1
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Musier-Forsyth K, Rein A, Hu WS. Transcription start site choice regulates HIV-1 RNA conformation and function. Curr Opin Struct Biol 2024; 88:102896. [PMID: 39146887 DOI: 10.1016/j.sbi.2024.102896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/17/2024]
Abstract
HIV-1, the causative agent of AIDS, is a retrovirus that packages two copies of unspliced viral RNA as a dimer into newly budding virions. The unspliced viral RNA also serves as an mRNA template for translation of two polyproteins. Recent studies suggest that the fate of the viral RNA (genome or mRNA) is determined at the level of transcription. RNA polymerase II uses heterogeneous transcription start sites to generate major transcripts that differ in only two guanosines at the 5' end. Remarkably, this two-nucleotide difference is sufficient to alter the structure of the 5'-untranslated region and generate two pools of RNA with distinct functions. The presence of both RNA species is needed for optimal viral replication and fitness.
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Affiliation(s)
- Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA.
| | - Alan Rein
- Retrovirus Assembly Section, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA.
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2
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Yasin S, Lesko SL, Kharytonchyk S, Brown JD, Chaudry I, Geleta SA, Tadzong NF, Zheng MY, Patel HB, Kengni G, Neubert E, Quiambao JMC, Becker G, Ghinger FG, Thapa S, Williams A, Radov MH, Boehlert KX, Hollmann NM, Singh K, Bruce JW, Marchant J, Telesnitsky A, Sherer NM, Summers MF. Role of RNA structural plasticity in modulating HIV-1 genome packaging and translation. Proc Natl Acad Sci U S A 2024; 121:e2407400121. [PMID: 39110735 PMCID: PMC11331132 DOI: 10.1073/pnas.2407400121] [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: 04/13/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
HIV-1 transcript function is controlled in part by twinned transcriptional start site usage, where 5' capped RNAs beginning with a single guanosine (1G) are preferentially packaged into progeny virions as genomic RNA (gRNA) whereas those beginning with three sequential guanosines (3G) are retained in cells as mRNAs. In 3G transcripts, one of the additional guanosines base pairs with a cytosine located within a conserved 5' polyA element, resulting in formation of an extended 5' polyA structure as opposed to the hairpin structure formed in 1G RNAs. To understand how this remodeling influences overall transcript function, we applied in vitro biophysical studies with in-cell genome packaging and competitive translation assays to native and 5' polyA mutant transcripts generated with promoters that differentially produce 1G or 3G RNAs. We identified mutations that stabilize the 5' polyA hairpin structure in 3G RNAs, which promote RNA dimerization and Gag binding without sequestering the 5' cap. None of these 3G transcripts were competitively packaged, confirming that cap exposure is a dominant negative determinant of viral genome packaging. For all RNAs examined, conformations that favored 5' cap exposure were both poorly packaged and more efficiently translated than those that favored 5' cap sequestration. We propose that structural plasticity of 5' polyA and other conserved RNA elements place the 5' leader on a thermodynamic tipping point for low-energetic (~3 kcal/mol) control of global transcript structure and function.
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Affiliation(s)
- Saif Yasin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Sydney L. Lesko
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI53705
- Department of Oncology, Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI53705
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109-5620
| | - Joshua D. Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Issac Chaudry
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Samuel A. Geleta
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Ndeh F. Tadzong
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Mei Y. Zheng
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Heer B. Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Gabriel Kengni
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Emma Neubert
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | | | - Ghazal Becker
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Frances Grace Ghinger
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Sreeyasha Thapa
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - A’Lyssa Williams
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Michelle H. Radov
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Kellie X. Boehlert
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Nele M. Hollmann
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
- HHMI, University of Maryland, Baltimore County, MD21250
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, MD21250
| | - Karndeep Singh
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - James W. Bruce
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI53705
- Department of Oncology, Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI53705
| | - Jan Marchant
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109-5620
| | - Nathan M. Sherer
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI53705
- Department of Oncology, Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI53705
| | - Michael F. Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, MD21250
- HHMI, University of Maryland, Baltimore County, MD21250
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, MD21250
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3
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Sung PY, Phelan JE, Luo D, Kulasegaran-Shylini R, Bohn P, Smyth RP, Roy P. Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network. Nucleic Acids Res 2024; 52:8500-8514. [PMID: 38769067 DOI: 10.1093/nar/gkae404] [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: 12/20/2023] [Revised: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
How do segmented RNA viruses correctly recruit their genome has yet to be clarified. Bluetongue virus is a double-stranded RNA virus with 10 segments of different sizes, but it assembles its genome in single-stranded form through a series of specific RNA-RNA interactions prior to packaging. In this study, we determined the structure of each BTV transcript, individually and in different combinations, using 2'-hydroxyl acylation analysed by primer extension and mutational profiling (SHAPE-MaP). SHAPE-MaP identified RNA structural changes during complex formation and putative RNA-RNA interaction sites. Our data also revealed a core RNA-complex of smaller segments which serves as the foundation ('anchor') for the assembly of a complete network composed of ten ssRNA segments. The same order of core RNA complex formation was identified in cells transfected with viral RNAs. No viral protein was required for these assembly reactions. Further, substitution mutations in the interacting bases within the core assemblies, altered subsequent segment addition and affected virus replication. These data identify a wholly RNA driven reaction that may offer novel opportunities for designed attenuation or antiviral therapeutics.
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Affiliation(s)
- Po-Yu Sung
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody E Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dongsheng Luo
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Polly Roy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
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4
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Duchon A, Hu WS. HIV-1 RNA genome packaging: it's G-rated. mBio 2024; 15:e0086123. [PMID: 38411060 PMCID: PMC11005445 DOI: 10.1128/mbio.00861-23] [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] [Indexed: 02/28/2024] Open
Abstract
A member of the Retroviridae, human immunodeficiency virus type 1 (HIV-1), uses the RNA genome packaged into nascent virions to transfer genetic information to its progeny. The genome packaging step is a highly regulated and extremely efficient process as a vast majority of virus particles contain two copies of full-length unspliced HIV-1 RNA that form a dimer. Thus, during virus assembly HIV-1 can identify and selectively encapsidate HIV-1 unspliced RNA from an abundant pool of cellular RNAs and various spliced HIV-1 RNAs. Several "G" features facilitate the packaging of a dimeric RNA genome. The viral polyprotein Gag orchestrates virus assembly and mediates RNA genome packaging. During this process, Gag preferentially binds unpaired guanosines within the highly structured 5' untranslated region (UTR) of HIV-1 RNA. In addition, the HIV-1 unspliced RNA provides a scaffold that promotes Gag:Gag interactions and virus assembly, thereby ensuring its packaging. Intriguingly, recent studies have shown that the use of different guanosines at the junction of U3 and R as transcription start sites results in HIV-1 unspliced RNA species with 99.9% identical sequences but dramatically distinct 5' UTR conformations. Consequently, one species of unspliced RNA is preferentially packaged over other nearly identical RNAs. These studies reveal how conformations affect the functions of HIV-1 RNA elements and the complex regulation of HIV-1 replication. In this review, we summarize cis- and trans-acting elements critical for HIV-1 RNA packaging, locations of Gag:RNA interactions that mediate genome encapsidation, and the effects of transcription start sites on the structure and packaging of HIV-1 RNA.
