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Castello A, Álvarez L, Kamel W, Iselin L, Hennig J. Exploring the expanding universe of host-virus interactions mediated by viral RNA. Mol Cell 2024; 84:3706-3721. [PMID: 39366356 DOI: 10.1016/j.molcel.2024.08.027] [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: 06/17/2024] [Revised: 08/16/2024] [Accepted: 08/23/2024] [Indexed: 10/06/2024]
Abstract
RNA is a central molecule in RNA virus biology; however, the interactions that it establishes with the host cell are only starting to be elucidated. In recent years, a methodology revolution has dramatically expanded the scope of host-virus interactions involving the viral RNA (vRNA). A second wave of method development has enabled the precise study of these protein-vRNA interactions in a life cycle stage-dependent manner, as well as providing insights into the interactome of specific vRNA species. This review discusses these technical advances and describes the new regulatory mechanisms that have been identified through their use. Among these, we discuss the importance of vRNA in regulating protein function through a process known as riboregulation. We envision that the elucidation of vRNA interactomes will open new avenues of research, including pathways to the discovery of host factors with therapeutic potential against viruses.
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Affiliation(s)
- Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G611QH, Scotland, UK.
| | - Lucía Álvarez
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany
| | - Wael Kamel
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G611QH, Scotland, UK
| | - Louisa Iselin
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G611QH, Scotland, UK
| | - Janosch Hennig
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany; Department of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
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2
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Arribas L, Menéndez-Arias L, Betancor G. May I Help You with Your Coat? HIV-1 Capsid Uncoating and Reverse Transcription. Int J Mol Sci 2024; 25:7167. [PMID: 39000271 PMCID: PMC11241228 DOI: 10.3390/ijms25137167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) capsid is a protein core formed by multiple copies of the viral capsid (CA) protein. Inside the capsid, HIV-1 harbours all the viral components required for replication, including the genomic RNA and viral enzymes reverse transcriptase (RT) and integrase (IN). Upon infection, the RT transforms the genomic RNA into a double-stranded DNA molecule that is subsequently integrated into the host chromosome by IN. For this to happen, the viral capsid must open and release the viral DNA, in a process known as uncoating. Capsid plays a key role during the initial stages of HIV-1 replication; therefore, its stability is intimately related to infection efficiency, and untimely uncoating results in reverse transcription defects. How and where uncoating takes place and its relationship with reverse transcription is not fully understood, but the recent development of novel biochemical and cellular approaches has provided unprecedented detail on these processes. In this review, we present the latest findings on the intricate link between capsid stability, reverse transcription and uncoating, the different models proposed over the years for capsid uncoating, and the role played by other cellular factors on these processes.
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Affiliation(s)
- Laura Arribas
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain;
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), 28049 Madrid, Spain;
| | - Gilberto Betancor
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain;
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3
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Heng X, Herrera AP, Song Z, Boris-Lawrie K. Retroviral PBS-segment sequence and structure: Orchestrating early and late replication events. Retrovirology 2024; 21:12. [PMID: 38886829 PMCID: PMC11181671 DOI: 10.1186/s12977-024-00646-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
An essential regulatory hub for retroviral replication events, the 5' untranslated region (UTR) encodes an ensemble of cis-acting replication elements that overlap in a logical manner to carry out divergent RNA activities in cells and in virions. The primer binding site (PBS) and primer activation sequence initiate the reverse transcription process in virions, yet overlap with structural elements that regulate expression of the complex viral proteome. PBS-segment also encompasses the attachment site for Integrase to cut and paste the 3' long terminal repeat into the host chromosome to form the provirus and purine residues necessary to execute the precise stoichiometry of genome-length transcripts and spliced viral RNAs. Recent genetic mapping, cofactor affinity experiments, NMR and SAXS have elucidated that the HIV-1 PBS-segment folds into a three-way junction structure. The three-way junction structure is recognized by the host's nuclear RNA helicase A/DHX9 (RHA). RHA tethers host trimethyl guanosine synthase 1 to the Rev/Rev responsive element (RRE)-containing RNAs for m7-guanosine Cap hyper methylation that bolsters virion infectivity significantly. The HIV-1 trimethylated (TMG) Cap licenses specialized translation of virion proteins under conditions that repress translation of the regulatory proteins. Clearly host-adaption and RNA shapeshifting comprise the fundamental basis for PBS-segment orchestrating both reverse transcription of virion RNA and the nuclear modification of m7G-Cap for biphasic translation of the complex viral proteome. These recent observations, which have exposed even greater complexity of retroviral RNA biology than previously established, are the impetus for this article. Basic research to fully comprehend the marriage of PBS-segment structures and host RNA binding proteins that carry out retroviral early and late replication events is likely to expose an immutable virus-specific therapeutic target to attenuate retrovirus proliferation.
