1
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Ne E, Crespo R, Izquierdo-Lara R, Rao S, Koçer S, Górska A, van Staveren T, Kan TW, van de Vijver D, Dekkers D, Rokx C, Moulos P, Hatzis P, Palstra RJ, Demmers J, Mahmoudi T. Catchet-MS identifies IKZF1-targeting thalidomide analogues as novel HIV-1 latency reversal agents. Nucleic Acids Res 2022; 50:5577-5598. [PMID: 35640596 PMCID: PMC9177988 DOI: 10.1093/nar/gkac407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/11/2022] [Accepted: 05/24/2022] [Indexed: 12/27/2022] Open
Abstract
A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and latency reversal, due to technical limitations, this has been challenging. Here we use a dCas9 targeted chromatin and histone enrichment strategy coupled to mass spectrometry (Catchet-MS) to probe the differential protein composition of the latent and activated HIV-1 5′LTR. Catchet-MS identified known and novel latent 5′LTR-associated host factors. Among these, IKZF1 is a novel HIV-1 transcriptional repressor, required for Polycomb Repressive Complex 2 recruitment to the LTR. We find the clinically advanced thalidomide analogue iberdomide, and the FDA approved analogues lenalidomide and pomalidomide, to be novel LRAs. We demonstrate that, by targeting IKZF1 for degradation, these compounds reverse HIV-1 latency in CD4+ T-cells isolated from virally suppressed people living with HIV-1 and that they are able to synergize with other known LRAs.
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Affiliation(s)
- Enrico Ne
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Ray Izquierdo-Lara
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Selin Koçer
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Alicja Górska
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Center, The Netherlands
| | - Dick Dekkers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rg-530, PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
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2
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García-de-Gracia F, Gaete-Argel A, Riquelme-Barrios S, Pereira-Montecinos C, Rojas-Araya B, Aguilera P, Oyarzún-Arrau A, Rojas-Fuentes C, Acevedo ML, Chnaiderman J, Valiente-Echeverría F, Toro-Ascuy D, Soto-Rifo R. CBP80/20-dependent translation initiation factor (CTIF) inhibits HIV-1 Gag synthesis by targeting the function of the viral protein Rev. RNA Biol 2021; 18:745-758. [PMID: 33103564 PMCID: PMC8078705 DOI: 10.1080/15476286.2020.1832375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Translation initiation of the human immunodeficiency virus type-1 (HIV-1) full-length RNA has been shown to occur through cap-dependent and IRES-driven mechanisms. Previous studies suggested that the nuclear cap-binding complex (CBC) rather than eIF4E drives cap-dependent translation of the full-length RNA and we have recently reported that the CBC subunit CBP80 supports the function of the viral protein Rev during nuclear export and translation of this viral transcript. Ribosome recruitment during CBC-dependent translation of cellular mRNAs relies on the activity CBP80/20 translation initiation factor (CTIF), which bridges CBP80 and the 40S ribosomal subunit through interactions with eIF3g. Here, we report that CTIF inhibits HIV-1 and HIV-2 Gag synthesis from the full-length RNA. Our results indicate that CTIF associates with HIV-1 Rev through its N-terminal domain and is recruited onto the full-length RNA ribonucleoprotein complex in order to interfere with Gag synthesis. We also demonstrate that CTIF induces the cytoplasmic accumulation of Rev impeding the association of the viral protein with CBP80. We finally show that Rev interferes with the association of CTIF with CBP80 indicating that CTIF and Rev compete for the CBC subunit.