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Affiliation(s)
- Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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5
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Hardy J, Demecheleer E, Schauvliege M, Staelens D, Mortier V, Verhofstede C. Reverse transcription of plasma-derived HIV-1 RNA generates multiple artifacts through tRNA(Lys-3)-priming. Microbiol Spectr 2024; 12:e0387223. [PMID: 38442427 PMCID: PMC10986323 DOI: 10.1128/spectrum.03872-23] [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: 11/06/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
In vitro reverse transcription of full-length HIV-1 RNA extracted from the blood plasma of people living with HIV-1 remains challenging. Here, we describe the initiation of reverse transcription of plasma-derived viral RNA in the absence of an exogenous primer. Real-time PCR and Sanger sequencing were applied to identify the source and to monitor the outcome of this reaction. Results demonstrated that during purification of viral RNA from plasma, tRNA(Lys-3) is co-extracted in a complex with the viral RNA. In the presence of a reverse transcription enzyme, this tRNA(Lys-3) can induce reverse transcription, a reaction that is not confined to transcription of the 5' end of the viral RNA. A range of cDNA products is generated, most of them indicative for the occurrence of in vitro strand transfer events that involve translocation of cDNA from the 5' end to random positions on the viral RNA. This process results in the formation of cDNAs with large internal deletions. However, near full-length cDNA and cDNA with sequence patterns resembling multiple spliced HIV-1 RNA were also detected. Despite its potential to introduce significant bias in the interpretation of results across various applications, tRNA(Lys-3)-driven reverse transcription has been overlooked thus far. A more in-depth study of this tRNA-driven in vitro reaction may provide new insight into the complex process of in vivo HIV-1 replication.IMPORTANCEThe use of silica-based extraction methods for purifying HIV-1 RNA from viral particles is a common practice, but it involves co-extraction of human tRNA(Lys-3) due to the strong interactions between these molecules. This co-extraction becomes particularly significant when the extracted RNA is used in reverse transcription reactions, as the tRNA(Lys-3) then serves as a primer. Reverse transcription from tRNA(Lys-3) is not confined to cDNA synthesis of the 5' end of the viral RNA but extends across various regions of the viral genome through in vitro strand transfer events. Co-extraction of tRNA(Lys-3) has been overlooked thus far, despite its potential to introduce bias in downstream, reverse transcription-related applications. The observed events in the tRNA(Lys-3)-induced in vitro reverse transcription resemble in vivo replication processes. Therefore, these reactions may offer a unique model to better understand the replication dynamics of HIV-1.
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Affiliation(s)
- Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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6
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Ying Y, Yang Y, Chen AK. Roles of RNA scaffolding in nanoscale Gag multimerization and selective protein sorting at HIV membranes. SCIENCE ADVANCES 2024; 10:eadk8297. [PMID: 38394201 PMCID: PMC10889351 DOI: 10.1126/sciadv.adk8297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
HIV-1 Gag proteins can multimerize upon the viral genomic RNA or multiple random cellular messenger RNAs to form a virus particle or a virus-like particle, respectively. To date, whether the two types of particles form via the same Gag multimerization process has remained unclarified. Using photoactivated localization microscopy to illuminate Gag organizations and dynamics at the nanoscale, here, we showed that genomic RNA mediates Gag multimerization in a more cluster-centric, cooperative, and spatiotemporally coordinated fashion, with the ability to drive dense Gag clustering dependent on its ability to act as a long-stranded scaffold not easily attainable by cellular messenger RNAs. These differences in Gag multimerization were further shown to affect downstream selective protein sorting into HIV membranes, indicating that the choice of RNA for packaging can modulate viral membrane compositions. These findings should advance the understanding of HIV assembly and further benefit the development of virus-like particle-based therapeutics.
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Affiliation(s)
- Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Peking University, Beijing 100871, China
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7
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Banerjee P, Voth GA. Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding. Biophys J 2024; 123:42-56. [PMID: 37978800 PMCID: PMC10808027 DOI: 10.1016/j.bpj.2023.11.017] [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: 08/15/2023] [Revised: 10/25/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-genomic RNA (gRNA) interactions play a crucial role in the multimerization process, which is yet to be fully understood. We performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to affect mainly the SP1 domain of the 18-mer and the matrix-capsid linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the nucleocapsid domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, and also regulates the dynamic organization of the local membrane region itself.
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Affiliation(s)
- Puja Banerjee
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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8
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Wu F, Simonetti FR. Learning from Persistent Viremia: Mechanisms and Implications for Clinical Care and HIV-1 Cure. Curr HIV/AIDS Rep 2023; 20:428-439. [PMID: 37955826 PMCID: PMC10719122 DOI: 10.1007/s11904-023-00674-w] [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] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
PURPOSE OF REVIEW In this review, we discuss what persistent viremia has taught us about the biology of the HIV-1 reservoir during antiretroviral therapy (ART). We will also discuss the implications of this phenomenon for HIV-1 cure research and its clinical management. RECENT FINDINGS While residual viremia (RV, 1-3 HIV-1 RNA copies/ml) can be detected in most of people on ART, some individuals experience non-suppressible viremia (NSV, > 20-50 copies/mL) despite optimal adherence. When issues of drug resistance and pharmacokinetics are ruled out, this persistent virus in plasma is the reflection of virus production from clonally expanded CD4+ T cells carrying proviruses. Recent work has shown that a fraction of the proviruses source of NSV are not infectious, due to defects in the 5'-Leader sequence. However, additional viruses and host determinants of NSV are not fully understood. The study of NSV is of prime importance because it represents a challenge for the clinical care of people on ART, and it sheds light on virus-host interactions that could advance HIV-1 remission research.
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Affiliation(s)
- Fengting Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA
| | - Francesco R Simonetti
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA.
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9
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Banerjee P, Voth GA. Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553549. [PMID: 37645781 PMCID: PMC10462060 DOI: 10.1101/2023.08.16.553549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-gRNA interactions play a crucial role in the multimerization process, which is yet to be fully understood. We have performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model (hENM) applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to impact mainly the SP1 domain of the 18-mer and the MA-CA linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the NC domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, as well as regulates the dynamic organization of the local membrane region itself. Significance Gag(Pr 55 Gag ) polyprotein orchestrates many essential events in HIV-1 assembly, including packaging of the genomic RNA (gRNA) in the immature virion. Although various experimental techniques, such as cryo-ET, X-ray, and NMR, have revealed structural properties of individual domains in the immature Gag clusters, structural and biophysical characterization of a full-length Gag molecule remains a challenge for existing experimental techniques. Using atomistic molecular dynamics simulations of the different model systems of Gag polyprotein, we present here a detailed structural characterization of Gag molecules in different multimerization states and interrogate the synergy between Gag-Gag, Gag-membrane, and Gag-gRNA interactions during the viral assembly process.
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10
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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11
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. RESEARCH SQUARE 2023:rs.3.rs-3060076. [PMID: 37461524 PMCID: PMC10350206 DOI: 10.21203/rs.3.rs-3060076/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
HIV-1 capsid assembly is an essential process in the virus infection cycle. Initiation of capsid assembly involves viral proteins, genomic RNA, and the inner leaflet of the plasma membrane, facilitated by a number of cellular factors1. The viral structural protein Gag plays a number of central roles in this process, including association with the membrane, selective binding of genomic RNA, and oligomerization and packaging to ultimately produce an immature budded pro-viral particle2. While there have been intensive studies regarding the early stages of Gag assembly, there is a lack of consensus on the mechanism for nucleation and growth of Gag complexes3-7. Here we show that myristoylated Gag forms a trimer nucleus in a model membrane that can selectively bind a dimeric RNA containing the packaging signal. Subsequent growth of myristoyl-Gag oligomers requires vRNA, and occurs by addition of 1 or 2 Gag monomers at a time from solution. These data support a model where the immature capsid lattice formation occurs by a gradual lattice edge expansion, following a trimeric nucleation event. The dynamic single molecule data that support this model were recorded using mass photometry, involving full length myristoylated protein, RNA, and lipid together. These data are the first to support a lattice edge expansion model of Gag during early stages of assembly in a biological-relevant setting, providing insights to the fundamental models of virus structural protein assembly process.