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Affiliation(s)
- Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
| | - Amanda Paz Herrera
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Zhenwei Song
- Department of Veterinary and Biomedical Sciences, Institute for Molecular Virology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, Institute for Molecular Virology, University of Minnesota, Saint Paul, MN, 55108, USA.
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4
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Zgheib S, Taha N, Zeiger M, Glushonkov O, Lequeu T, Anton H, Didier P, Boutant E, Mély Y, Réal E. The human cellular protein NoL12 is a specific partner of the HIV-1 nucleocapsid protein NCp7. J Virol 2023; 97:e0004023. [PMID: 37695057 PMCID: PMC10537728 DOI: 10.1128/jvi.00040-23] [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: 01/06/2023] [Accepted: 07/12/2023] [Indexed: 09/12/2023] Open
Abstract
The human immunodeficiency virus-1 (HIV-1) nucleocapsid protein (NCp7) is a nucleic acid chaperone protein with two highly conserved zinc fingers. To exert its key roles in the viral cycle, NCp7 interacts with several host proteins. Among them, the human NoL12 protein (hNoL12) was previously identified in genome wide screens as a potential partner of NCp7. hNoL12 is a highly conserved 25 kDa nucleolar RNA-binding protein implicated in the 5'end processing of ribosomal RNA in the nucleolus and thus in the assembly and maturation of ribosomes. In this work, we confirmed the NCp7/hNoL12 interaction in cells by Förster resonance energy transfer visualized by Fluorescence Lifetime Imaging Microscopy and co-immunoprecipitation. The interaction between NCp7 and hNoL12 was found to strongly depend on their both binding to RNA, as shown by the loss of interaction when the cell lysates were pretreated with RNase. Deletion mutants of hNoL12 were tested for their co-immunoprecipitation with NCp7, leading to the identification of the exonuclease domain of hNoL12 as the binding domain for NCp7. Finally, the interaction with hNoL12 was found to be specific of the mature NCp7 and to require NCp7 basic residues. IMPORTANCE HIV-1 mature nucleocapsid (NCp7) results from the maturation of the Gag precursor in the viral particle and is thus mostly abundant in the first phase of the infection which ends with the genomic viral DNA integration in the cell genome. Most if not all the nucleocapsid partners identified so far are not specific of the mature form. We described here the specific interaction in the nucleolus between NCp7 and the human nucleolar protein 12, a protein implicated in ribosomal RNA maturation and DNA damage response. This interaction takes place in the cell nucleolus, a subcellular compartment where NCp7 accumulates. The absence of binding between hNoL12 and Gag makes hNoL12 one of the few known specific cellular partners of NCp7.
