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Lambert GS, Rice BL, Kaddis Maldonado RJ, Chang J, Parent LJ. Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome. bioRxiv 2024:2024.01.18.575255. [PMID: 38293010 PMCID: PMC10827203 DOI: 10.1101/2024.01.18.575255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Retroviruses exploit a variety of host proteins to assemble and release virions from infected cells. To date, most studies that examined possible interacting partners of retroviral Gag proteins focused on host proteins that localize primarily to the cytoplasm or plasma membrane. Given the recent findings that several full-length Gag proteins localize to the nucleus, identifying the Gag-nuclear interactome has high potential for novel findings that reveal previously unknown host processes. In this study, we systematically compared nuclear factors identified in published HIV-1 proteomic studies which had used a variety of experimental approaches. In addition, to contribute to this body of knowledge, we report results from a mass spectrometry approach using affinity-tagged (His6) HIV-1 and RSV Gag proteins mixed with nuclear extracts. Taken together, the previous studies-as well as our own-identified potential binding partners of HIV-1 and RSV Gag involved in several nuclear processes, including transcription, splicing, RNA modification, and chromatin remodeling. Although a subset of host proteins interacted with both Gag proteins, there were also unique host proteins belonging to each interactome dataset. To validate one of the novel findings, we demonstrated the interaction of RSV Gag with a member of the Mediator complex, Med26, which is required for RNA polymerase II-mediated transcription. These results provide a strong premise for future functional studies to investigate roles for these nuclear host factors that may have shared functions in the biology of both retroviruses, as well as functions specific to RSV and HIV-1, given their distinctive hosts and molecular pathology.
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Affiliation(s)
- Gregory S. Lambert
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Breanna L. Rice
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Rebecca J. Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Jordan Chang
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Leslie J. Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
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Kumar R, Christensen ND, Kaddis Maldonado RJ, Bewley MC, Ostman A, Sudol M, Chen EC, Buchkovich NW, Gontu A, Surendran Nair M, Nissly RH, Minns AM, Kapur V, Rossi R, Kuchipudi SV, Lindner SE, Parent LJ, Flanagan JM, Buchkovich NJ. Monoclonal Antibodies to S and N SARS-CoV-2 Proteins as Probes to Assess Structural and Antigenic Properties of Coronaviruses. Viruses 2021; 13:v13101899. [PMID: 34696329 PMCID: PMC8537396 DOI: 10.3390/v13101899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023] Open
Abstract
Antibodies targeting the spike (S) and nucleocapsid (N) proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential tools. In addition to important roles in the treatment and diagnosis of infection, the availability of high-quality specific antibodies for the S and N proteins is essential to facilitate basic research of virus replication and in the characterization of mutations responsible for variants of concern. We have developed panels of mouse and rabbit monoclonal antibodies (mAbs) to the SARS-CoV-2 spike receptor-binding domain (S-RBD) and N protein for functional and antigenic analyses. The mAbs to the S-RBD were tested for neutralization of native SARS-CoV-2, with several exhibiting neutralizing activity. The panels of mAbs to the N protein were assessed for cross-reactivity with the SARS-CoV and Middle East respiratory syndrome (MERS)-CoV N proteins and could be subdivided into sets that showed unique specificity for SARS-CoV-2 N protein, cross-reactivity between SARS-CoV-2 and SARS-CoV N proteins only, or cross-reactivity to all three coronavirus N proteins tested. Partial mapping of N-reactive mAbs were conducted using truncated fragments of the SARS-CoV-2 N protein and revealed near complete coverage of the N protein. Collectively, these sets of mouse and rabbit monoclonal antibodies can be used to examine structure/function studies for N proteins and to define the surface location of virus neutralizing epitopes on the RBD of the S protein.
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Affiliation(s)
- Rinki Kumar
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Neil D. Christensen
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Correspondence: (N.D.C.); (N.J.B.)
| | - Rebecca J. Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Maria C. Bewley
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Alexandria Ostman
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Malgorzata Sudol
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Eunice C. Chen
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Natalie W. Buchkovich
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Ruth H. Nissly
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Allen M. Minns
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Animal Science, Penn State University, University Park, PA 16802, USA
| | - Vivek Kapur
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Animal Science, Penn State University, University Park, PA 16802, USA
| | - Randall Rossi
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
| | - Suresh V. Kuchipudi
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Scott E. Lindner
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Leslie J. Parent
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - John M. Flanagan
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Nicholas J. Buchkovich
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
- Correspondence: (N.D.C.); (N.J.B.)