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Affiliation(s)
- Anne X.-Z. Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - John A. Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - David P. Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
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12
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Bohn P, Gribling-Burrer AS, Ambi UB, Smyth RP. Nano-DMS-MaP allows isoform-specific RNA structure determination. Nat Methods 2023; 20:849-859. [PMID: 37106231 PMCID: PMC10250195 DOI: 10.1038/s41592-023-01862-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experiments is that short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, information is acquired as a population average in regions that are shared between transcripts, thus blurring the underlying structural landscape. Here, we present nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP)-a method that exploits long-read sequencing to provide isoform-resolved structural information of highly similar RNA molecules. We demonstrate the value of Nano-DMS-MaP by resolving the complex structural landscape of human immunodeficiency virus-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures at the packaging site within the common 5' untranslated region, likely explaining why spliced viral RNAs are excluded from viral particles. Thus, Nano-DMS-MaP is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short-read ensemble analyses.
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Affiliation(s)
- Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Uddhav B Ambi
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Julius-Maximilians-Universität Würzburg, Faculty of Medicine, Würzburg, Germany.
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13
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White JA, Wu F, Yasin S, Moskovljevic M, Varriale J, Dragoni F, Camilo-Contreras A, Duan J, Zheng MY, Tadzong NF, Patel HB, Quiambao JMC, Rhodehouse K, Zhang H, Lai J, Beg SA, Delannoy M, Kilcrease C, Hoffmann CJ, Poulin S, Chano F, Tremblay C, Cherian J, Barditch-Crovo P, Chida N, Moore RD, Summers MF, Siliciano RF, Siliciano JD, Simonetti FR. Clonally expanded HIV-1 proviruses with 5'-leader defects can give rise to nonsuppressible residual viremia. J Clin Invest 2023; 133:165245. [PMID: 36602866 PMCID: PMC10014112 DOI: 10.1172/jci165245] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
BackgroundAntiretroviral therapy (ART) halts HIV-1 replication, decreasing viremia to below the detection limit of clinical assays. However, some individuals experience persistent nonsuppressible viremia (NSV) originating from CD4+ T cell clones carrying infectious proviruses. Defective proviruses represent over 90% of all proviruses persisting during ART and can express viral genes, but whether they can cause NSV and complicate ART management is unknown.MethodsWe undertook an in-depth characterization of proviruses causing NSV in 4 study participants with optimal adherence and no drug resistance. We investigated the impact of the observed defects on 5'-leader RNA properties, virus infectivity, and gene expression. Integration-site specific assays were used to track these proviruses over time and among cell subsets.ResultsClones carrying proviruses with 5'-leader defects can cause persistent NSV up to approximately 103 copies/mL. These proviruses had small, often identical deletions or point mutations involving the major splicing donor (MSD) site and showed partially reduced RNA dimerization and nucleocapsid binding. Nevertheless, they were inducible and produced noninfectious virions containing viral RNA, but lacking envelope.ConclusionThese findings show that proviruses with 5'-leader defects in CD4+ T cell clones can give rise to NSV, affecting clinical care. Sequencing of the 5'-leader can help in understanding failure to completely suppress viremia.FundingOffice of the NIH Director and National Institute of Dental and Craniofacial Research, NIH; Howard Hughes Medical Institute; Johns Hopkins University Center for AIDS Research; National Institute for Allergy and Infectious Diseases (NIAID), NIH, to the PAVE, BEAT-HIV, and DARE Martin Delaney collaboratories.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saif Yasin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Milica Moskovljevic
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Filippo Dragoni
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mei Y Zheng
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Ndeh F Tadzong
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Heer B Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Jeanelle Mae C Quiambao
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Delannoy
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christin Kilcrease
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher J Hoffmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Canada
| | - Jerald Cherian
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia Barditch-Crovo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natasha Chida
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Chameettachal A, Mustafa F, Rizvi TA. Understanding Retroviral Life Cycle and its Genomic RNA Packaging. J Mol Biol 2023; 435:167924. [PMID: 36535429 DOI: 10.1016/j.jmb.2022.167924] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Members of the family Retroviridae are important animal and human pathogens. Being obligate parasites, their replication involves a series of steps during which the virus hijacks the cellular machinery. Additionally, many of the steps of retrovirus replication are unique among viruses, including reverse transcription, integration, and specific packaging of their genomic RNA (gRNA) as a dimer. Progress in retrovirology has helped identify several molecular mechanisms involved in each of these steps, but many are still unknown or remain controversial. This review summarizes our present understanding of the molecular mechanisms involved in various stages of retrovirus replication. Furthermore, it provides a comprehensive analysis of our current understanding of how different retroviruses package their gRNA into the assembling virions. RNA packaging in retroviruses holds a special interest because of the uniqueness of packaging a dimeric genome. Dimerization and packaging are highly regulated and interlinked events, critical for the virus to decide whether its unspliced RNA will be packaged as a "genome" or translated into proteins. Finally, some of the outstanding areas of exploration in the field of RNA packaging are highlighted, such as the role of epitranscriptomics, heterogeneity of transcript start sites, and the necessity of functional polyA sequences. An in-depth knowledge of mechanisms that interplay between viral and cellular factors during virus replication is critical in understanding not only the virus life cycle, but also its pathogenesis, and development of new antiretroviral compounds, vaccines, as well as retroviral-based vectors for human gene therapy.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates. https://twitter.com/chameettachal
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
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15
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Yang X, Liu Y, Cui W, Liu M, Wang W. Distinct Gag interaction properties of HIV-1 RNA 5' leader conformers reveal a mechanism for dimeric genome selection. RNA (NEW YORK, N.Y.) 2023; 29:217-227. [PMID: 36384962 PMCID: PMC9891258 DOI: 10.1261/rna.079347.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
During HIV-1 assembly, two copies of viral genomic RNAs (gRNAs) are selectively packaged into new viral particles. This process is mediated by specific interactions between HIV-1 Gag and the packaging signals at the 5' leader (5'L) of viral gRNA. 5'L is able to adopt different conformations, which promotes either gRNA dimerization and packaging or Gag translation. Dimerization and packaging are coupled. Whether the selective packaging of the gRNA dimer is due to favorable interactions between Gag and 5'L in the packaging conformation is not known. Here, using RNAs mimicking the two 5'L conformers, we show that the 5'L conformation dramatically affects Gag-RNA interactions. Compared to the RNA in the translation conformation (5'LT), the RNA in the packaging conformation (5'LP) can bind more Gag molecules. Gag associates with 5'LP faster than it binds to 5'LT, whereas Gag dissociates from 5'LP more slowly. The Gag-5'LP complex is more stable at high salt concentrations. The NC-SP2-p6 region of Gag likely accounts for the faster association and slower dissociation kinetics for the Gag-5'LP interaction and for the higher stability. In summary, our data suggest that conformational changes play an important role in the selection of dimeric genomes, probably by affecting the binding kinetics and stability of the Gag-5'L complex.
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Affiliation(s)
- Xin Yang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yong Liu
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Wen Cui
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Mengmeng Liu
- Office of Research Administration, Chongqing Medical University, Chongqing 400016, China
| | - Wei Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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16
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525415. [PMID: 36747785 PMCID: PMC9901173 DOI: 10.1101/2023.01.27.525415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mass photometry (MP) was used to investigate the assembly of myristoylated full-length HIV-1 Gag (myr-Gag) and vRNA 5’ UTR fragment in a supported lipid bilayer (SLB) model system. The MP trajectories demonstrated that Gag trimerization on the membrane is a key step of early Gag assembly in the presence of vRNA. Growth of myr-Gag oligomers requires vRNA, occuring by addition of 1 or 2 monomers at a time from solution. These data support a model where formation of the Gag hexamers characteristic of the immature capsid lattice occurs by a gradual edge expansion, following a trimeric nucleation event. These dynamic single molecule data involving protein, RNA, and lipid components together, provide novel and fundamental insights into the initiation of virus capsid assembly.