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Affiliation(s)
- Sarwat Zgheib
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Nedal Taha
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Manon Zeiger
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Oleksandr Glushonkov
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Thiebault Lequeu
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Halina Anton
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Pascal Didier
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Emmanuel Boutant
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Yves Mély
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Eléonore Réal
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
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5
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Heaton SM, Gorry PR, Borg NA. DExD/H-box helicases in HIV-1 replication and their inhibition. Trends Microbiol 2023; 31:393-404. [PMID: 36463019 DOI: 10.1016/j.tim.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Antiretroviral therapy (ART) reduces human immunodeficiency virus type 1 (HIV-1) infection, but selection of treatment-refractory variants remains a major challenge. HIV-1 encodes 16 canonical proteins, a small number of which are the singular targets of nearly all antiretrovirals developed to date. Cellular factors are increasingly being explored, which may present more therapeutic targets, more effectively target certain aspects of the viral replication cycle, and/or limit viral escape. Unlike most other positive-sense RNA viruses that encode at least one helicase, retroviruses are limited to the host repertoire. Accordingly, HIV-1 subverts DEAD-box helicase 3X (DDX3X) and numerous other cellular helicases of the Asp-Glu-x-Asp/His (DExD/H)-box family to service multiple aspects of its replication cycle. Here we review DDX3X and other DExD/H-box helicases in HIV-1 replication and their inhibition.
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Affiliation(s)
- Steven M Heaton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Current affiliation: RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, 1-chōme-7-22 Suehirochō, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan.
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Natalie A Borg
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
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6
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Nuclear export inhibitor Selinexor targeting XPO1 enhances coronavirus replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527884. [PMID: 36824761 PMCID: PMC9948980 DOI: 10.1101/2023.02.09.527884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Nucleocytoplasmic transport of proteins using XPO1 (exportin 1) plays a vital role in cell proliferation and survival. Many viruses also exploit this pathway to promote infection and replication. Thus, inhibiting XPO1-mediated nuclear export with selective inhibitors activates multiple antiviral and anti-inflammatory pathways. The XPO1 inhibitor, Selinexor, is an FDA-approved anticancer drug predicted to have antiviral function against many viruses, including SARS-CoV-2. Unexpectedly, we observed that pretreatment of cultured human cells with Selinexor actually enhanced protein expression and replication of coronaviruses, including SARS-CoV-2. Knockdown of cellular XPO1 protein expression significantly enhanced the replication of coronaviruses in human cells. We further demonstrate that Selinexor treatment reduced the formation of unique cytoplasmic antiviral granules that include RNA helicase DHX9 in the virus-infected cells. These results, for the first time, show that the anti-cancer drug Selinexor enhances the replication of coronaviruses in human cells in vitro and thus should be further explored in vivo for the potential impact on the dual use for anticancer and antiviral therapy.
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7
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Bonaventure B, Goujon C. DExH/D-box helicases at the frontline of intrinsic and innate immunity against viral infections. J Gen Virol 2022; 103. [PMID: 36006669 DOI: 10.1099/jgv.0.001766] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
DExH/D-box helicases are essential nucleic acid and ribonucleoprotein remodelers involved in all aspects of nucleic acid metabolism including replication, gene expression and post-transcriptional modifications. In parallel to their importance in basic cellular functions, DExH/D-box helicases play multiple roles in viral life cycles, with some of them highjacked by viruses or negatively regulating innate immune activation. However, other DExH/D-box helicases have recurrently been highlighted as direct antiviral effectors or as positive regulators of innate immune activation. Innate immunity relies on the ability of Pathogen Recognition Receptors to recognize viral signatures and trigger the production of interferons (IFNs) and pro-inflammatory cytokines. Secreted IFNs interact with their receptors to establish antiviral cellular reprogramming via expression regulation of the interferon-stimulated genes (ISGs). Several DExH/D-box helicases have been reported to act as viral sensors (DDX3, DDX41, DHX9, DDX1/DDX21/DHX36 complex), and others to play roles in innate immune activation (DDX60, DDX60L, DDX23). In contrast, the DDX39A, DDX46, DDX5 and DDX24 helicases act as negative regulators and impede IFN production upon viral infection. Beyond their role in viral sensing, the ISGs DDX60 and DDX60L act as viral inhibitors. Interestingly, the constitutively expressed DEAD-box helicases DDX56, DDX17, DDX42 intrinsically restrict viral replication. Hence, DExH/D-box helicases appear to form a multilayer network of primary and secondary factors involved in both intrinsic and innate antiviral immunity. In this review, we highlight recent findings on the extent of antiviral defences played by helicases and emphasize the need to better understand their immune functions as well as their complex interplay.