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Affiliation(s)
- Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Camila Pereira-Montecinos
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Bárbara Rojas-Araya
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Paulina Aguilera
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aarón Oyarzún-Arrau
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Cecilia Rojas-Fuentes
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Mónica L. Acevedo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jonás Chnaiderman
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Daniela Toro-Ascuy
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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3
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Panwar U, Chandra I, Selvaraj C, Singh SK. Current Computational Approaches for the Development of Anti-HIV Inhibitors: An Overview. Curr Pharm Des 2020; 25:3390-3405. [PMID: 31538884 DOI: 10.2174/1381612825666190911160244] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Today, HIV-1 infection has become an extensive problem to public health and a greater challenge to all working researchers throughout the world. Since the beginning of HIV-1 virus, several antiviral therapeutic agents have been developed at various stages to combat HIV-1 infection. But, many of antiviral drugs are on the platform of drug resistance and toxicology issues, needs an urgent constructive investigation for the development of productive and protective therapeutics to make an improvement of individual life suffering with viral infection. As developing a novel agent is very costly, challenging and time taking route in the recent times. METHODS The review summarized about the modern approaches of computational aided drug discovery to developing a novel inhibitor within a short period of time and less cost. RESULTS The outcome suggests on the premise of reported information that the computational drug discovery is a powerful technology to design a defensive and fruitful therapeutic agents to combat HIV-1 infection and recover the lifespan of suffering one. CONCLUSION Based on survey of the reported information, we concluded that the current computational approaches is highly supportive in the progress of drug discovery and controlling the viral infection.
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Affiliation(s)
- Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
| | - Ishwar Chandra
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
| | - Chandrabose Selvaraj
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, Czech Republic
| | - Sanjeev K Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
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4
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Quaranta P, Lottini G, Chesi G, Contrafatto F, Russotto R, Macera L, Lai M, Spezia PG, Brai A, Botta M, Freer G, Pistello M. DDX3 inhibitors show antiviral activity against positive-sense single-stranded RNA viruses but not against negative-sense single-stranded RNA viruses: The coxsackie B model. Antiviral Res 2020; 178:104750. [DOI: 10.1016/j.antiviral.2020.104750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/08/2020] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
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5
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Barrera A, Olguín V, Vera-Otarola J, López-Lastra M. Cap-independent translation initiation of the unspliced RNA of retroviruses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194583. [PMID: 32450258 DOI: 10.1016/j.bbagrm.2020.194583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Retroviruses are a unique family of RNA viruses that utilize a virally encoded reverse transcriptase (RT) to replicate their genomic RNA (gRNA) through a proviral DNA intermediate. The provirus is permanently integrated into the host cell chromosome and is expressed by the host cell transcription, RNA processing, and translation machinery. Retroviral messenger RNAs (mRNAs) entirely resemble a cellular mRNA as they have a 5'cap structure, 5'untranslated region (UTR), an open reading frame (ORF), 3'UTR, and a 3'poly(A) tail. The primary transcription product interacts with the cellular RNA processing machinery and is spliced, exported to the cytoplasm, and translated. However, a proportion of the pre-mRNA subverts typical RNA processing giving rise to the full-length RNA. In the cytoplasm, the full-length retroviral RNA fulfills a dual role acting as mRNA and as the gRNA. Simple retroviruses generate two pools of full-length RNA, one for each purpose. However, complex retroviruses have a single pool of full-length RNA, which is destined for translation or encapsidation. As for eukaryotic mRNAs, translational control of retroviral protein synthesis is mostly exerted at the step of initiation. Interestingly, some retroviral mRNAs, both simple and complex, use a dual mechanism to initiate protein synthesis, a cap-dependent initiation mechanism, or via internal initiation using an internal ribosome entry site (IRES). In this review, we describe and discuss data regarding the molecular mechanism driving the canonical cap-dependent and IRES-mediated translation initiation for retroviral mRNA, focusing the discussion mainly on the most studied retroviral mRNA, the HIV-1 mRNA.
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Affiliation(s)
- Aldo Barrera
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Valeria Olguín
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile.
