1
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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: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Rebensburg SV, Wei G, Larue RC, Lindenberger J, Francis AC, Annamalai AS, Morrison J, Shkriabai N, Huang SW, KewalRamani V, Poeschla EM, Melikyan GB, Kvaratskhelia M. Sec24C is an HIV-1 host dependency factor crucial for virus replication. Nat Microbiol 2021; 6:435-444. [PMID: 33649557 PMCID: PMC8012256 DOI: 10.1038/s41564-021-00868-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
Early events of the human immunodeficiency virus 1 (HIV-1) lifecycle, such as post-entry virus trafficking, uncoating and nuclear import, are poorly characterized because of limited understanding of virus-host interactions. Here, we used mass spectrometry-based proteomics to delineate cellular binding partners of curved HIV-1 capsid lattices and identified Sec24C as an HIV-1 host dependency factor. Gene deletion and complementation in Jurkat cells revealed that Sec24C facilitates infection and markedly enhances HIV-1 spreading infection. Downregulation of Sec24C in HeLa cells substantially reduced HIV-1 core stability and adversely affected reverse transcription, nuclear import and infectivity. Live-cell microscopy showed that Sec24C co-trafficked with HIV-1 cores in the cytoplasm during virus ingress. Biochemical assays demonstrated that Sec24C directly and specifically interacted with hexameric capsid lattices. A 2.3-Å resolution crystal structure of Sec24C228-242 in the complex with a capsid hexamer revealed that the Sec24C FG-motif bound to a pocket comprised of two adjoining capsid subunits. Combined with previous data1-4, our findings indicate that a capsid-binding FG-motif is conserved in unrelated proteins present in the cytoplasm (Sec24C), the nuclear pore (Nup153; refs. 3,4) and the nucleus (CPSF6; refs. 1,2). We propose that these virus-host interactions during HIV-1 trafficking across different cellular compartments are crucial for productive infection of target cells.
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Affiliation(s)
- Stephanie V. Rebensburg
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Guochao Wei
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ross C. Larue
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Jared Lindenberger
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ashwanth C. Francis
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Arun S. Annamalai
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James Morrison
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Szu-Wei Huang
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Vineet KewalRamani
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Eric M. Poeschla
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Gregory B. Melikyan
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Correspondence to:
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3
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Bester SM, Wei G, Zhao H, Adu-Ampratwum D, Iqbal N, Courouble VV, Francis AC, Annamalai AS, Singh PK, Shkriabai N, Van Blerkom P, Morrison J, Poeschla EM, Engelman AN, Melikyan GB, Griffin PR, Fuchs JR, Asturias FJ, Kvaratskhelia M. Structural and mechanistic bases for a potent HIV-1 capsid inhibitor. Science 2020; 370:360-364. [PMID: 33060363 PMCID: PMC7831379 DOI: 10.1126/science.abb4808] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo-electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies.
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Affiliation(s)
- Stephanie M Bester
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Guochao Wei
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Daniel Adu-Ampratwum
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Naseer Iqbal
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Valentine V Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ashwanth C Francis
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Arun S Annamalai
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter Van Blerkom
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - James Morrison
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory B Melikyan
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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4
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Al-Saleem J, Dirksen WP, Martinez MP, Shkriabai N, Kvaratskhelia M, Ratner L, Green PL. HTLV-1 Tax-1 interacts with SNX27 to regulate cellular localization of the HTLV-1 receptor molecule, GLUT1. PLoS One 2019; 14:e0214059. [PMID: 30897179 PMCID: PMC6428263 DOI: 10.1371/journal.pone.0214059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/06/2019] [Indexed: 12/23/2022] Open
Abstract
An estimated 10-20 million people worldwide are infected with human T cell leukemia virus type 1 (HTLV-1), with endemic areas of infection in Japan, Australia, the Caribbean, and Africa. HTLV-1 is the causative agent of adult T cell leukemia (ATL) and HTLV-1 associated myopathy/tropic spastic paraparesis (HAM/TSP). HTLV-1 expresses several regulatory and accessory genes that function at different stages of the virus life cycle. The regulatory gene Tax-1 is required for efficient virus replication, as it drives transcription of viral gene products, and has also been demonstrated to play a key role in the pathogenesis of the virus. Several studies have identified a PDZ binding motif (PBM) at the carboxyl terminus of Tax-1 and demonstrated the importance of this domain for HTLV-1 induced cellular transformation. Using a mass spectrometry-based proteomics approach we identified sorting nexin 27 (SNX27) as a novel interacting partner of Tax-1. Further, we demonstrated that their interaction is mediated by the Tax-1 PBM and SNX27 PDZ domains. SNX27 has been shown to promote the plasma membrane localization of glucose transport 1 (GLUT1), one of the receptor molecules of the HTLV-1 virus, and the receptor molecule required for HTLV-1 fusion and entry. We postulated that Tax-1 alters GLUT1 localization via its interaction with SNX27. We demonstrate that over expression of Tax-1 in cells causes a reduction of GLUT1 on the plasma membrane. Furthermore, we show that knockdown of SNX27 results in increased virion release and decreased HTLV-1 infectivity. Collectively, we demonstrate the first known mechanism by which HTLV-1 regulates a receptor molecule post-infection.