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Affiliation(s)
- Boris Bonaventure
- IRIM, CNRS, Montpellier University, France.,Present address: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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8
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Wang Z, Cherukupalli S, Xie M, Wang W, Jiang X, Jia R, Pannecouque C, De Clercq E, Kang D, Zhan P, Liu X. Contemporary Medicinal Chemistry Strategies for the Discovery and Development of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2022; 65:3729-3757. [PMID: 35175760 DOI: 10.1021/acs.jmedchem.1c01758] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a major component of the highly active anti-retroviral therapy (HAART) regimen. However, the occurrence of drug-resistant strains and adverse reactions after long-term usage have inevitably compromised the clinical application of NNRTIs. Therefore, the development of novel inhibitors with distinct anti-resistance profiles and better pharmacological properties is still an enormous challenge. Herein, we summarize state-of-the-art medicinal chemistry strategies for the discovery of potent NNRTIs, such as structure-based design strategies, contemporary computer-aided drug design, covalent-binding strategies, and the application of multi-target-directed ligands. The strategies described here will facilitate the identification of promising HIV-1 NNRTIs.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Wenbo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
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9
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Ma Y, Mao G, Wu G, Zhang XE. Single-Particle Tracking Reveals the Interplay between HIV-1 Reverse Transcription and Uncoating. Anal Chem 2022; 94:2648-2654. [PMID: 35080851 DOI: 10.1021/acs.analchem.1c05199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reverse transcription uses the reverse transcriptase enzyme to synthesize deoxyribonucleic acid (DNA) from a ribonucleic acid (RNA) template. This plays an essential role in viral replication. There are still, however, many unknown facts regarding the timing and dynamic processes involved in this life stage. Here, three types of dual-fluorescence human immunodeficiency virus type-1 (HIV-1) particles were constructed with high infectivity, and the sequential process of reverse transcription was observed by real-time imaging of a single HIV-1 particle. Viral uncoating occurred at 60-120 min post infection. Subsequently, at 120-180 min post infection, the viral genome was separated into two parts and reverse-transcribed to generate a DNA product. Nevirapine (NVP), a reverse transcriptase inhibitor, can delay the dynamic process. This study revealed a delicate, sequential, and complex relationship between uncoating and reverse transcription, which may facilitate the development of antiviral drugs.
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Affiliation(s)
- Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guoqiang Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,National Key Laboratory of Biomacromolecules Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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10
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HIV-1 hypermethylated guanosine cap licenses specialized translation unaffected by mTOR. Proc Natl Acad Sci U S A 2022; 119:2105153118. [PMID: 34949712 PMCID: PMC8740576 DOI: 10.1073/pnas.2105153118] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/29/2022] Open
Abstract
The proliferation of viral pathogens is restricted by hosts, but resilient pathogens antagonize the restriction by hosts. Findings explain that HIV-1 blocked mono-methylated guanosine cap by hypermethylation and engaged novel cap-binding complex for virion protein translation unaffected by global translation inhibition. The hypermethylated cap activity required RNA-structure-dependent binding of RNA helicase A/DHX9. eIF4E interaction proceeded on completely spliced HIV messenger RNA templates encoding viral regulatory proteins, thus eIF4E inactivation by catalytic site mTOR inhibitor suppressed regulatory protein translation, while structural/accessory protein translation was maintained. Two mutually exclusive translation pathways antagonize hosts and facilitate HIV-1 proliferation in primary CD4+ T cells to the detriment of hosts. eIF4E inactivation imposed an operational rheostat that suppressed regulatory proteins, while maintaining virion production in immune cells. Appended to the 5′ end of nascent RNA polymerase II transcripts is 7-methyl guanosine (m7G-cap) that engages nuclear cap-binding complex (CBC) to facilitate messenger RNA (mRNA) maturation. Mature mRNAs exchange CBC for eIF4E, the rate-limiting translation factor that is controlled through mTOR. Experiments in immune cells have now documented HIV-1 incompletely processed transcripts exhibited hypermethylated m7G-cap and that the down-regulation of the trimethylguanosine synthetase-1–reduced HIV-1 infectivity and virion protein synthesis by several orders of magnitude. HIV-1 cap hypermethylation required nuclear RNA helicase A (RHA)/DHX9 interaction with the shape of the 5′ untranslated region (UTR) primer binding site (PBS) segment. Down-regulation of RHA or the anomalous shape of the PBS segment abrogated hypermethylated caps and derepressed eIF4E binding for virion protein translation during global down-regulation of host translation. mTOR inhibition was detrimental to HIV-1 proliferation and attenuated Tat, Rev, and Nef synthesis. This study identified mutually exclusive translation pathways and the calibration of virion structural/accessory protein synthesis with de novo synthesis of the viral regulatory proteins. The hypermethylation of select, viral mRNA resulted in CBC exchange to heterodimeric CBP80/NCBP3 that expanded the functional capacity of HIV-1 in immune cells.