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6
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Saha S, Hafren A, Mäkinen K. Dynamics of Protein Accumulation from the 3' End of Viral RNA Are Different from Those in the Rest of the Genome in Potato Virus A Infection. J Virol 2019; 93:e00721-19. [PMID: 31341041 PMCID: PMC6744237 DOI: 10.1128/jvi.00721-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/14/2019] [Indexed: 01/18/2023] Open
Abstract
One large open reading frame (ORF) encodes 10 potyviral proteins. We compared the accumulation of cylindrical inclusion (CI) protein from the middle, coat protein (CP) from the 3'end, and Renilla luciferase (RLUC) from two distinct locations in potato virus A (PVA) RNA. 5' RLUC was expressed from an rluc gene inserted between the P1 and helper component proteinase (HCPro) cistrons, and 3' RLUC was expressed from the gene inserted between the RNA polymerase and CP cistrons. Viral protein and RNA accumulation were quantitated (i) when expressed from PVA RNA in the presence of ectopically expressed genome-linked viral protein (VPg) and auxiliary proteins and (ii) at different time points during natural infection. The rate and timing of 3' RLUC and CP accumulation were found to be different from those of 5' RLUC and CI. Ectopic expression of VPg boosted PVA RNA, 3' RLUC, and, together with HCPro, CP accumulation, whereas 5' RLUC and CI accumulation remained unaffected regardless of the increased viral RNA amount. In natural infection, the rate of the noteworthy minute early accumulation of 3' RLUC accelerated toward the end of infection. 5' RLUC accumulation, which was already pronounced at 2 days postinfection, increased moderately and stabilized to a constant level by day 5, whereas PVA RNA and CP levels continued to increase throughout the infection. We propose that these observations connect with the mechanisms by which potyvirus infection limits CP accumulation during early infection and specifically supports its accumulation late in infection, but follow-up studies are required to understand the mechanism of how this occurs.IMPORTANCE The results of this study suggest that the dynamics of potyviral protein accumulation are regulated differentially from the 3' end of viral RNA than from the rest of the genome, the significance of which would be to satisfy the needs of replication early and particle assembly late in infection.
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Affiliation(s)
- Shreya Saha
- Faculty of Agriculture and Forestry, Department of Microbiology, Viikki Plant Sciences Center, University of Helsinki, Helsinki, Finland
| | - Anders Hafren
- Faculty of Agriculture and Forestry, Department of Microbiology, Viikki Plant Sciences Center, University of Helsinki, Helsinki, Finland
| | - Kristiina Mäkinen
- Faculty of Agriculture and Forestry, Department of Microbiology, Viikki Plant Sciences Center, University of Helsinki, Helsinki, Finland
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7
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Riquelme-Barrios S, Pereira-Montecinos C, Valiente-Echeverría F, Soto-Rifo R. Emerging Roles of N 6-Methyladenosine on HIV-1 RNA Metabolism and Viral Replication. Front Microbiol 2018; 9:576. [PMID: 29643844 PMCID: PMC5882793 DOI: 10.3389/fmicb.2018.00576] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/13/2018] [Indexed: 01/07/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification present in Eukaryotic mRNA. The functions of this chemical modification are mediated by m6A-binding proteins (m6A readers) and regulated by methyltransferases (m6A writers) and demethylases (m6A erasers), which together are proposed to be responsible of a new layer of post-transcriptional control of gene expression. Despite the presence of m6A in a retroviral genome was reported more than 40 years ago, the recent development of sequencing-based technologies allowing the mapping of m6A in a transcriptome-wide manner made it possible to identify the topology and dynamics of m6A during replication of HIV-1 as well as other viruses. As such, three independent groups recently reported the presence of m6A along the HIV-1 genomic RNA (gRNA) and described the impact of cellular m6A writers, erasers and readers on different steps of viral RNA metabolism and replication. Interestingly, while two groups reported a positive role of m6A at different steps of viral gene expression it was also proposed that the presence of m6A within the gRNA reduces viral infectivity by inducing the early degradation of the incoming viral genome. This review summarizes the recent advances in this emerging field and discusses the relevance of m6A during HIV-1 replication.