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Affiliation(s)
- Jacob Al-Saleem
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Wessel P. Dirksen
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Michael P. Martinez
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Lee Ratner
- Division of Oncology, Washington University, St Louis, Missouri, United States of America
| | - Patrick L. Green
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
- Comprehensive Cancer Center and Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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5
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Panfil AR, Al-Saleem J, Howard CM, Shkriabai N, Kvaratskhelia M, Green PL. Stability of the HTLV-1 Antisense-Derived Protein, HBZ, Is Regulated by the E3 Ubiquitin-Protein Ligase, UBR5. Front Microbiol 2018; 9:80. [PMID: 29441057 PMCID: PMC5797633 DOI: 10.3389/fmicb.2018.00080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/12/2018] [Indexed: 12/25/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) encodes a protein derived from the antisense strand of the proviral genome designated HBZ (HTLV-1 basic leucine zipper factor). HBZ is the only viral gene consistently expressed in infected patients and adult T-cell leukemia/lymphoma (ATL) tumor cell lines. It functions to antagonize many activities of the Tax viral transcriptional activator, suppresses apoptosis, and supports proliferation of ATL cells. Factors that regulate the stability of HBZ are thus important to the pathophysiology of ATL development. Using affinity-tagged protein and shotgun proteomics, we identified UBR5 as a novel HBZ-binding partner. UBR5 is an E3 ubiquitin-protein ligase that functions as a key regulator of the ubiquitin proteasome system in both cancer and developmental biology. Herein, we investigated the role of UBR5 in HTLV-1-mediated T-cell transformation and leukemia/lymphoma development. The UBR5/HBZ interaction was verified in vivo using over-expression constructs, as well as endogenously in T-cells. shRNA-mediated knockdown of UBR5 enhanced HBZ steady-state levels by stabilizing the HBZ protein. Interestingly, the related HTLV-2 antisense-derived protein, APH-2, also interacted with UBR5 in vivo. However, knockdown of UBR5 did not affect APH-2 protein stability. Co-immunoprecipitation assays identified ubiquitination of HBZ and knockdown of UBR5 resulted in a decrease in HBZ ubiquitination. MS/MS analysis identified seven ubiquitinated lysines in HBZ. Interestingly, UBR5 expression was upregulated in established T lymphocytic leukemia/lymphoma cell lines and the later stage of T-cell transformation in vitro. Finally, we demonstrated loss of UBR5 decreased cellular proliferation in transformed T-cell lines. Overall, our study provides evidence for UBR5 as a host cell E3 ubiquitin-protein ligase responsible for regulating HBZ protein stability. Additionally, our data suggests UBR5 plays an important role in maintaining the proliferative phenotype of transformed T-cell lines.
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Affiliation(s)
- Amanda R Panfil
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States
| | - Jacob Al-Saleem
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States
| | - Cory M Howard
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Patrick L Green
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States.,Comprehensive Cancer Center and Solove Research Institute, The Ohio State University, Columbus, OH, United States
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6
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Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis D. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science 2017; 355:89-92. [PMID: 28059769 DOI: 10.1126/science.aah5163] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/02/2016] [Indexed: 12/25/2022]
Abstract
Like all retroviruses, HIV-1 irreversibly inserts a viral DNA (vDNA) copy of its RNA genome into host target DNA (tDNA). The intasome, a higher-order nucleoprotein complex composed of viral integrase (IN) and the ends of linear vDNA, mediates integration. Productive integration into host chromatin results in the formation of the strand transfer complex (STC) containing catalytically joined vDNA and tDNA. HIV-1 intasomes have been refractory to high-resolution structural studies. We used a soluble IN fusion protein to facilitate structural studies, through which we present a high-resolution cryo-electron microscopy (cryo-EM) structure of the core tetrameric HIV-1 STC and a higher-order form that adopts carboxyl-terminal domain rearrangements. The distinct STC structures highlight how HIV-1 can use the common retroviral intasome core architecture to accommodate different IN domain modules for assembly.
