RNA, and over 90 proteins previously shown to impact HIV replication. Further analysis using siRNA knockdown techniques against several of these proteins revealed significant changes to HIV expression. These results demonstrate the utility of the approach for the discovery of host proteins involved in HIV replication. Additionally, because this strategy only requires availability of 30 nucleotides of the HIV-RNA for hybridization with a capture oligonucleotide, it is readily applicable to any HIV system of interest regardless of cell type, HIV-1 virus strain, or experimental perturbation.
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Wang X, Sun B, Mbondji C, Biswas S, Zhao J, Hewlett I. Differences in Activation of HIV-1 Replication by Superinfection With HIV-1 and HIV-2 in U1 Cells. J Cell Physiol 2016; 232:1746-1753. [PMID: 27662631 DOI: 10.1002/jcp.25614] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022]
Abstract
Macrophages contribute to HIV-1 pathogenesis by forming a viral reservoir that serve as a viral source for the infection of CD4 T cells. The relationship between HIV-1 latent infection and superinfection in macrophages has not been well studied. Using susceptible U1 cells chronically infected with HIV-1, we studied the effects of HIV superinfection on latency and differences in superinfection with HIV-1 and HIV-2 in macrophages. We found that HIV-1 (MN) superinfection displayed increased HIV-1 replication in a time-dependent manner; while cells infected with HIV-2 (Rod) initially showed increased HIV-1 replication, followed by a decrease in HIV-1 RNA production. HIV-1 superinfection upregulated/activated NF-ĸB, NFAT, AP-1, SP-1, and MAPK Erk through expression/activation of molecules, CD4, CD3, TCRβ, Zap-70, PLCγ1, and PKCΘ in T cell receptor-related signaling pathways; while HIV-2 superinfection initially increased expression/activation of these molecules followed by decreased protein expression/activation. HIV superinfection initially downregulated HDAC1 and upregulated acetyl-histone H3 and histone H3 (K4), while HIV-2 superinfection demonstrated an increase in HDAC1 and a decrease in acetyl-histone H3 and histone H3 (K4) relative to HIV-1 superinfection. U1 cells superinfected with HIV-1 or HIV-2 showed differential expression of proteins, IL-2, PARP-1, YB-1, and LysRS. These findings indicate that superinfection with HIV-1 or HIV-2 has different effects on reactivation of HIV-1 replication. HIV-1 superinfection with high load of viral replication may result in high levels of cytotoxicity relative to HIV-2 superinfection. Cells infected with HIV-2 showed lower level of HIV-1 replication, suggesting that co-infection with HIV-2 may result in slower progression toward AIDS. J. Cell. Physiol. 232: 1746-1753, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Xue Wang
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Bing Sun
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Christelle Mbondji
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Santanu Biswas
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Indira Hewlett
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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Shurtleff MJ, Temoche-Diaz MM, Karfilis KV, Ri S, Schekman R. Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction. eLife 2016; 5. [PMID: 27559612 PMCID: PMC5047747 DOI: 10.7554/elife.19276] [Citation(s) in RCA: 460] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022] Open
Abstract
Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration, development and metastasis. To study the mechanisms of RNA packaging into exosomes, we devised a purification scheme based on the membrane marker CD63 to isolate a single exosome species secreted from HEK293T cells. Using immunoisolated CD63-containing exosomes we identified a set of miRNAs that are highly enriched with respect to their cellular levels. To explore the biochemical requirements for exosome biogenesis and RNA packaging, we devised a cell-free reaction that recapitulates the species-selective enclosure of miR-223 in isolated membranes supplemented with cytosol. We found that the RNA-binding protein Y-box protein I (YBX1) binds to and is required for the sorting of miR-223 in the cell-free reaction. Furthermore, YBX1 serves an important role in the secretion of miRNAs in exosomes by HEK293T cells. DOI:http://dx.doi.org/10.7554/eLife.19276.001 Human cells release molecules into their surroundings via membrane-bound packets called exosomes. These molecules can then circulate throughout the body and are protected from degradation. Among the cargos carried by exosomes are small molecules of RNA known as microRNAs, which are involved in regulating gene activity. Only a select subset of the hundreds of microRNAs in a human cell end up packaged into exosomes. This suggests that there might be a specific mechanism that sorts those microRNAs that are destined for export. However, few proteins or other factors that might be involved in this sorting process had been