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11
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Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Res 2021; 49:5925-5942. [PMID: 33978756 PMCID: PMC8191761 DOI: 10.1093/nar/gkab342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.
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Affiliation(s)
- Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas Gremminger
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Cheng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Jun Li
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Liming Qiu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Juan Ji
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
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12
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Dicker K, Järvelin AI, Garcia-Moreno M, Castello A. The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity. Semin Cell Dev Biol 2021; 111:108-118. [PMID: 32921578 PMCID: PMC7482619 DOI: 10.1016/j.semcdb.2020.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022]
Abstract
RNA is a central molecule in RNA virus biology due to its dual function as messenger and genome. However, the small number of proteins encoded by viral genomes is insufficient to enable virus infection. Hence, viruses hijack cellular RNA-binding proteins (RBPs) to aid replication and spread. In this review we discuss the 'knowns' and 'unknowns' regarding the contribution of host RBPs to the formation of viral particles and the initial steps of infection in the newly infected cell. Through comparison of the virion proteomes of ten different human RNA viruses, we confirm that a pool of cellular RBPs are typically incorporated into viral particles. We describe here illustrative examples supporting the important functions of these RBPs in viral particle formation and infectivity and we propose that the role of host RBPs in these steps can be broader than previously anticipated. Understanding how cellular RBPs regulate virus infection can lead to the discovery of novel therapeutic targets against viruses.
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Affiliation(s)
- Kate Dicker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK.
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13
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Gremminger T, Song Z, Ji J, Foster A, Weng K, Heng X. Extended Interactions between HIV-1 Viral RNA and tRNA Lys3 Are Important to Maintain Viral RNA Integrity. Int J Mol Sci 2020; 22:ijms22010058. [PMID: 33374603 PMCID: PMC7793103 DOI: 10.3390/ijms22010058] [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: 11/06/2020] [Revised: 12/09/2020] [Accepted: 12/19/2020] [Indexed: 01/19/2023] Open
Abstract
The reverse transcription of the human immunodeficiency virus 1 (HIV-1) initiates upon annealing of the 3′-18-nt of tRNALys3 onto the primer binding site (PBS) in viral RNA (vRNA). Additional intermolecular interactions between tRNALys3 and vRNA have been reported, but their functions remain unclear. Here, we show that abolishing one potential interaction, the A-rich loop: tRNALys3 anticodon interaction in the HIV-1 MAL strain, led to a decrease in viral infectivity and reduced the synthesis of reverse transcription products in newly infected cells. In vitro biophysical and functional experiments revealed that disruption of the extended interaction resulted in an increased affinity for reverse transcriptase (RT) and enhanced primer extension efficiency. In the absence of deoxyribose nucleoside triphosphates (dNTPs), vRNA was degraded by the RNaseH activity of RT, and the degradation rate was slower in the complex with the extended interaction. Consistently, the loss of vRNA integrity was detected in virions containing A-rich loop mutations. Similar results were observed in the HIV-1 NL4.3 strain, and we show that the nucleocapsid (NC) protein is necessary to promote the extended vRNA: tRNALys3 interactions in vitro. In summary, our data revealed that the additional intermolecular interaction between tRNALys3 and vRNA is likely a conserved mechanism among various HIV-1 strains and protects the vRNA from RNaseH degradation in mature virions.