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Affiliation(s)
- Dario Oliveira Passos
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renbin Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie V Rebensburg
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Youngmin Jeon
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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7
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Ablenas CJ, Liu HW, Shkriabai N, Kvaratskhelia M, Cosa G, Götte M. Dynamic Interconversions of HCV Helicase Binding Modes on the Nucleic Acid Substrate. ACS Infect Dis 2017; 3:99-109. [PMID: 28081608 DOI: 10.1021/acsinfecdis.6b00177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The dynamics involved in the interaction between hepatitis C virus nonstructural protein 3 (NS3) C-terminal helicase and its nucleic acid substrate have been the subject of interest for some time given the key role of this enzyme in viral replication. Here, we employed fluorescence-based techniques and focused on events that precede the unwinding process. Both ensemble Förster resonance energy transfer (FRET) and ensemble protein induced fluorescence enhancement (PIFE) assays show binding on the 3' single-stranded overhang of model DNA substrates (>5 nucleotides) with no preference for the single-stranded/double-stranded (ss/ds) junction. Single-molecule PIFE experiments revealed three enhancement levels that correspond to three discrete binding sites at adjacent bases. The enzyme is able to transition between binding sites in both directions without dissociating from the nucleic acid. In contrast, the NS3 mutant W501A, which is unable to engage in stacking interactions with the DNA, is severely compromised in this switching activity. Altogether our data are consistent with a model for NS3 dynamics that favors ATP-independent random binding and sliding by one and two nucleotides along the overhang of the loading strand.
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Affiliation(s)
| | - Hsiao-Wei Liu
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gonzalo Cosa
- Department of Chemistry and the Centre for Self-Assembled Chemical
Structures (CSACS/CRMAA), McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Matthias Götte
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
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8
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Kessl JJ, Kutluay SB, Townsend D, Rebensburg S, Slaughter A, Larue RC, Shkriabai N, Bakouche N, Fuchs JR, Bieniasz PD, Kvaratskhelia M. HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis. Cell 2016; 166:1257-1268.e12. [PMID: 27565348 DOI: 10.1016/j.cell.2016.07.044] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/16/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
Abstract
While an essential role of HIV-1 integrase (IN) for integration of viral cDNA into human chromosome is established, studies with IN mutants and allosteric IN inhibitors (ALLINIs) have suggested that IN can also influence viral particle maturation. However, it has remained enigmatic as to how IN contributes to virion morphogenesis. Here, we demonstrate that IN directly binds the viral RNA genome in virions. These interactions have specificity, as IN exhibits distinct preference for select viral RNA structural elements. We show that IN substitutions that selectively impair its binding to viral RNA result in eccentric, non-infectious virions without affecting nucleocapsid-RNA interactions. Likewise, ALLINIs impair IN binding to viral RNA in virions of wild-type, but not escape mutant, virus. These results reveal an unexpected biological role of IN binding to the viral RNA genome during virion morphogenesis and elucidate the mode of action of ALLINIs.
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Affiliation(s)
- Jacques J Kessl
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
| | - Dana Townsend
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie Rebensburg
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Alison Slaughter
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Ross C Larue
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Nikoloz Shkriabai
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Nordine Bakouche
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - James R Fuchs
- College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA; Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA.