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17
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Lei X, Gonçalves-Carneiro D, Zang TM, Bieniasz PD. Initiation of HIV-1 Gag lattice assembly is required for recognition of the viral genome packaging signal. eLife 2023; 12:e83548. [PMID: 36688533 PMCID: PMC9908077 DOI: 10.7554/elife.83548] [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: 09/18/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
The encapsidation of HIV-1 gRNA into virions is enabled by the binding of the nucleocapsid (NC) domain of the HIV-1 Gag polyprotein to the structured viral RNA packaging signal (Ψ) at the 5' end of the viral genome. However, the subcellular location and oligomeric status of Gag during the initial Gag-Ψ encounter remain uncertain. Domains other than NC, such as capsid (CA), may therefore indirectly affect RNA recognition. To investigate the contribution of Gag domains to Ψ recognition in a cellular environment, we performed protein-protein crosslinking and protein-RNA crosslinking immunoprecipitation coupled with sequencing (CLIP-seq) experiments. We demonstrate that NC alone does not bind specifically to Ψ in living cells, whereas full-length Gag and a CANC subdomain bind to Ψ with high specificity. Perturbation of the Ψ RNA structure or NC zinc fingers affected CANC:Ψ binding specificity. Notably, CANC variants with substitutions that disrupt CA:CA dimer, trimer, or hexamer interfaces in the immature Gag lattice also affected RNA binding, and mutants that were unable to assemble a nascent Gag lattice were unable to specifically bind to Ψ. Artificially multimerized NC domains did not specifically bind Ψ. CA variants with substitutions in inositol phosphate coordinating residues that prevent CA hexamerization were also deficient in Ψ binding and second-site revertant mutants that restored CA assembly also restored specific binding to Ψ. Overall, these data indicate that the correct assembly of a nascent immature CA lattice is required for the specific interaction between Gag and Ψ in cells.
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Affiliation(s)
- Xiao Lei
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
| | | | - Trinity M Zang
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew York, New YorkUnited States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew York, New YorkUnited States
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18
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes. Virus Res 2022; 321:198910. [PMID: 36070810 DOI: 10.1016/j.virusres.2022.198910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.
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Affiliation(s)
- Margarita I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Andriy L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Iryna M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Leonid G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine.
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19
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Olsthoorn RCL. Replication of alphaviruses requires a pseudoknot that involves the poly(A) tail. RNA (NEW YORK, N.Y.) 2022; 28:1348-1358. [PMID: 35906005 PMCID: PMC9479738 DOI: 10.1261/rna.079243.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Alphaviruses, such as the Sindbis virus and the Chikungunya virus, are RNA viruses with a positive sense single-stranded RNA genome that infect various vertebrates, including humans. A conserved sequence element (CSE) of ∼19 nt in the 3' noncoding region is important for replication. Despite extensive mutational analysis of the CSE, no comprehensive model of this element exists to date. Here, it is shown that the CSE can form an RNA pseudoknot with part of the poly(A) tail and is similar to the human telomerase pseudoknot with which it shares 17 nt. Mutants that alter the stability of the pseudoknot were investigated in the context of a replicon of the Sindbis virus and by native gel electrophoresis. These studies reveal that the pseudoknot is required for virus replication and is stabilized by UAU base triples. The new model is discussed in relation to previous data on Sindbis virus mutants and revertants lacking (part of) the CSE.
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Affiliation(s)
- René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
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20
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Ding P, Summers MF. Sequestering the 5′‐cap for viral RNA packaging. Bioessays 2022; 44:e2200104. [PMID: 36101513 DOI: 10.1002/bies.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/11/2022]
Abstract
Many viruses evolved mechanisms for capping the 5'-ends of their plus-strand RNAs as a means of hijacking the eukaryotic messenger RNA (mRNA) splicing/translation machinery. Although capping is critical for replication, the RNAs of these viruses have other essential functions including their requirement to be packaged as either genomes or pre-genomes into progeny viruses. Recent studies indicate that human immunodeficiency virus type-1 (HIV-1) RNAs are segregated between splicing/translation and packaging functions by a mechanism that involves structural sequestration of the 5'-cap. Here, we examined studies reported for other viruses and retrotransposons that require both selective packaging of their RNAs and 5'-RNA capping for host-mediated translation. Our findings suggest that viruses and retrotransposons have evolved multiple mechanisms to control 5'-cap accessibility, consistent with the hypothesis that removal or sequestration of the 5' cap enables packageable RNAs to avoid capture by the cellular RNA processing and translation machinery.
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Affiliation(s)
- Pengfei Ding
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
| | - Michael F. Summers
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
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21
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Upstream of N-Ras (Unr/CSDE1) Interacts with NCp7 and Gag, Modulating HIV-1 IRES-Mediated Translation Initiation. Viruses 2022; 14:v14081798. [PMID: 36016420 PMCID: PMC9413769 DOI: 10.3390/v14081798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
The Human Immunodeficiency Virus-1 (HIV-1) nucleocapsid protein (NC) as a mature protein or as a domain of the Gag precursor plays important roles in the early and late phases of the infection. To better understand its roles, we searched for new cellular partners and identified the RNA-binding protein Unr/CSDE1, Upstream of N-ras, whose interaction with Gag and NCp7 was confirmed by co-immunoprecipitation and FRET-FLIM. Unr interaction with Gag was found to be RNA-dependent and mediated by its NC domain. Using a dual luciferase assay, Unr was shown to act as an ITAF (IRES trans-acting factor), increasing the HIV-1 IRES-dependent translation. Point mutations of the HIV-1 IRES in a consensus Unr binding motif were found to alter both the IRES activity and its activation by Unr, suggesting a strong dependence of the IRES on Unr. Interestingly, Unr stimulatory effect is counteracted by NCp7, while Gag increases the Unr-promoted IRES activity, suggesting a differential Unr effect on the early and late phases of viral infection. Finally, knockdown of Unr in HeLa cells leads to a decrease in infection by a non-replicative lentivector, proving its functional implication in the early phase of viral infection.
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22
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Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
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23
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Pak A, Gupta M, Yeager M, Voth GA. Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly toward Kinetically Trapped Morphologies. J Am Chem Soc 2022; 144:10417-10428. [PMID: 35666943 PMCID: PMC9204763 DOI: 10.1021/jacs.2c02568] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
During the late stages of the HIV-1 lifecycle, immature virions are produced by the concerted activity of Gag polyproteins, primarily mediated by the capsid (CA) and spacer peptide 1 (SP1) domains, which assemble into a spherical lattice, package viral genomic RNA, and deform the plasma membrane. Recently, inositol hexakisphosphate (IP6) has been identified as an essential assembly cofactor that efficiently produces both immature virions in vivo and immature virus-like particles in vitro. To date, however, several distinct mechanistic roles for IP6 have been proposed on the basis of independent functional, structural, and kinetic studies. In this work, we investigate the molecular influence of IP6 on the structural outcomes and dynamics of CA/SP1 assembly using coarse-grained (CG) molecular dynamics (MD) simulations and free energy calculations. Here, we derive a bottom-up, low-resolution, and implicit-solvent CG model of CA/SP1 and IP6, and simulate their assembly under conditions that emulate both in vitro and in vivo systems. Our analysis identifies IP6 as an assembly accelerant that promotes curvature generation and fissure-like defects throughout the lattice. Our findings suggest that IP6 induces kinetically trapped immature morphologies, which may be physiologically important for later stages of viral morphogenesis and potentially useful for virus-like particle technologies.