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Affiliation(s)
- Sebastián Riquelme-Barrios
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Camila Pereira-Montecinos
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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8
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Baxter AE, O'Doherty U, Kaufmann DE. Beyond the replication-competent HIV reservoir: transcription and translation-competent reservoirs. Retrovirology 2018; 15:18. [PMID: 29394935 PMCID: PMC5797386 DOI: 10.1186/s12977-018-0392-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
Recent years have seen a substantial increase in the number of tools available to monitor and study HIV reservoirs. Here, we discuss recent technological advances that enable an understanding of reservoir dynamics beyond classical assays to measure the frequency of cells containing provirus able to propagate a spreading infection (replication-competent reservoir). Specifically, we focus on the characterization of cellular reservoirs containing proviruses able to transcribe viral mRNAs (so called transcription-competent) and translate viral proteins (translation-competent). We suggest that the study of these alternative reservoirs provides complementary information to classical approaches, crucially at a single-cell level. This enables an in-depth characterization of the cellular reservoir, both following reactivation from latency and, importantly, directly ex vivo at baseline. Furthermore, we propose that the study of cellular reservoirs that may not contain fully replication-competent virus, but are able to produce HIV mRNAs and proteins, is of biological importance. Lastly, we detail some of the key contributions that the study of these transcription and translation-competent reservoirs has made thus far to investigations into HIV persistence, and outline where these approaches may take the field next.
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Affiliation(s)
- Amy E Baxter
- CR-CHUM, Université de Montréal, Montréal, QC, Canada.,Scripps CHAVI-ID, La Jolla, CA, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine and Therapeutic Pathology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Daniel E Kaufmann
- CR-CHUM, Université de Montréal, Montréal, QC, Canada. .,Scripps CHAVI-ID, La Jolla, CA, USA.
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9
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Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Sci Rep 2017; 7:16965. [PMID: 29208937 PMCID: PMC5717263 DOI: 10.1038/s41598-017-16793-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/17/2017] [Indexed: 02/05/2023] Open
Abstract
HIV-1 replication requires myriad interactions between cellular proteins and the viral unspliced RNA. These interactions are important in archetypal RNA processes such as transcription and translation as well as for more specialized functions including alternative splicing and packaging of unspliced genomic RNA into virions. We present here a hybridization capture strategy for purification of unspliced full-length HIV RNA-protein complexes preserved in vivo by formaldehyde crosslinking, and coupled with mass spectrometry to identify HIV RNA-protein interactors in HIV-1 infected cells. One hundred eighty-nine proteins were identified to interact with unspliced HIV RNA including Rev and Gag/Gag-Pol, 24 host proteins previously shown to bind segments of HIV RNA, and over 90 proteins previously shown to impact HIV replication. Further analysis using siRNA knockdown techniques against several of these proteins revealed significant changes to HIV expression. These results demonstrate the utility of the approach for the discovery of host proteins involved in HIV replication. Additionally, because this strategy only requires availability of 30 nucleotides of the HIV-RNA for hybridization with a capture oligonucleotide, it is readily applicable to any HIV system of interest regardless of cell type, HIV-1 virus strain, or experimental perturbation.
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10
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Antzin-Anduetza I, Mahiet C, Granger LA, Odendall C, Swanson CM. Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication. Retrovirology 2017; 14:49. [PMID: 29121951 PMCID: PMC5679385 DOI: 10.1186/s12977-017-0374-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The human immunodeficiency virus type 1 (HIV-1) structural protein Gag is necessary and sufficient to form viral particles. In addition to encoding the amino acid sequence for Gag, the underlying RNA sequence could encode cis-acting elements or nucleotide biases that are necessary for viral replication. Furthermore, RNA sequences that inhibit viral replication could be suppressed in gag. However, the functional relevance of RNA elements and nucleotide biases that promote or repress HIV-1 replication remain poorly understood. RESULTS To characterize if the RNA sequence in gag controls HIV-1 replication, the matrix (MA) region was codon modified, allowing the RNA sequence to be altered without affecting the protein sequence. Codon modification of nucleotides (nt) 22-261 or 22-378 in gag inhibited viral replication by decreasing genomic RNA (gRNA) abundance, gRNA stability, Gag expression, virion production and infectivity. Comparing the effect of these point mutations to deletions of the same region revealed that the mutations inhibited infectious virus production while the deletions did not. This demonstrated that codon modification introduced inhibitory sequences. There is a much lower than expected frequency of CpG dinucleotides in HIV-1 and codon modification introduced a substantial increase in CpG abundance. To determine if they are necessary for inhibition of HIV-1 replication, codons introducing CpG dinucleotides were mutated back to the wild type codon, which restored efficient Gag expression and infectious virion production. To determine if they are sufficient to inhibit viral replication, CpG dinucleotides were inserted into gag in the absence of other changes. The increased CpG dinucleotide content decreased HIV-1 infectivity and viral replication. CONCLUSIONS The HIV-1 RNA sequence contains low abundance of CpG dinucleotides. Increasing the abundance of CpG dinucleotides inhibits multiple steps of the viral life cycle, providing a functional explanation for why CpG dinucleotides are suppressed in HIV-1.
