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Payen SH, Andrada K, Tara E, Petereit J, Verma SC, Rossetto CC. The cellular paraspeckle component SFPQ associates with the viral processivity factor ORF59 during lytic replication of Kaposi's Sarcoma-associated herpesvirus (KSHV). Virus Res 2024; 349:199456. [PMID: 39214388 PMCID: PMC11406446 DOI: 10.1016/j.virusres.2024.199456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) relies on many cellular proteins to complete replication and generate new virions. Paraspeckle nuclear bodies consisting of core ribonucleoproteins splicing factor proline/glutamine-rich (SFPQ), Non-POU domain-containing octamer-binding protein (NONO), and paraspeckle protein component 1 (PSPC1) along with the long non-coding RNA NEAT1, form a complex that has been speculated to play an important role in viral replication. Paraspeckle bodies are multifunctional and involved in various processes including gene expression, mRNA splicing, and anti-viral defenses. To better understand the role of SFPQ during KSHV replication, we performed SFPQ immunoprecipitation followed by mass spectrometry from KSHV-infected cells. Proteomic analysis showed that during lytic reactivation, SFPQ associates with viral proteins, including ORF10, ORF59, and ORF61. These results are consistent with a previously reported ORF59 proteomics assay identifying SFPQ. To test if the association between ORF59 and SFPQ is important for replication, we first identified the region of ORF59 that associates with SFPQ using a series of 50 amino acid deletion mutants of ORF59 in the KSHV BACmid system. By performing co-immunoprecipitations, we identified the region spanning amino acids 101-150 of ORF59 as the association domain with SFPQ. Using this information, we generated a dominant negative polypeptide of ORF59 encompassing amino acids 101-150, that disrupted the association between SFPQ and full-length ORF59, and decreased virus production. Interestingly, when we tested other human herpesvirus processivity factors (EBV BMRF1, HSV-1 UL42, and HCMV UL44) by transfection of each expression plasmid followed by co-immunoprecipitation, we found a conserved association with SFPQ. These are limited studies that remain to be done in the context of infection but suggest a potential association of SFPQ with processivity factors across multiple herpesviruses.
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Affiliation(s)
- Shannon Harger Payen
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Kayla Andrada
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Evelyn Tara
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Juli Petereit
- University of Nevada, Reno, Nevada Bioinformatics Center (RRID: SCR_017802), Reno, NV 89557, USA
| | - Subhash C Verma
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Cyprian C Rossetto
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA.
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Kulkarni V, Jayakumar S, Mohan M, Kulkarni S. Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections. Cells 2023; 12:987. [PMID: 37048060 PMCID: PMC10093752 DOI: 10.3390/cells12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets.
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Affiliation(s)
- Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Sahana Jayakumar
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Mahesh Mohan
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Smita Kulkarni
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
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Swain M, Ageeli AA, Kasprzak W, Li M, Miller JT, Sztuba-Solinska J, Schneekloth J, Koirala D, Piccirili J, Fraboni AJ, Murelli RP, Wlodawer A, Shapiro B, Baird N, Le Grice SFJ. Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands. Nucleic Acids Res 2021; 49:13179-13193. [PMID: 34871450 PMCID: PMC8682744 DOI: 10.1093/nar/gkab1170] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 10/24/2021] [Accepted: 11/18/2021] [Indexed: 11/14/2022] Open
Abstract
Cellular and virus-coded long non-coding (lnc) RNAs support multiple roles related to biological and pathological processes. Several lncRNAs sequester their 3' termini to evade cellular degradation machinery, thereby supporting disease progression. An intramolecular triplex involving the lncRNA 3' terminus, the element for nuclear expression (ENE), stabilizes RNA transcripts and promotes persistent function. Therefore, such ENE triplexes, as presented here in Kaposi's sarcoma-associated herpesvirus (KSHV) polyadenylated nuclear (PAN) lncRNA, represent targets for therapeutic development. Towards identifying novel ligands targeting the PAN ENE triplex, we screened a library of immobilized small molecules and identified several triplex-binding chemotypes, the tightest of which exhibits micromolar binding affinity. Combined biophysical, biochemical, and computational strategies localized ligand binding to a platform created near a dinucleotide bulge at the base of the triplex. Crystal structures of apo (3.3 Å) and ligand-soaked (2.5 Å) ENE triplexes, which include a stabilizing basal duplex, indicate significant local structural rearrangements within this dinucleotide bulge. MD simulations and a modified nucleoside analog interference technique corroborate the role of the bulge and the base of the triplex in ligand binding. Together with recently discovered small molecules that reduce nuclear MALAT1 lncRNA levels by engaging its ENE triplex, our data supports the potential of targeting RNA triplexes with small molecules.
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MESH Headings
- Base Sequence
- Crystallography, X-Ray
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/metabolism
- Herpesvirus 8, Human/physiology
- Humans
- Ligands
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Molecular Structure
- Nucleic Acid Conformation
- Nucleotides/genetics
- Nucleotides/metabolism
- Poly A/chemistry
- Poly A/genetics
- Poly A/metabolism
- RNA Stability/genetics
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sarcoma, Kaposi/virology
- Small Molecule Libraries/chemistry
- Small Molecule Libraries/metabolism
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Affiliation(s)
- Monalisa Swain
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Abeer A Ageeli
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104, USA
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mi Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Jennifer T Miller
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | | | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Joseph Piccirili
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Americo J Fraboni
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, 11210, USA
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, 11210, USA
- PhD Program in Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Nathan Baird
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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