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Affiliation(s)
- Alexander
J. Pak
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Manish Gupta
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Mark Yeager
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States,Center
for Membrane Biology, University of Virginia
School of Medicine, Charlottesville, Virginia 22908, United States, United States,Cardiovascular
Research Center, University of Virginia
School of Medicine, Charlottesville, Virginia 22908, United States,Department
of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States,E-mail:
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24
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Hanson HM, Willkomm NA, Yang H, Mansky LM. Human Retrovirus Genomic RNA Packaging. Viruses 2022; 14:1094. [PMID: 35632835 PMCID: PMC9142903 DOI: 10.3390/v14051094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 02/07/2023] Open
Abstract
Two non-covalently linked copies of the retrovirus genome are specifically recruited to the site of virus particle assembly and packaged into released particles. Retroviral RNA packaging requires RNA export of the unspliced genomic RNA from the nucleus, translocation of the genome to virus assembly sites, and specific interaction with Gag, the main viral structural protein. While some aspects of the RNA packaging process are understood, many others remain poorly understood. In this review, we provide an update on recent advancements in understanding the mechanism of RNA packaging for retroviruses that cause disease in humans, i.e., HIV-1, HIV-2, and HTLV-1, as well as advances in the understanding of the details of genomic RNA nuclear export, genome translocation to virus assembly sites, and genomic RNA dimerization.
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Affiliation(s)
- Heather M. Hanson
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
| | - Nora A. Willkomm
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
| | - Louis M. Mansky
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
- Masonic Cancer Center, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
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25
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Zuber J, Schroeder SJ, Sun H, Turner DH, Mathews DH. Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects. Nucleic Acids Res 2022; 50:5251-5262. [PMID: 35524574 PMCID: PMC9122537 DOI: 10.1093/nar/gkac261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/29/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
Nearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. We curated an expanded database of helix stabilities determined by optical melting experiments. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. Prior parameter sets treated 5′GGUC3′ paired to 3′CUGG5′ separately from other 5′GU3′/3′UG5′ stacks. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Introduction of the additional terms was tested with three optical melting experiments. The average absolute difference between measured and predicted free energy changes at 37°C for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. This confirms the need for the additional sequence dependence in the model.
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Affiliation(s)
- Jeffrey Zuber
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Susan J Schroeder
- Department of Chemistry and Biochemistry, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Hongying Sun
- Department of Biochemistry & Biophysics, University of Rochester, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Douglas H Turner
- Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.,Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.,Department of Biostatistics & Computational Biology, University of Rochester, Rochester, NY 14642, USA
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26
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Sumner C, Ono A. Relationship between HIV-1 Gag Multimerization and Membrane Binding. Viruses 2022; 14:v14030622. [PMID: 35337029 PMCID: PMC8949992 DOI: 10.3390/v14030622] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022] Open
Abstract
HIV-1 viral particle assembly occurs specifically at the plasma membrane and is driven primarily by the viral polyprotein Gag. Selective association of Gag with the plasma membrane is a key step in the viral assembly pathway, which is traditionally attributed to the MA domain. MA regulates specific plasma membrane binding through two primary mechanisms including: (1) specific interaction of the MA highly basic region (HBR) with the plasma membrane phospholipid phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2], and (2) tRNA binding to the MA HBR, which prevents Gag association with non-PI(4,5)P2 containing membranes. Gag multimerization, driven by both CA–CA inter-protein interactions and NC-RNA binding, also plays an essential role in viral particle assembly, mediating the establishment and growth of the immature Gag lattice on the plasma membrane. In addition to these functions, the multimerization of HIV-1 Gag has also been demonstrated to enhance its membrane binding activity through the MA domain. This review provides an overview of the mechanisms regulating Gag membrane binding through the MA domain and multimerization through the CA and NC domains, and examines how these two functions are intertwined, allowing for multimerization mediated enhancement of Gag membrane binding.
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27
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Gilmer O, Mailler E, Paillart JC, Mouhand A, Tisné C, Mak J, Smyth RP, Marquet R, Vivet-Boudou V. Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55 Gag and its maturation products. RNA Biol 2022; 19:191-205. [PMID: 35067194 PMCID: PMC8786341 DOI: 10.1080/15476286.2021.2021677] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55Gag precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55Gag or its maturation products (NCp15, NCp9 and NCp7) and the 5ʹ gRNA region and their structural consequences, in vitro. We show that Pr55Gag and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55Gag maturation products on the gRNA structural maturation.
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Affiliation(s)
- Orian Gilmer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Elodie Mailler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Assia Mouhand
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-chimique, Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-chimique, Paris, France
| | - Johnson Mak
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Redmond P Smyth
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
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28
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Durand S, Seigneuret F, Burlaud-Gaillard J, Lemoine R, Tassi MF, Moreau A, Mougel M, Roingeard P, Tauber C, de Rocquigny H. Quantitative analysis of the formation of nucleoprotein complexes between HIV-1 Gag protein and genomic RNA using transmission electron microscopy. J Biol Chem 2022; 298:101500. [PMID: 34929171 PMCID: PMC8760521 DOI: 10.1016/j.jbc.2021.101500] [Citation(s) in RCA: 2] [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: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 01/06/2023] Open
Abstract
In HIV, the polyprotein precursor Gag orchestrates the formation of the viral capsid. In the current view of this viral assembly, Gag forms low-order oligomers that bind to the viral genomic RNA triggering the formation of high-ordered ribonucleoprotein complexes. However, this assembly model was established using biochemical or imaging methods that do not describe the cellular location hosting Gag-gRNA complex nor distinguish gRNA packaging in single particles. Here, we studied the intracellular localization of these complexes by electron microscopy and monitored the distances between the two partners by morphometric analysis of gold beads specifically labeling Gag and gRNA. We found that formation of these viral clusters occurred shortly after the nuclear export of the gRNA. During their transport to the plasma membrane, the distance between Gag and gRNA decreases together with an increase of gRNA packaging. Point mutations in the zinc finger patterns of the nucleocapsid domain of Gag caused an increase in the distance between Gag and gRNA as well as a sharp decrease of gRNA packaged into virions. Finally, we show that removal of stem loop 1 of the 5'-untranslated region does not interfere with gRNA packaging, whereas combined with the removal of stem loop 3 is sufficient to decrease but not abolish Gag-gRNA cluster formation and gRNA packaging. In conclusion, this morphometric analysis of Gag-gRNA cluster formation sheds new light on HIV-1 assembly that can be used to describe at nanoscale resolution other viral assembly steps involving RNA or protein-protein interactions.
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Affiliation(s)
- Stéphanie Durand
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Florian Seigneuret
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Julien Burlaud-Gaillard
- Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Roxane Lemoine
- B Cell Ressources Platform, EA4245 "Transplantation, Immunology and Inflammation", University of Tours, Tours Cedex 1, France
| | - Marc-Florent Tassi
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Alain Moreau
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Marylène Mougel
- Équipe R2D2 Retroviral RNA Dynamics and Delivery, IRIM, CNRS UMR9004, University of Montpellier, Montpellier, France
| | - Philippe Roingeard
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France; Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Clovis Tauber
- UMR U1253 iBrain, Inserm, University of Tours, Tours Cedex 1, France
| | - Hugues de Rocquigny
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France.