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Affiliation(s)
- Irati Antzin-Anduetza
- Department of Infectious Diseases, King's College London, 3rd Floor Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Charlotte Mahiet
- Department of Infectious Diseases, King's College London, 3rd Floor Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Luke A Granger
- Department of Infectious Diseases, King's College London, 3rd Floor Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Charlotte Odendall
- Department of Infectious Diseases, King's College London, 3rd Floor Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, 3rd Floor Borough Wing, Guy's Hospital, London, SE1 9RT, UK.
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11
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Deforges J, de Breyne S, Ameur M, Ulryck N, Chamond N, Saaidi A, Ponty Y, Ohlmann T, Sargueil B. Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame. Nucleic Acids Res 2017; 45:7382-7400. [PMID: 28449096 PMCID: PMC5499600 DOI: 10.1093/nar/gkx303] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/12/2017] [Indexed: 02/06/2023] Open
Abstract
In the late phase of the HIV virus cycle, the unspliced genomic RNA is exported to the cytoplasm for the necessary translation of the Gag and Gag-pol polyproteins. Three distinct translation initiation mechanisms ensuring Gag production have been described with little rationale for their multiplicity. The Gag-IRES has the singularity to be located within Gag ORF and to directly interact with ribosomal 40S. Aiming at elucidating the specificity and the relevance of this interaction, we probed HIV-1 Gag-IRES structure and developed an innovative integrative modelling strategy to take into account all the gathered information. We propose a novel Gag-IRES secondary structure strongly supported by all experimental data. We further demonstrate the presence of two regions within Gag-IRES that independently and directly interact with the ribosome. Importantly, these binding sites are functionally relevant to Gag translation both in vitro and ex vivo. This work provides insight into the Gag-IRES molecular mechanism and gives compelling evidence for its physiological importance. It allows us to propose original hypotheses about the IRES physiological role and conservation among primate lentiviruses.
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Affiliation(s)
- Jules Deforges
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Sylvain de Breyne
- CIRI (International Center for Infectiology Research), INSERM U1111, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5308, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Melissa Ameur
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Nathalie Ulryck
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Nathalie Chamond
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Afaf Saaidi
- CNRS UMR 7161, Laboratoire de Recherche en Informatique de l'Ecole Polytechnique (LIX), Ecole Polytechnique, 1 rue Estienne d'Orves, 91120 Palaiseau, France.,AMIB, Inria Saclay, bat Alan Turing, 1 rue Estienne d'Orves, 91120 Palaiseau, France
| | - Yann Ponty
- CNRS UMR 7161, Laboratoire de Recherche en Informatique de l'Ecole Polytechnique (LIX), Ecole Polytechnique, 1 rue Estienne d'Orves, 91120 Palaiseau, France.,AMIB, Inria Saclay, bat Alan Turing, 1 rue Estienne d'Orves, 91120 Palaiseau, France
| | - Theophile Ohlmann
- CIRI (International Center for Infectiology Research), INSERM U1111, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5308, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Bruno Sargueil
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
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Boeras I, Seufzer B, Brady S, Rendahl A, Heng X, Boris-Lawrie K. The basal translation rate of authentic HIV-1 RNA is regulated by 5'UTR nt-pairings at junction of R and U5. Sci Rep 2017; 7:6902. [PMID: 28761163 PMCID: PMC5537239 DOI: 10.1038/s41598-017-06883-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/19/2017] [Indexed: 11/25/2022] Open
Abstract