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14
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Guo F, Xing L. RNA helicase A as co-factor for DNA viruses during replication. Virus Res 2020; 291:198206. [PMID: 33132162 DOI: 10.1016/j.virusres.2020.198206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022]
Abstract
RNA helicase A (RHA) is a ubiquitously expressed DExH-box helicase enzyme that is involved in a wide range of biological processes including transcription, translation, and RNA processing. A number of RNA viruses recruit RHA to the viral RNA to facilitate virus replication. DNA viruses contain a DNA genome and replicate using a DNA-dependent DNA polymerase. RHA has also been reported to associate with some DNA viruses during replication, in which the enzyme acts on the viral RNA or protein products. As shown for Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, RHA has potential to allow the virus to control a switch in cellular gene expression to modulate the antiviral response. While the study of the interaction of RHA with DNA viruses is still at an early stage, preliminary evidence indicates that the underlying molecular mechanisms are diverse. We now review the current status of this emerging field.
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Affiliation(s)
- Fan Guo
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, PR China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, PR China.
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15
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Osmer PS, Singh G, Boris-Lawrie K. A New Approach to 3D Modeling of Inhomogeneous Populations of Viral Regulatory RNA. Viruses 2020; 12:v12101108. [PMID: 33003639 PMCID: PMC7650772 DOI: 10.3390/v12101108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of experimentally-determined input constraints of HIVNL4-3 trans-activation responsive sequence (TAR) and pairings of unique-5′ (U5) with dimerization (DIS) or AUG motifs, we calculated a series of 3D models that differ in proximity of 5′-Cap and the junction of TAR and PolyA helices; configuration of primer binding site (PBS)-segment; and two host cofactors binding sites. Input constraints on U5-AUG pairings were most compatible with intramolecular folding of 5′-UTR motifs in energetic minima. Introducing theoretical constraints predicted metastable PolyA region drives orientation of 5′-Cap with TAR, U5 and PBS-segment helices. SimRNA and the workflow developed herein provides viable options to predict 3D conformations of inhomogeneous populations of large RNAs that have been intractable to conventional ensemble methods.
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Affiliation(s)
- Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
- Correspondence: ; Tel.: +1-612-625-2100
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16
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Anisenko A, Kan M, Shadrina O, Brattseva A, Gottikh M. Phosphorylation Targets of DNA-PK and Their Role in HIV-1 Replication. Cells 2020; 9:E1907. [PMID: 32824372 PMCID: PMC7464883 DOI: 10.3390/cells9081907] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
The DNA dependent protein kinase (DNA-PK) is a trimeric nuclear complex consisting of a large protein kinase and the Ku heterodimer. The kinase activity of DNA-PK is required for efficient repair of DNA double-strand breaks (DSB) by non-homologous end joining (NHEJ). We also showed that the kinase activity of DNA-PK is essential for post-integrational DNA repair in the case of HIV-1 infection. Besides, DNA-PK is known to participate in such cellular processes as protection of mammalian telomeres, transcription, and some others where the need for its phosphorylating activity is not clearly elucidated. We carried out a systematic search and analysis of DNA-PK targets described in the literature and identified 67 unique DNA-PK targets phosphorylated in response to various in vitro and/or in vivo stimuli. A functional enrichment analysis of DNA-PK targets and determination of protein-protein associations among them were performed. For 27 proteins from these 67 DNA-PK targets, their participation in the HIV-1 life cycle was demonstrated. This information may be useful for studying the functioning of DNA-PK in various cellular processes, as well as in various stages of HIV-1 replication.
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Affiliation(s)
- Andrey Anisenko
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (O.S.); (M.G.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia;; (M.K.); (A.B.)
| | - Marina Kan
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia;; (M.K.); (A.B.)
| | - Olga Shadrina
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (O.S.); (M.G.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia;; (M.K.); (A.B.)
| | - Anna Brattseva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia;; (M.K.); (A.B.)
| | - Marina Gottikh
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (O.S.); (M.G.)