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Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem. Proc Natl Acad Sci U S A 2021; 118:2114494118. [PMID: 34873042 DOI: 10.1073/pnas.2114494118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 01/08/2023] Open
Abstract
To generate infectious virus, HIV-1 must package two copies of its full-length RNA into particles. HIV-1 transcription initiates from multiple, neighboring sites, generating RNA species that only differ by a few nucleotides at the 5' end, including those with one (1G) or three (3G) 5' guanosines. Strikingly, 1G RNA is preferentially packaged into virions over 3G RNA. We investigated how HIV-1 distinguishes between these nearly identical RNAs using in-gel chemical probing combined with recently developed computational tools for determining RNA conformational ensembles, as well as cell-based assays to quantify the efficiency of RNA packaging into viral particles. We found that 1G and 3G RNAs fold into distinct structural ensembles. The 1G RNA, but not the 3G RNA, primarily adopts conformations with an intact polyA stem, exposed dimerization initiation site, and multiple, unpaired guanosines known to mediate Gag binding. Furthermore, we identified mutants that exhibited altered genome selectivity and packaged 3G RNA efficiently. In these mutants, both 1G and 3G RNAs fold into similar conformational ensembles, such that they can no longer be distinguished. Our findings demonstrate that polyA stem stability guides RNA-packaging selectivity. These studies also uncover the mechanism by which HIV-1 selects its genome for packaging: 1G RNA is preferentially packaged because it exposes structural elements that promote RNA dimerization and Gag binding.
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D’Souza AR, Jayaraman D, Long Z, Zeng J, Prestwood LJ, Chan C, Kappei D, Lever AML, Kenyon JC. HIV-1 Packaging Visualised by In-Gel SHAPE. Viruses 2021; 13:v13122389. [PMID: 34960658 PMCID: PMC8707378 DOI: 10.3390/v13122389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
HIV-1 packages two copies of its gRNA into virions via an interaction with the viral structural protein Gag. Both copies and their native RNA structure are essential for virion infectivity. The precise stepwise nature of the packaging process has not been resolved. This is largely due to a prior lack of structural techniques that follow RNA structural changes within an RNA-protein complex. Here, we apply the in-gel SHAPE (selective 2'OH acylation analysed by primer extension) technique to study the initiation of HIV-1 packaging, examining the interaction between the packaging signal RNA and the Gag polyprotein, and compare it with that of the NC domain of Gag alone. Our results imply interactions between Gag and monomeric packaging signal RNA in switching the RNA conformation into a dimerisation-competent structure, and show that the Gag-dimer complex then continues to stabilise. These data provide a novel insight into how HIV-1 regulates the translation and packaging of its genome.
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Affiliation(s)
- Aaron R. D’Souza
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (A.R.D.); (D.J.)
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
| | - Dhivya Jayaraman
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (A.R.D.); (D.J.)
| | - Ziqi Long
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
| | - Jingwei Zeng
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
| | - Liam J. Prestwood
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andrew M. L. Lever
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (A.R.D.); (D.J.)
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)1-2237-47308 (J.C.K.)
| | - Julia C. Kenyon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Homerton College, University of Cambridge, Cambridge CB2 8PH, UK
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)1-2237-47308 (J.C.K.)
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31
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Liu S, Koneru PC, Li W, Pathirage C, Engelman AN, Kvaratskhelia M, Musier-Forsyth K. HIV-1 integrase binding to genomic RNA 5'-UTR induces local structural changes in vitro and in virio. Retrovirology 2021; 18:37. [PMID: 34809662 PMCID: PMC8609798 DOI: 10.1186/s12977-021-00582-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/03/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND During HIV-1 maturation, Gag and Gag-Pol polyproteins are proteolytically cleaved and the capsid protein polymerizes to form the honeycomb capsid lattice. HIV-1 integrase (IN) binds the viral genomic RNA (gRNA) and impairment of IN-gRNA binding leads to mis-localization of the nucleocapsid protein (NC)-condensed viral ribonucleoprotein complex outside the capsid core. IN and NC were previously demonstrated to bind to the gRNA in an orthogonal manner in virio; however, the effect of IN binding alone or simultaneous binding of both proteins on gRNA structure is not yet well understood. RESULTS Using crosslinking-coupled selective 2'-hydroxyl acylation analyzed by primer extension (XL-SHAPE), we characterized the interaction of IN and NC with the HIV-1 gRNA 5'-untranslated region (5'-UTR). NC preferentially bound to the packaging signal (Psi) and a UG-rich region in U5, irrespective of the presence of IN. IN alone also bound to Psi but pre-incubation with NC largely abolished this interaction. In contrast, IN specifically bound to and affected the nucleotide (nt) dynamics of the apical loop of the transactivation response element (TAR) and the polyA hairpin even in the presence of NC. SHAPE probing of the 5'-UTR RNA in virions produced from allosteric IN inhibitor (ALLINI)-treated cells revealed that while the global secondary structure of the 5'-UTR remained unaltered, the inhibitor treatment induced local reactivity differences, including changes in the apical loop of TAR that are consistent with the in vitro results. CONCLUSIONS Overall, the binding interactions of NC and IN with the 5'-UTR are largely orthogonal in vitro. This study, together with previous probing experiments, suggests that IN and NC binding in vitro and in virio lead to only local structural changes in the regions of the 5'-UTR probed here. Accordingly, disruption of IN-gRNA binding by ALLINI treatment results in local rather than global secondary structure changes of the 5'-UTR in eccentric virus particles.
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Affiliation(s)
- Shuohui Liu
- grid.261331.40000 0001 2285 7943Department of Chemistry and Biochemistry, Centers for RNA Biology and Retroviral Research, The Ohio State University, Columbus, OH USA
| | - Pratibha C. Koneru
- grid.430503.10000 0001 0703 675XDivision of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO USA
| | - Wen Li
- grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Chathuri Pathirage
- grid.261331.40000 0001 2285 7943Department of Chemistry and Biochemistry, Centers for RNA Biology and Retroviral Research, The Ohio State University, Columbus, OH USA
| | - Alan N. Engelman
- grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Mamuka Kvaratskhelia
- grid.430503.10000 0001 0703 675XDivision of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO USA
| | - Karin Musier-Forsyth
- grid.261331.40000 0001 2285 7943Department of Chemistry and Biochemistry, Centers for RNA Biology and Retroviral Research, The Ohio State University, Columbus, OH USA
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32
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Blakemore RJ, Burnett C, Swanson C, Kharytonchyk S, Telesnitsky A, Munro JB. Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR. Biophys J 2021; 120:4874-4890. [PMID: 34529947 PMCID: PMC8595565 DOI: 10.1016/j.bpj.2021.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
During HIV-1 assembly, the viral Gag polyprotein specifically selects the dimeric RNA genome for packaging into new virions. The 5′ untranslated region (5′UTR) of the dimeric genome may adopt a conformation that is optimal for recognition by Gag. Further conformational rearrangement of the 5′UTR, promoted by the nucleocapsid (NC) domain of Gag, is predicted during virus maturation. Two 5′UTR dimer conformations, the kissing dimer (KD) and the extended dimer (ED), have been identified in vitro, which differ in the extent of intermolecular basepairing. Whether 5′UTRs from different HIV-1 strains with distinct sequences have access to the same dimer conformations has not been determined. Here, we applied fluorescence cross-correlation spectroscopy and single-molecule Förster resonance energy transfer imaging to demonstrate that 5′UTRs from two different HIV-1 subtypes form (KDs) with divergent stabilities. We further show that both 5′UTRs convert to a stable dimer in the presence of the viral NC protein, adopting a conformation consistent with extensive intermolecular contacts. These results support a unified model in which the genomes of diverse HIV-1 strains adopt an ED conformation.
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Affiliation(s)
- Robert J Blakemore
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Graduate Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Canessa Swanson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore Country, Baltimore, Maryland
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.