The paradigm protein synthesis rate is regulated by structural complexity of the 5′untranslated region (UTR) derives from bacterial and other riboswitches. In-solution, HIV-1 5′UTR forms two interchangeable long-range nucleotide (nt) -pairings, one sequesters the gag start codon promoting dimerization while the other sequesters the dimer initiation signal preventing dimerization. While the effect of these nt-pairings on dimerization and packaging has been documented their effect on authentic HIV translation in cellulo has remained elusive until now. HIVNL4-3 5′UTR substitutions were designed to individually stabilize the dimer-prone or monomer-prone conformations, validated in-solution, and introduced to molecular clones. The effect of 5′UTR conformation on ribosome loading to HIV unspliced RNA and rate of Gag polypeptide synthesis was quantified in cellulo. Monomer- and dimer-prone 5′UTRs displayed equivalent, basal rate of translation. Gain-of-function substitution U103, in conjunction with previously defined nt-pairings that reorient AUG to flexible nt-pairing, significantly activated the translation rate, indicating the basal translation rate is under positive selection. The observed translation up-mutation focuses attention to nt-pairings at the junction of R and U5, a poorly characterized structure upstream of the characterized HIV riboswitch and demonstrates the basal translation rate of authentic HIV RNA is regulated independently of monomer:dimer equilibrium of the 5′UTR.
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Affiliation(s)
- I Boeras
- University of Minnesota, Department of Veterinary and Biomedical Sciences, 1971 Commonwealth, Saint Paul, MN, 55108, USA
| | - B Seufzer
- University of Minnesota, Department of Veterinary and Biomedical Sciences, 1971 Commonwealth, Saint Paul, MN, 55108, USA
| | - S Brady
- University of Missouri, Department of Biochemistry, 503 S. College Ave, Columbia, MO, 65211, USA
| | - A Rendahl
- University of Minnesota, Department of Veterinary and Biomedical Sciences, 1971 Commonwealth, Saint Paul, MN, 55108, USA
| | - X Heng
- University of Missouri, Department of Biochemistry, 503 S. College Ave, Columbia, MO, 65211, USA.
| | - K Boris-Lawrie
- University of Minnesota, Department of Veterinary and Biomedical Sciences, 1971 Commonwealth, Saint Paul, MN, 55108, USA.
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Epitranscriptomic regulation of viral replication. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:460-471. [PMID: 28219769 DOI: 10.1016/j.bbagrm.2017.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/11/2022]
Abstract
RNA plays central roles in biology and novel functions and regulation mechanisms are constantly emerging. To accomplish some of their functions within the cell, RNA molecules undergo hundreds of chemical modifications from which N6-methyladenosine (m6A), inosine (I), pseudouridine (ψ) and 5-methylcytosine (5mC) have been described in eukaryotic mRNA. Interestingly, the m6A modification was shown to be reversible, adding novel layers of regulation of gene expression through what is now recognized as epitranscriptomics. The development of molecular mapping strategies coupled to next generation sequencing allowed the identification of thousand of modified transcripts in different tissues and under different physiological conditions such as viral infections. As intracellular parasites, viruses are confronted to cellular RNA modifying enzymes and, as a consequence, viral RNA can be chemically modified at some stages of the replication cycle. This review focuses on the chemical modifications of viral RNA and the impact that these modifications have on viral gene expression and the output of infection. A special emphasis is given to m6A, which was recently shown to play important yet controversial roles in different steps of the HIV-1, HCV and ZIKV replication cycles.
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14
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Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries. Viruses 2016; 8:v8110320. [PMID: 27886048 PMCID: PMC5127034 DOI: 10.3390/v8110320] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 02/06/2023] Open
Abstract
The human immunodeficiency virus type-1 (HIV-1) unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs) containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1), Staufen double-stranded RNA binding protein 1/2 (STAU1/2), or components of miRNA-induced silencing complex (miRISC) and processing bodies (PBs). More recently, the HIV-1 unspliced mRNA was shown to contain N⁶-methyladenosine (m⁶A), allowing the recruitment of YTH N⁶-methyladenosine RNA binding protein 2 (YTHDF2), an m⁶A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.