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9
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Ngure M, Issur M, Shkriabai N, Liu HW, Cosa G, Kvaratskhelia M, Götte M. Interactions of the Disordered Domain II of Hepatitis C Virus NS5A with Cyclophilin A, NS5B, and Viral RNA Show Extensive Overlap. ACS Infect Dis 2016; 2:839-851. [PMID: 27676132 DOI: 10.1021/acsinfecdis.6b00143] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Domain II of the nonstructural protein 5 (NS5A) of the hepatitis C virus (HCV) is involved in intermolecular interactions with the viral RNA genome, the RNA-dependent RNA polymerase NS5B, and the host factor cyclophilin A (CypA). However, domain II of NS5A (NS5ADII) is largely disordered, which makes it difficult to characterize the protein-protein or protein-nucleic acid interfaces. Here we utilized a mass spectrometry-based protein footprinting approach in attempts to characterize regions forming contacts between NS5ADII and its binding partners. In particular, we compared surface topologies of lysine and arginine residues in the context of free and bound NS5ADII. These experiments have led to the identification of an RNA binding motif (305RSRKFPR311) in an arginine-rich region of NS5ADII. Furthermore, we show that K308 is indispensable for both RNA and NS5B binding, whereas W316, further downstream, is essential for protein-protein interactions with CypA and NS5B. Most importantly, NS5ADII binding to NS5B involves a region associated with RNA binding within NS5B. This interaction down-regulated RNA synthesis by NS5B, suggesting that NS5ADII modulates the activity of NS5B and potentially regulates HCV replication.
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Affiliation(s)
- Marianne Ngure
- Department of Medical Microbiology and
Immunology, University of Alberta, 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
| | - Moheshwarnath Issur
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hsiao-Wei Liu
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
| | - Gonzalo Cosa
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Quebec H3A 0B8, Canada
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Matthias Götte
- Department of Medical Microbiology and
Immunology, University of Alberta, 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montréal, Quebec H3G 1Y6, Canada
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10
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Chen TH, Tanimoto A, Shkriabai N, Kvaratskhelia M, Wysocki V, Gopalan V. Use of chemical modification and mass spectrometry to identify substrate-contacting sites in proteinaceous RNase P, a tRNA processing enzyme. Nucleic Acids Res 2016; 44:5344-55. [PMID: 27166372 PMCID: PMC4914120 DOI: 10.1093/nar/gkw391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/28/2016] [Indexed: 02/07/2023] Open
Abstract
Among all enzymes in nature, RNase P is unique in that it can use either an RNA- or a protein-based active site for its function: catalyzing cleavage of the 5′-leader from precursor tRNAs (pre-tRNAs). The well-studied catalytic RNase P RNA uses a specificity module to recognize the pre-tRNA and a catalytic module to perform cleavage. Similarly, the recently discovered proteinaceous RNase P (PRORP) possesses two domains – pentatricopeptide repeat (PPR) and metallonuclease (NYN) – that are present in some other RNA processing factors. Here, we combined chemical modification of lysines and multiple-reaction monitoring mass spectrometry to identify putative substrate-contacting residues in Arabidopsis thaliana PRORP1 (AtPRORP1), and subsequently validated these candidate sites by site-directed mutagenesis. Using biochemical studies to characterize the wild-type (WT) and mutant derivatives, we found that AtPRORP1 exploits specific lysines strategically positioned at the tips of it's V-shaped arms, in the first PPR motif and in the NYN domain proximal to the catalytic center, to bind and cleave pre-tRNA. Our results confirm that the protein- and RNA-based forms of RNase P have distinct modules for substrate recognition and cleavage, an unanticipated parallel in their mode of action.
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Affiliation(s)
- Tien-Hao Chen
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Akiko Tanimoto
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Nikoloz Shkriabai
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | | | - Vicki Wysocki
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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11
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Cherian MA, Baydoun HH, Al-Saleem J, Shkriabai N, Kvaratskhelia M, Green P, Ratner L. Akt Pathway Activation by Human T-cell Leukemia Virus Type 1 Tax Oncoprotein. J Biol Chem 2015; 290:26270-81. [PMID: 26324707 DOI: 10.1074/jbc.m115.684746] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Indexed: 12/12/2022] Open
Abstract
Human T-cell leukemia virus (HTLV) type 1, the etiological agent of adult T-cell leukemia, expresses the viral oncoprotein Tax1. In contrast, HTLV-2, which expresses Tax2, is non-leukemogenic. One difference between these homologous proteins is the presence of a C-terminal PDZ domain-binding motif (PBM) in Tax1, previously reported to be important for non-canonical NFκB activation. In contrast, this study finds no defect in non-canonical NFκB activity by deletion of the Tax1 PBM. Instead, Tax1 PBM was found to be important for Akt activation. Tax1 attenuates the effects of negative regulators of the PI3K-Akt-mammalian target of rapamycin pathway, phosphatase and tensin homologue (PTEN), and PHLPP. Tax1 competes with PTEN for binding to DLG-1, unlike a PBM deletion mutant of Tax1. Forced membrane expression of PTEN or PHLPP overcame the effects of Tax1, as measured by levels of Akt phosphorylation, and rates of Akt dephosphorylation. The current findings suggest that Akt activation may explain the differences in transforming activity of HTLV-1 and -2.