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33
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Lee GQ. Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness. Viruses 2021; 13:1874. [PMID: 34578455 PMCID: PMC8473067 DOI: 10.3390/v13091874] [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: 07/21/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 12/20/2022] Open
Abstract
HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences at single molecule resolution (FLIP-seq) or to co-capture full-length viral genome sequences in conjunction with its associated viral integration site (MIP-seq). This commentary aims to provide an overview on both FLIP-seq and MIP-seq, discuss their strengths and limitations, and outline specific chemistry and bioinformatics concerns when using these assays to study HIV persistence.
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Affiliation(s)
- Guinevere Q Lee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
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34
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5'-Cap sequestration is an essential determinant of HIV-1 genome packaging. Proc Natl Acad Sci U S A 2021; 118:2112475118. [PMID: 34493679 PMCID: PMC8449379 DOI: 10.1073/pnas.2112475118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
HIV-1 selectively packages two copies of its 5'-capped RNA genome (gRNA) during virus assembly, a process mediated by the nucleocapsid (NC) domain of the viral Gag polyprotein and encapsidation signals located within the dimeric 5' leader of the viral RNA. Although residues within the leader that promote packaging have been identified, the determinants of authentic packaging fidelity and efficiency remain unknown. Here, we show that a previously characterized 159-nt region of the leader that possesses all elements required for RNA dimerization, high-affinity NC binding, and packaging in a noncompetitive RNA packaging assay (ΨCES) is unexpectedly poorly packaged when assayed in competition with the intact 5' leader. ΨCES lacks a 5'-tandem hairpin element that sequesters the 5' cap, suggesting that cap sequestration may be important for packaging. Consistent with this hypothesis, mutations within the intact leader that expose the cap without disrupting RNA structure or NC binding abrogated RNA packaging, and genetic addition of a 5' ribozyme to ΨCES to enable cotranscriptional shedding of the 5' cap promoted ΨCES-mediated RNA packaging to wild-type levels. Additional mutations that either block dimerization or eliminate subsets of NC binding sites substantially attenuated competitive packaging. Our studies indicate that packaging is achieved by a bipartite mechanism that requires both sequestration of the 5' cap and exposure of NC binding sites that reside fully within the ΨCES region of the dimeric leader. We speculate that cap sequestration prevents irreversible capture by the cellular RNA processing and translation machinery, a mechanism likely employed by other viruses that package 5'-capped RNA genomes.
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35
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Zhang C, Forsdyke DR. Potential Achilles heels of SARS-CoV-2 are best displayed by the base order-dependent component of RNA folding energy. Comput Biol Chem 2021; 94:107570. [PMID: 34500325 PMCID: PMC8410225 DOI: 10.1016/j.compbiolchem.2021.107570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 "Achilles heel," the signal can be targeted by a new antiviral compound. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e. g. NSP3, ORF3a), we suggest that their nucleic acid level functions can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The ribosomal frameshifting element scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein.
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Affiliation(s)
- Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Donald R Forsdyke
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L3N6, Canada.
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RNA Structures and Their Role in Selective Genome Packaging. Viruses 2021; 13:v13091788. [PMID: 34578369 PMCID: PMC8472981 DOI: 10.3390/v13091788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
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Bou-Nader C, Muecksch F, Brown JB, Gordon JM, York A, Peng C, Ghirlando R, Summers MF, Bieniasz PD, Zhang J. HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization. Cell Host Microbe 2021; 29:1421-1436.e7. [PMID: 34384537 PMCID: PMC8650744 DOI: 10.1016/j.chom.2021.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/24/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
The HIV-1 virion structural polyprotein, Gag, is directed to particle assembly sites at the plasma membrane by its N-terminal matrix (MA) domain. MA also binds to host tRNAs. To understand the molecular basis of MA-tRNA interaction and its potential function, we present a co-crystal structure of HIV-1 MA-tRNALys3 complex. The structure reveals a specialized group of MA basic and aromatic residues preconfigured to recognize the distinctive structure of the tRNA elbow. Mutational, cross-linking, fluorescence, and NMR analyses show that the crystallographically defined interface drives MA-tRNA binding in solution and living cells. The structure indicates that MA is unlikely to bind tRNA and membrane simultaneously. Accordingly, single-amino-acid substitutions that abolish MA-tRNA binding caused striking redistribution of Gag to the plasma membrane and reduced HIV-1 replication. Thus, HIV-1 exploits host tRNAs to occlude a membrane localization signal and control the subcellular distribution of its major structural protein.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Ashley York
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Chen Peng
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA; Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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Bauby H, Ward CC, Hugh-White R, Swanson CM, Schulz R, Goujon C, Malim MH. HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 + T Cells Early Postinfection. mBio 2021; 12:e0136921. [PMID: 34154423 PMCID: PMC8263007 DOI: 10.1128/mbio.01369-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
The interactions between a virus and its host are complex but can be broadly categorized as either viral manipulation of cellular functions or cellular responses to infection. These processes begin at the earliest point of contact between virus and cell and frequently result in changes to cellular gene expression, making genome-wide transcriptomics a useful tool to study them. Several previous studies have used transcriptomics to evaluate the cellular responses to human immunodeficiency virus type 1 (HIV-1) infection; however, none have examined events in primary CD4+ T cells during the first 24 h of infection. Here, we analyzed CD4+ T cells at 4.5, 8, 12, 24, and 48 h following infection. We describe global changes to host gene expression commencing at 4.5 h postinfection and evolving over the ensuing time points. We identify upregulation of genes related to innate immunity, cytokine production, and apoptosis and downregulation of those involved in transcription and translation. We further demonstrate that the viral accessory protein Vpr is necessary for almost all gene expression changes seen at 12 h postinfection and the majority of those seen at 48 h. Identifying this new role for Vpr not only provides fresh perspective on its possible function but also adds further insight into the interplay between HIV-1 and its host at the cellular level. IMPORTANCE HIV-1, while now treatable, remains an important human pathogen causing significant morbidity and mortality globally. The virus predominantly infects CD4+ T cells and, if not treated with medication, ultimately causes their depletion, resulting in AIDS and death. Further refining our understanding of the interaction between HIV-1 and these cells has the potential to inform further therapeutic development. Previous studies have used transcriptomics to assess gene expression changes in CD4+ T cells following HIV-1 infection; here, we provide a detailed examination of changes occurring in the first 24 h of infection. Importantly, we define the viral protein Vpr as essential for the changes observed at this early stage. This finding has significance for understanding the role of Vpr in infection and pathogenesis and also for interpreting previous transcriptomic analyses of HIV-1 infection.