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Jan E, Mohr I, Walsh D. A Cap-to-Tail Guide to mRNA Translation Strategies in Virus-Infected Cells. Annu Rev Virol 2016; 3:283-307. [PMID: 27501262 DOI: 10.1146/annurev-virology-100114-055014] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although viruses require cellular functions to replicate, their absolute dependence upon the host translation machinery to produce polypeptides indispensable for their reproduction is most conspicuous. Despite their incredible diversity, the mRNAs produced by all viruses must engage cellular ribosomes. This has proven to be anything but a passive process and has revealed a remarkable array of tactics for rapidly subverting control over and dominating cellular regulatory pathways that influence translation initiation, elongation, and termination. Besides enforcing viral mRNA translation, these processes profoundly impact host cell-intrinsic immune defenses at the ready to deny foreign mRNA access to ribosomes and block protein synthesis. Finally, genome size constraints have driven the evolution of resourceful strategies for maximizing viral coding capacity. Here, we review the amazing strategies that work to regulate translation in virus-infected cells, highlighting both virus-specific tactics and the tremendous insight they provide into fundamental translational control mechanisms in health and disease.
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Affiliation(s)
- Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada;
| | - Ian Mohr
- Department of Microbiology and New York University Cancer Institute, New York University School of Medicine, New York, NY 10016;
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611;
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16
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Meyer F. Viral interactions with components of the splicing machinery. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 142:241-68. [PMID: 27571697 DOI: 10.1016/bs.pmbts.2016.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Eukaryotic genes are often interrupted by stretches of sequence with no protein coding potential or obvious function. After transcription, these interrupting sequences must be removed to give rise to the mature messenger RNA. This fundamental process is called RNA splicing and is achieved by complicated machinery made of protein and RNA that assembles around the RNA to be edited. Viruses also use RNA splicing to maximize their coding potential and economize on genetic space, and use clever strategies to manipulate the splicing machinery to their advantage. This article gives an overview of the splicing process and provides examples of viral strategies that make use of various components of the splicing system to promote their replicative cycle. Representative virus families have been selected to illustrate the interaction with various regulatory proteins and ribonucleoproteins. The unifying theme is fine regulation through protein-protein and protein-RNA interactions with the spliceosome components and associated factors to promote or prevent spliceosome assembly on given splice sites, in addition to a strong influence from cis-regulatory sequences on viral transcripts. Because there is an intimate coupling of splicing with the processes that direct mRNA biogenesis, a description of how these viruses couple the regulation of splicing with the retention or stability of mRNAs is also included. It seems that a unique balance of suppression and activation of splicing and nuclear export works optimally for each family of viruses.
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Affiliation(s)
- F Meyer
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, USA.
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Fernandes JD, Booth DS, Frankel AD. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:470-86. [PMID: 26929078 DOI: 10.1002/wrna.1342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/28/2023]
Abstract
HIV replication requires the nuclear export of essential, intron-containing viral RNAs. To facilitate export, HIV encodes the viral accessory protein Rev which binds unspliced and partially spliced viral RNAs and creates a ribonucleoprotein complex that recruits the cellular Chromosome maintenance factor 1 export machinery. Exporting RNAs in this manner bypasses the necessity for complete splicing as a prerequisite for mRNA export, and allows intron-containing RNAs to reach the cytoplasm intact for translation and virus packaging. Recent structural studies have revealed that this entire complex exhibits remarkable plasticity at many levels of organization, including RNA folding, protein-RNA recognition, multimer formation, and host factor recruitment. In this review, we explore each aspect of plasticity from structural, functional, and possible therapeutic viewpoints. WIREs RNA 2016, 7:470-486. doi: 10.1002/wrna.1342 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jason D Fernandes
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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Smirnova VV, Terenin IM, Khutornenko AA, Andreev DE, Dmitriev SE, Shatsky IN. Does HIV-1 mRNA 5'-untranslated region bear an internal ribosome entry site? Biochimie 2016; 121:228-37. [DOI: 10.1016/j.biochi.2015.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/11/2015] [Indexed: 12/18/2022]
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