identified to date. Shurtleff et al. set out to identify these factors and started by purifying exosomes from human cells grown in the laboratory and looking for microRNAs that were more abundant in the exosomes than the cells. One exosome-specific microRNA, called miR-223, was further studied via a test-tube based system that uses extracts from cells rather than cells themselves. These experiments confirmed that miR-223 is selectively packed into exosomes that formed in the test tube. Using this system, Shurtleff et al. then isolated a protein called Y-box Protein I (or YBX1 for short) that binds to RNA molecules and found that it was required for this selective packaging. YBX1 is known to be a constituent of exosomes released from intact cells and may therefore be required to sort other RNA molecules into exosomes. Future studies will explore how YBX1 recognizes those RNA molecules to be exported from cells via exosomes. Also, because exosomes have been implicated in some diseases such as cancer, it will be important to explore what role exosome-specific microRNAs play in both health and disease. DOI:http://dx.doi.org/10.7554/eLife.19276.002
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Affiliation(s)
- Matthew J Shurtleff
- Department of Plant and Microbial Biology, University of California, Berkeley, United States
| | - Morayma M Temoche-Diaz
- Department of Plant and Microbial Biology, University of California, Berkeley, United States
| | - Kate V Karfilis
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Sayaka Ri
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Randy Schekman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
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Bann DV, Beyer AR, Parent LJ. A murine retrovirus co-Opts YB-1, a translational regulator and stress granule-associated protein, to facilitate virus assembly. J Virol 2014; 88:4434-50. [PMID: 24501406 PMCID: PMC3993753 DOI: 10.1128/jvi.02607-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/28/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Gag protein of the murine retrovirus mouse mammary tumor virus (MMTV) orchestrates the assembly of immature virus particles in the cytoplasm which are subsequently transported to the plasma membrane for release from the cell. The morphogenetic pathway of MMTV assembly is similar to that of Saccharomyces cerevisiae retrotransposons Ty1 and Ty3, which assemble virus-like particles (VLPs) in intracytoplasmic ribonucleoprotein (RNP) complexes. Assembly of Ty1 and Ty3 VLPs depends upon cellular mRNA processing factors, prompting us to examine whether MMTV utilizes a similar set of host proteins to facilitate viral capsid assembly. Our data revealed that MMTV Gag colocalized with YB-1, a translational regulator found in stress granules and P bodies, in intracytoplasmic foci. The association of MMTV Gag and YB-1 in cytoplasmic granules was not disrupted by cycloheximide treatment, suggesting that these sites were not typical stress granules. However, the association of MMTV Gag and YB-1 was RNA dependent, and an MMTV RNA reporter construct colocalized with Gag and YB-1 in cytoplasmic RNP complexes. Knockdown of YB-1 resulted in a significant decrease in MMTV particle production, indicating that YB-1 plays a role in MMTV capsid formation. Analysis by live-cell imaging with fluorescence recovery after photobleaching (FRAP) revealed that the population of Gag proteins localized within YB-1 complexes was relatively immobile, suggesting that Gag forms stable complexes in association with YB-1. Together, our data imply that the formation of intracytoplasmic Gag-RNA complexes is facilitated by YB-1, which promotes MMTV virus assembly. IMPORTANCE Cellular mRNA processing factors regulate the posttranscriptional fates of mRNAs, affecting localization and utilization of mRNAs under normal conditions and in response to stress. RNA viruses such as retroviruses interact with cellular mRNA processing factors that accumulate in ribonucleoprotein complexes known as P bodies and stress granules. This report shows for the first time that mouse mammary tumor virus (MMTV), a mammalian retrovirus that assembles intracytoplasmic virus particles, commandeers the cellular factor YB-1, a key regulator of translation involved in the cellular stress response. YB-1 is essential for the efficient production of MMTV particles, a process directed by the viral Gag protein. We found that Gag and YB-1 localize together in cytoplasmic granules. Functional studies of Gag/YB-1 granules suggest that they may be sites where virus particles assemble. These studies provide significant insights into the interplay between mRNA processing factors and retroviruses.
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Affiliation(s)
- Darrin V. Bann
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Andrea R. Beyer
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Leslie J. Parent
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
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