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Singh G, Fritz SE, Seufzer B, Boris-Lawrie K. The mRNA encoding the JUND tumor suppressor detains nuclear RNA-binding proteins to assemble polysomes that are unaffected by mTOR. J Biol Chem 2020; 295:7763-7773. [PMID: 32312751 DOI: 10.1074/jbc.ra119.012005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
One long-standing knowledge gap is the role of nuclear proteins in mRNA translation. Nuclear RNA helicase A (DHX9/RHA) is necessary for the translation of the mRNAs of JUND (JunD proto-oncogene AP-1 transcription factor subunit) and HIV-1 genes, and nuclear cap-binding protein 1 (NCBP1)/CBP80 is a component of HIV-1 polysomes. The protein kinase mTOR activates canonical messenger ribonucleoproteins by post-translationally down-regulating the eIF4E inhibitory protein 4E-BP1. We posited here that NCBP1 and DHX9/RHA (RHA) support a translation pathway of JUND RNA that is independent of mTOR. We present evidence from reciprocal immunoprecipitation experiments indicating that NCBP1 and RHA both are components of messenger ribonucleoproteins in several cell types. Moreover, tandem affinity and RT-quantitative PCR results revealed that JUND mRNA is a component of a previously unknown ribonucleoprotein complex. Results from the tandem IP indicated that another component of the JUND-containing ribonucleoprotein complex is NCBP3, a recently identified ortholog of NCBP2/CBP20. We also found that NCBP1, NCBP3, and RHA, but not NCBP2, are components of JUND-containing polysomes. Mutational analysis uncovered two dsRNA-binding domains of RHA that are necessary to tether JUND-NCBP1/NCBP3 to polysomes. We also found that JUND translation is unaffected by inhibition of mTOR, unless RHA was down-regulated by siRNA. These findings uncover a noncanonical cap-binding complex consisting of NCBP1/NCBP3 and RHA substitutes for the eukaryotic translation initiation factors 4E and 4G and activates mTOR-independent translation of the mRNA encoding the tumor suppressor JUND.
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Affiliation(s)
- Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Sarah E Fritz
- Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
| | - Bradley Seufzer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108 .,Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
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Kamjula V, Kanneganti A, Metla R, Nidamanuri K, Idupulapati S, Runthala A. Decoding the vital segments in human ATP-dependent RNA helicase. Bioinformation 2020; 16:160-170. [PMID: 32405168 PMCID: PMC7196165 DOI: 10.6026/97320630016160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/20/2020] [Indexed: 12/28/2022] Open
Abstract
An analysis of the ATP-dependent RNA helicase using known functionally close analogs helps disclose the structural and functional information of the enzyme. The enzyme plays several interlinked biological functions and there is an urgent need to interpret its key active-site residues to infer function and establish role. The human protein q96c10.1 is annotated using tools such as interpro, go and cdd. The physicochemical properties are estimated using the tool protparam. We describe the enzyme protein model developed using modeller to identify active site residues. We used consurf to estimate the structural conservation and is evolutionary relationship is inferred using known close sequence homologs. The active site is predicted using castp and its topological flexibility is estimated through cabs-flex. The protein is annotated as a hydrolase using available data and ddx58 is found as its top-ranked interacting protein partner. We show that about 124 residues are found to be highly conserved among 259 homologs, clustered in 7 clades with the active-site showing low sequence conservation. It is further shown that only 9 loci among the 42 active-site residues are conserved with limited structural fluctuation from the wild type structure. Thus, we document various useful information linked to function, sequence similarity and phylogeny of the enzyme for annotation as potential helicase as designated by uniprot. Data shows limited degree of conserved sequence segments with topological flexibility unlike in other subfamily members of the protein.
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Affiliation(s)
- Vandana Kamjula
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Ananya Kanneganti
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Rohan Metla
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Kusuma Nidamanuri
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Sudarshan Idupulapati
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Ashish Runthala
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
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