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Affiliation(s)
- Mathew A Cherian
- From the Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 and
| | - Hicham H Baydoun
- From the Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 and
| | - Jacob Al-Saleem
- the Center for Retrovirus Research and Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Nikoloz Shkriabai
- the Center for Retrovirus Research and Departments of Pharmaceutics and Pharmaceutical Chemistry and
| | - Mamuka Kvaratskhelia
- the Center for Retrovirus Research and Departments of Pharmaceutics and Pharmaceutical Chemistry and
| | - Patrick Green
- the Center for Retrovirus Research and Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Lee Ratner
- From the Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 and
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12
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Slaughter A, Jurado KA, Deng N, Feng L, Kessl JJ, Shkriabai N, Larue RC, Fadel HJ, Patel PA, Jena N, Fuchs JR, Poeschla E, Levy RM, Engelman A, Kvaratskhelia M. The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase. Retrovirology 2014; 11:100. [PMID: 25421939 PMCID: PMC4251946 DOI: 10.1186/s12977-014-0100-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/24/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an important new class of anti-HIV-1 agents. ALLINIs bind at the IN catalytic core domain (CCD) dimer interface occupying the principal binding pocket of its cellular cofactor LEDGF/p75. Consequently, ALLINIs inhibit HIV-1 IN interaction with LEDGF/p75 as well as promote aberrant IN multimerization. Selection of viral strains emerging under the inhibitor pressure has revealed mutations at the IN dimer interface near the inhibitor binding site. RESULTS We have investigated the effects of one of the most prevalent substitutions, H171T IN, selected under increasing pressure of ALLINI BI-D. Virus containing the H171T IN substitution exhibited an ~68-fold resistance to BI-D treatment in infected cells. These results correlated with ~84-fold reduced affinity for BI-D binding to recombinant H171T IN CCD protein compared to its wild type (WT) counterpart. However, the H171T IN substitution only modestly affected IN-LEDGF/p75 binding and allowed HIV-1 containing this substitution to replicate at near WT levels. The x-ray crystal structures of BI-D binding to WT and H171T IN CCD dimers coupled with binding free energy calculations revealed the importance of the Nδ- protonated imidazole group of His171 for hydrogen bonding to the BI-D tert-butoxy ether oxygen and establishing electrostatic interactions with the inhibitor carboxylic acid, whereas these interactions were compromised upon substitution to Thr171. CONCLUSIONS Our findings reveal a distinct mechanism of resistance for the H171T IN mutation to ALLINI BI-D and indicate a previously undescribed role of the His171 side chain for binding the inhibitor.
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Affiliation(s)
- Alison Slaughter
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Kellie A Jurado
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215 USA
| | - Nanjie Deng
- Department of Chemistry and Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA
| | - Lei Feng
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Jacques J Kessl
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Ross C Larue
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Hind J Fadel
- Department of Molecular Medicine & Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | - Pratiq A Patel
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210 USA
| | - Nivedita Jena
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210 USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210 USA
| | - Eric Poeschla
- Department of Molecular Medicine & Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | - Ronald M Levy
- Department of Chemistry and Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA
| | - Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215 USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
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13
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Shkriabai N, Dharmarajan V, Slaughter A, Kessl JJ, Larue RC, Feng L, Fuchs JR, Griffin PR, Kvaratskhelia M. A critical role of the C-terminal segment for allosteric inhibitor-induced aberrant multimerization of HIV-1 integrase. J Biol Chem 2014; 289:26430-26440. [PMID: 25118283 DOI: 10.1074/jbc.m114.589572] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a promising class of antiretroviral agents for clinical development. Although ALLINIs promote aberrant IN multimerization and inhibit IN interaction with its cellular cofactor LEDGF/p75 with comparable potencies in vitro, their primary mechanism of action in infected cells is through inducing aberrant multimerization of IN. Crystal structures have shown that ALLINIs bind at the IN catalytic core domain dimer interface and bridge two interacting subunits. However, how these interactions promote higher-order protein multimerization is not clear. Here, we used mass spectrometry-based protein footprinting to monitor surface topology changes in full-length WT and the drug-resistant A128T mutant INs in the presence of ALLINI-2. These experiments have identified protein-protein interactions that extend beyond the direct inhibitor binding site and which lead to aberrant multimerization of WT but not A128T IN. Specifically, we demonstrate that C-terminal residues Lys-264 and Lys-266 play an important role in the inhibitor induced aberrant multimerization of the WT protein. Our findings provide structural clues for exploiting IN multimerization as a new, attractive therapeutic target and are expected to facilitate development of improved inhibitors.