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Chen EC, Maldonado RJK, Parent LJ. Visualizing Rous Sarcoma Virus Genomic RNA Dimerization in the Nucleus, Cytoplasm, and at the Plasma Membrane. Viruses 2021; 13:v13050903. [PMID: 34068261 PMCID: PMC8153106 DOI: 10.3390/v13050903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 01/01/2023] Open
Abstract
Retroviruses are unique in that they package their RNA genomes as non-covalently linked dimers. Failure to dimerize their genomes results in decreased infectivity and reduced packaging of genomic RNA into virus particles. Two models of retrovirus genome dimerization have been characterized: in murine leukemia virus (MLV), genomic RNA dimerization occurs co-transcriptionally in the nucleus, resulting in the preferential formation of genome homodimers; whereas in human immunodeficiency virus (HIV-1), genomic RNA dimerization occurs in the cytoplasm and at the plasma membrane, with a random distribution of heterodimers and homodimers. Although in vitro studies have identified the genomic RNA sequences that facilitate dimerization in Rous sarcoma virus (RSV), in vivo characterization of the location and preferences of genome dimerization has not been performed. In this study, we utilized three single molecule RNA imaging approaches to visualize genome dimers of RSV in cultured quail fibroblasts. The formation of genomic RNA heterodimers within cells was dependent on the presence of the dimerization initiation site (DIS) sequence in the L3 stem. Subcellular localization analysis revealed that heterodimers were present the nucleus, cytoplasm, and at the plasma membrane, indicating that genome dimers can form in the nucleus. Furthermore, single virion analysis revealed that RSV preferentially packages genome homodimers into virus particles. Therefore, the mechanism of RSV genomic RNA dimer formation appears more similar to MLV than HIV-1.
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Affiliation(s)
- Eunice C. Chen
- Department of Medicine, Division of Infectious Diseases and Epidemiology, Penn State College of Medicine, Hershey, PA 17033, USA; (E.C.C.); (R.J.K.M.)
| | - Rebecca J. Kaddis Maldonado
- Department of Medicine, Division of Infectious Diseases and Epidemiology, Penn State College of Medicine, Hershey, PA 17033, USA; (E.C.C.); (R.J.K.M.)
| | - Leslie J. Parent
- Department of Medicine, Division of Infectious Diseases and Epidemiology, Penn State College of Medicine, Hershey, PA 17033, USA; (E.C.C.); (R.J.K.M.)
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
- Correspondence: ; Tel.: +1-717-531-7199
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Maldonado RJK, Rice B, Chen EC, Tuffy KM, Chiari EF, Fahrbach KM, Hope TJ, Parent LJ. Visualizing Association of the Retroviral Gag Protein with Unspliced Viral RNA in the Nucleus. mBio 2020; 11:e00524-20. [PMID: 32265329 PMCID: PMC7157774 DOI: 10.1128/mbio.00524-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
Packaging of genomic RNA (gRNA) by retroviruses is essential for infectivity, yet the subcellular site of the initial interaction between the Gag polyprotein and gRNA remains poorly defined. Because retroviral particles are released from the plasma membrane, it was previously thought that Gag proteins initially bound to gRNA in the cytoplasm or at the plasma membrane. However, the Gag protein of the avian retrovirus Rous sarcoma virus (RSV) undergoes active nuclear trafficking, which is required for efficient gRNA encapsidation (L. Z. Scheifele, R. A. Garbitt, J. D. Rhoads, and L. J. Parent, Proc Natl Acad Sci U S A 99:3944-3949, 2002, https://doi.org/10.1073/pnas.062652199; R. Garbitt-Hirst, S. P. Kenney, and L. J. Parent, J Virol 83:6790-6797, 2009, https://doi.org/10.1128/JVI.00101-09). These results raise the intriguing possibility that the primary contact between Gag and gRNA might occur in the nucleus. To examine this possibility, we created a RSV proviral construct that includes 24 tandem repeats of MS2 RNA stem-loops, making it possible to track RSV viral RNA (vRNA) in live cells in which a fluorophore-conjugated MS2 coat protein is coexpressed. Using confocal microscopy, we observed that both wild-type Gag and a nuclear export mutant (Gag.L219A) colocalized with vRNA in the nucleus. In live-cell time-lapse images, the wild-type Gag protein trafficked together with vRNA as a single ribonucleoprotein (RNP) complex in the nucleoplasm near the nuclear periphery, appearing to traverse the nuclear envelope into the cytoplasm. Furthermore, biophysical imaging methods suggest that Gag and the unspliced vRNA physically interact in the nucleus. Taken together, these data suggest that RSV Gag binds unspliced vRNA to export it from the nucleus, possibly for packaging into virions as the viral genome.IMPORTANCE Retroviruses cause severe diseases in animals and humans, including cancer and acquired immunodeficiency syndromes. To propagate infection, retroviruses assemble new virus particles that contain viral proteins and unspliced vRNA to use as gRNA. Despite the critical requirement for gRNA packaging, the molecular mechanisms governing the identification and selection of gRNA by the Gag protein remain poorly understood. In this report, we demonstrate that the Rous sarcoma virus (RSV) Gag protein colocalizes with unspliced vRNA in the nucleus in the interchromatin space. Using live-cell confocal imaging, RSV Gag and unspliced vRNA were observed to move together from inside the nucleus across the nuclear envelope, suggesting that the Gag-gRNA complex initially forms in the nucleus and undergoes nuclear export into the cytoplasm as a viral ribonucleoprotein (vRNP) complex.
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Affiliation(s)
| | - Breanna Rice
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Eunice C Chen
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Kevin M Tuffy
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Estelle F Chiari
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Kelly M Fahrbach
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois, USA
| | - Thomas J Hope
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois, 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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