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Affiliation(s)
- Hélène Bauby
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Christopher C. Ward
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rupert Hugh-White
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Reiner Schulz
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Caroline Goujon
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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Chen SC, Olsthoorn RCL, Yu CH. Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Virus Evol 2021; 7:veab021. [PMID: 34141447 PMCID: PMC8206606 DOI: 10.1093/ve/veab021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In many single-stranded (ss) RNA viruses, the cis-acting packaging signal that confers selectivity genome packaging usually encompasses short structured RNA repeats. These structural units, termed repetitive structural motifs (RSMs), potentially mediate capsid assembly by specific RNA–protein interactions. However, general knowledge of the conservation and/or the diversity of RSMs in the positive-sense ssRNA coronaviruses (CoVs) is limited. By performing structural phylogenetic analysis, we identified a variety of RSMs in nearly all CoV genomic RNAs, which are exclusively located in the 5′-untranslated regions (UTRs) and/or in the inter-domain regions of poly-protein 1ab coding sequences in a lineage-specific manner. In all alpha- and beta-CoVs, except for Embecovirus spp, two to four copies of 5′-gUUYCGUc-3′ RSMs displaying conserved hexa-loop sequences were generally identified in Stem-loop 5 (SL5) located in the 5′-UTRs of genomic RNAs. In Embecovirus spp., however, two to eight copies of 5′-agc-3′/guAAu RSMs were found in the coding regions of non-structural protein (NSP) 3 and/or NSP15 in open reading frame (ORF) 1ab. In gamma- and delta-CoVs, other types of RSMs were found in several clustered structural elements in 5′-UTRs and/or ORF1ab. The identification of RSM-encompassing structural elements in all CoVs suggests that these RNA elements play fundamental roles in the life cycle of CoVs. In the recently emerged SARS-CoV-2, beta-CoV-specific RSMs are also found in its SL5, displaying two copies of 5′-gUUUCGUc-3′ motifs. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. In conclusion, the comprehensive exploration for RSMs reveals phylogenetic insights into the RNA structural elements in CoVs as a whole and provides a new perspective on variations currently found in SARS-CoV-2.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - René C L Olsthoorn
- Department of Supramolecular Biomaterials Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden,The Netherlands
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
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Chameettachal A, Vivet-Boudou V, Pitchai F, Pillai V, Ali L, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi T. A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag. Nucleic Acids Res 2021; 49:4668-4688. [PMID: 33836091 PMCID: PMC8096270 DOI: 10.1093/nar/gkab223] [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: 06/11/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 12/22/2022] Open
Abstract
Retroviral RNA genome (gRNA) harbors cis-acting sequences that facilitate its specific packaging from a pool of other viral and cellular RNAs by binding with high-affinity to the viral Gag protein during virus assembly. However, the molecular intricacies involved during selective gRNA packaging are poorly understood. Binding and footprinting assays on mouse mammary tumor virus (MMTV) gRNA with purified Pr77Gag along with in cell gRNA packaging study identified two Pr77Gag binding sites constituting critical, non-redundant packaging signals. These included: a purine loop in a bifurcated stem-loop containing the gRNA dimerization initiation site, and the primer binding site (PBS). Despite these sites being present on both unspliced and spliced RNAs, Pr77Gag specifically bound to unspliced RNA, since only that could adopt the native bifurcated stem-loop structure containing looped purines. These results map minimum structural elements required to initiate MMTV gRNA packaging, distinguishing features that are conserved amongst divergent retroviruses from those perhaps unique to MMTV. Unlike purine-rich motifs frequently associated with packaging signals, direct involvement of PBS in gRNA packaging has not been documented in retroviruses. These results enhance our understanding of retroviral gRNA packaging/assembly, making it not only a target for novel therapeutic interventions, but also development of safer gene therapy vectors.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Anjana Krishnan
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
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Identification of a Novel Cis-Acting Regulator of HIV-1 Genome Packaging. Int J Mol Sci 2021; 22:ijms22073435. [PMID: 33810482 PMCID: PMC8036536 DOI: 10.3390/ijms22073435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) uptakes homo-dimerized viral RNA genome into its own particle. A cis-acting viral RNA segment responsible for this event, termed packaging signal (psi), is located at the 5′-end of the viral genome. Although the psi segment exhibits nucleotide variation in nature, its effects on the psi function largely remain unknown. Here we show that a psi sequence from an HIV-1 regional variant, subtype D, has a lower packaging ability compared with that from another regional variant, HIV-1 subtype B, despite maintaining similar genome dimerization activities. A series of molecular genetic investigations narrowed down the responsible element of the selective attenuation to the two sequential nucleotides at positions 226 and 227 in the psi segment. Molecular dynamics simulations predicted that the dinucleotide substitution alters structural dynamics, fold, and hydrogen-bond networks primarily of the psi-SL2 element that contains the binding interface of viral nucleocapsid protein for the genome packaging. In contrast, such structural changes were minimal within the SL1 element involved in genome dimerization. These results suggest that the psi 226/227 dinucleotide pair functions as a cis-acting regulator to control the psi structure to selectively tune the efficiency of packaging, but not dimerization of highly variable HIV-1 genomes.
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Pitchai FNN, Chameettachal A, Vivet-Boudou V, Ali LM, Pillai VN, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi TA. Identification of Pr78 Gag Binding Sites on the Mason-Pfizer Monkey Virus Genomic RNA Packaging Determinants. J Mol Biol 2021; 433:166923. [PMID: 33713677 DOI: 10.1016/j.jmb.2021.166923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 02/04/2023]
Abstract
How retroviral Gag proteins recognize the packaging signals (Psi) on their genomic RNA (gRNA) is a key question that we addressed here using Mason-Pfizer monkey virus (MPMV) as a model system by combining band-shift assays and footprinting experiments. Our data show that Pr78Gag selects gRNA against spliced viral RNA by simultaneously binding to two single stranded loops on the MPMV Psi RNA: (1) a large purine loop (ssPurines), and (2) a loop which partially overlaps with a mostly base-paired purine repeat (bpPurines) and extends into a GU-rich binding motif. Importantly, this second Gag binding site is located immediately downstream of the major splice donor (mSD) and is thus absent from the spliced viral RNAs. Identifying elements crucial for MPMV gRNA packaging should help in understanding not only the mechanism of virion assembly by retroviruses, but also facilitate construction of safer retroviral vectors for human gene therapy.
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Affiliation(s)
- Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Anjana Krishnan
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, United Arab Emirates.
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43
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
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Mouhand A, Pasi M, Catala M, Zargarian L, Belfetmi A, Barraud P, Mauffret O, Tisné C. Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States. Viruses 2020; 12:v12101109. [PMID: 33003650 PMCID: PMC7601788 DOI: 10.3390/v12101109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/17/2022] Open
Abstract
HIV-1 Gag polyprotein orchestrates the assembly of viral particles. Its C-terminus consists of the nucleocapsid (NC) domain that interacts with nucleic acids, and p1 and p6, two unstructured regions, p6 containing the motifs to bind ALIX, the cellular ESCRT factor TSG101 and the viral protein Vpr. The processing of Gag by the viral protease subsequently liberates NCp15 (NC-p1-p6), NCp9 (NC-p1) and NCp7, NCp7 displaying the optimal chaperone activity of nucleic acids. This review focuses on the nucleic acid binding properties of the NC domain in the different maturation states during the HIV-1 viral cycle.
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Affiliation(s)
- Assia Mouhand
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Marco Pasi
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Loussiné Zargarian
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Anissa Belfetmi
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Pierre Barraud
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Olivier Mauffret
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
- Correspondence: (O.M.); (C.T.)
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
- Correspondence: (O.M.); (C.T.)
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Elliott JL, Kutluay SB. Going beyond Integration: The Emerging Role of HIV-1 Integrase in Virion Morphogenesis. Viruses 2020; 12:E1005. [PMID: 32916894 PMCID: PMC7551943 DOI: 10.3390/v12091005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022] Open
Abstract
The HIV-1 integrase enzyme (IN) plays a critical role in the viral life cycle by integrating the reverse-transcribed viral DNA into the host chromosome. This function of IN has been well studied, and the knowledge gained has informed the design of small molecule inhibitors that now form key components of antiretroviral therapy regimens. Recent discoveries unveiled that IN has an under-studied yet equally vital second function in human immunodeficiency virus type 1 (HIV-1) replication. This involves IN binding to the viral RNA genome in virions, which is necessary for proper virion maturation and morphogenesis. Inhibition of IN binding to the viral RNA genome results in mislocalization of the viral genome inside the virus particle, and its premature exposure and degradation in target cells. The roles of IN in integration and virion morphogenesis share a number of common elements, including interaction with viral nucleic acids and assembly of higher-order IN multimers. Herein we describe these two functions of IN within the context of the HIV-1 life cycle, how IN binding to the viral genome is coordinated by the major structural protein, Gag, and discuss the value of targeting the second role of IN in virion morphogenesis.
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Affiliation(s)
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA;
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47
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