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Affiliation(s)
- Nikoloz Shkriabai
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | | | - Alison Slaughter
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Jacques J Kessl
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Ross C Larue
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Lei Feng
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, and
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210,.
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14
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Larue RC, Plumb MR, Crowe BL, Shkriabai N, Sharma A, DiFiore J, Malani N, Aiyer SS, Roth MJ, Bushman FD, Foster MP, Kvaratskhelia M. Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes. Nucleic Acids Res 2014; 42:4868-81. [PMID: 24520112 PMCID: PMC4005663 DOI: 10.1093/nar/gku135] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The importance of understanding the molecular mechanisms of murine leukemia virus (MLV) integration into host chromatin is highlighted by the development of MLV-based vectors for human gene-therapy. We have recently identified BET proteins (Brd2, 3 and 4) as the main cellular binding partners of MLV integrase (IN) and demonstrated their significance for effective MLV integration at transcription start sites. Here we show that recombinant Brd4, a representative of the three BET proteins, establishes complementary high-affinity interactions with MLV IN and mononucleosomes (MNs). Brd4(1–720) but not its N- or C-terminal fragments effectively stimulate MLV IN strand transfer activities in vitro. Mass spectrometry- and NMR-based approaches have enabled us to map key interacting interfaces between the C-terminal domain of BRD4 and the C-terminal tail of MLV IN. Additionally, the N-terminal fragment of Brd4 binds to both DNA and acetylated histone peptides, allowing it to bind tightly to MNs. Comparative analyses of the distributions of various histone marks along chromatin revealed significant positive correlations between H3- and H4-acetylated histones, BET protein-binding sites and MLV-integration sites. Our findings reveal a bimodal mechanism for BET protein-mediated MLV integration into select chromatin locations.
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Affiliation(s)
- Ross C Larue
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
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15
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Sharma A, Larue R, Plumb M, Malani N, Male F, Slaughter A, Kessl J, Shkriabai N, Coward E, Aiyer S, Green P, Wu L, Roth M, Bushman F, Kvaratskhelia M. BET proteins target murine leukemia virus integration to transcription start sites. Retrovirology 2013. [PMCID: PMC3848285 DOI: 10.1186/1742-4690-10-s1-o19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Eidahl JO, Crowe BL, North JA, McKee CJ, Shkriabai N, Feng L, Plumb M, Graham RL, Gorelick RJ, Hess S, Poirier MG, Foster MP, Kvaratskhelia M. Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res 2013; 41:3924-36. [PMID: 23396443 PMCID: PMC3616739 DOI: 10.1093/nar/gkt074] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/27/2012] [Accepted: 01/18/2013] [Indexed: 01/19/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75 is tightly bound to mononucleosomes (MNs). Our proteomic experiments indicate that this interaction is direct and not mediated by other cellular factors. We determined the solution structure of LEDGF PWWP and monitored binding to the histone H3 tail containing trimethylated Lys36 (H3K36me3) and DNA by NMR. Results reveal two distinct functional interfaces of LEDGF PWWP: a well-defined hydrophobic cavity, which selectively interacts with the H3K36me3 peptide and adjacent basic surface, which non-specifically binds DNA. LEDGF PWWP exhibits nanomolar binding affinity to purified native MNs, but displays markedly lower affinities for the isolated H3K36me3 peptide and DNA. Furthermore, we show that LEDGF PWWP preferentially and tightly binds to in vitro reconstituted MNs containing a tri-methyl-lysine analogue at position 36 of H3 and not to their unmodified counterparts. We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin.
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Affiliation(s)
- Jocelyn O. Eidahl
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Brandon L. Crowe
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Justin A. North
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher J. McKee
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nikoloz Shkriabai
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lei Feng
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew Plumb
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert L. Graham
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert J. Gorelick
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sonja Hess
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Michael G. Poirier
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark P. Foster
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mamuka Kvaratskhelia
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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