1
|
Gien H, Morse M, McCauley MJ, Rouzina I, Gorelick RJ, Williams MC. Cationic Residues of the HIV-1 Nucleocapsid Protein Enable DNA Condensation to Maintain Viral Core Particle Stability during Reverse Transcription. Viruses 2024; 16:872. [PMID: 38932164 PMCID: PMC11209390 DOI: 10.3390/v16060872] [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: 03/29/2024] [Revised: 04/30/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a multifunctional viral protein necessary for HIV-1 replication. Recent studies have demonstrated that reverse transcription (RT) completes in the intact viral capsid, and the timing of RT and uncoating are correlated. How the small viral core stably contains the ~10 kbp double stranded (ds) DNA product of RT, and the role of NC in this process, are not well understood. We showed previously that NC binds and saturates dsDNA in a non-specific electrostatic binding mode that triggers uniform DNA self-attraction, condensing dsDNA into a tight globule against extending forces up to 10 pN. In this study, we use optical tweezers and atomic force microscopy to characterize the role of NC's basic residues in dsDNA condensation. Basic residue mutations of NC lead to defective interaction with the dsDNA substrate, with the constant force plateau condensation observed with wild-type (WT) NC missing or diminished. These results suggest that NC's high positive charge is essential to its dsDNA condensing activity, and electrostatic interactions involving NC's basic residues are responsible in large part for the conformation, size, and stability of the dsDNA-protein complex inside the viral core. We observe DNA re-solubilization and charge reversal in the presence of excess NC, consistent with the electrostatic nature of NC-induced DNA condensation. Previous studies of HIV-1 replication in the presence of the same cationic residue mutations in NC showed significant defects in both single- and multiple-round viral infectivity. Although NC participates in many stages of viral replication, our results are consistent with the hypothesis that cationic residue mutations inhibit genomic DNA condensation, resulting in increased premature capsid uncoating and contributing to viral replication defects.
Collapse
Affiliation(s)
- Helena Gien
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| |
Collapse
|
2
|
Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024; 21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [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: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.
Collapse
Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| | - Harish Vashisth
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| |
Collapse
|
3
|
González SA, Affranchino JL. The impact of mutations affecting highly conserved amino acids in the simian immunodeficiency virus nucleocapsid protein on virion assembly, genomic RNA packaging and viral infectivity. Virology 2023; 578:163-170. [PMID: 36580863 DOI: 10.1016/j.virol.2022.12.007] [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: 11/15/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The nucleocapsid (NC) domain of the retroviral Gag polyproteins mediates the incorporation of the viral genomic RNA into virions. Although SIV is widely used as a model for human immunodeficiency virus type 1 (HIV-1) infections, the SIV NC has been the subject of few studies which have provided discrepant data on the relative contribution of the two NC zinc finger motifs to genomic RNA encapsidation. Here, we demonstrate that mutations affecting the first cysteine in the distal zinc finger motif (C33S) or the N-terminal NC basic domain (R7A/K8A) drastically impair virion assembly and viral RNA binding. By contrast, amino acid substitutions targeting the first cysteine of the proximal zinc finger (C12S) or the basic region connecting both zinc fingers (R29A/R30A) allow substantial particle production and genomic RNA encapsidation. Our results help define the relative contribution of the SIV NC zinc finger motifs and basic regions to the NC biological properties.
Collapse
Affiliation(s)
- Silvia A González
- Laboratorio de Virología, Facultad de Ciencias Exactas y Naturales, Universidad de Belgrano (UB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - José L Affranchino
- Centro de Virología Humana y Animal (CEVHAN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Abierta Interamericana (UAI), Buenos Aires, Argentina
| |
Collapse
|
4
|
Sosic A, Olivato G, Carraro C, Göttlich R, Fabris D, Gatto B. In Vitro Evaluation of Bis-3-Chloropiperidines as RNA Modulators Targeting TAR and TAR-Protein Interaction. Int J Mol Sci 2022; 23:ijms23020582. [PMID: 35054766 PMCID: PMC8776071 DOI: 10.3390/ijms23020582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
After a long limbo, RNA has gained its credibility as a druggable target, fully earning its deserved role in the next generation of pharmaceutical R&D. We have recently probed the trans-activation response (TAR) element, an RNA stem–bulge–loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabilizing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analytical approaches for the study of multicomponent RNA-based interactions.
Collapse
Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Giulia Olivato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany;
| | - Dan Fabris
- Department of Chemistry, University of Connecticut, 55 North Eagleville Rd., Storrs, CT 06269, USA;
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
- Correspondence:
| |
Collapse
|
5
|
Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C, Lamb DC, Tuma R, Calabrese AN, Borodavka A. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proc Natl Acad Sci U S A 2021; 118:e2100198118. [PMID: 34615715 PMCID: PMC8521686 DOI: 10.1073/pnas.2100198118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 01/13/2023] Open
Abstract
Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA-RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo-electron microscopy reconstructions of an NSP2-RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling.
Collapse
Affiliation(s)
- Jack P K Bravo
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Kira Bartnik
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Luca Venditti
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Julia Acker
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, European Molecular Biology Laboratory (EMBL) Australia, Clayton, VIC 3800, Australia
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, European Molecular Biology Laboratory (EMBL) Australia, Clayton, VIC 3800, Australia
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| |
Collapse
|
6
|
Bis-3-Chloropiperidines Targeting TAR RNA as A Novel Strategy to Impair the HIV-1 Nucleocapsid Protein. Molecules 2021; 26:molecules26071874. [PMID: 33810333 PMCID: PMC8038054 DOI: 10.3390/molecules26071874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Specific RNA sequences regulate functions essential to life. The Trans-Activation Response element (TAR) is an RNA stem-bulge-loop structure involved in several steps of HIV-1 replication. In this work, we show how RNA targeting can inhibit HIV-1 nucleocapsid (NC), a highly conserved protein known to catalyze nucleic acid melting and strand transfers during reverse transcription. Our RNA targeting strategy consists of the employment of bis-3-chloropiperidines (B-CePs) to impair RNA melting through bifunctional alkylation. Specific interactions between B-CePs and TAR RNA were analytically investigated by gel electrophoresis and mass spectrometry, allowing the elucidation of B-CePs' recognition of TAR, and highlighting an RNA-directed mechanism of protein inhibition. We propose that B-CePs can freeze TAR tridimensional conformation, impairing NC-induced dynamics and finally inhibiting its functions in vitro.
Collapse
|
7
|
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.
Collapse
|
8
|
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.
Collapse
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.)
| |
Collapse
|
9
|
Significant Differences in RNA Structure Destabilization by HIV-1 GagDp6 and NCp7 Proteins. Viruses 2020; 12:v12050484. [PMID: 32344834 PMCID: PMC7290599 DOI: 10.3390/v12050484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 01/12/2023] Open
Abstract
Retroviral nucleocapsid (NC) proteins are nucleic acid chaperones that play distinct roles in the viral life cycle. During reverse transcription, HIV-1 NC facilitates the rearrangement of nucleic acid secondary structures, allowing the transactivation response (TAR) RNA hairpin to be transiently destabilized and annealed to a complementary RNA hairpin. In contrast, during viral assembly, NC, as a domain of the group-specific antigen (Gag) polyprotein, binds the genomic RNA and facilitates packaging into new virions. It is not clear how the same protein, alone or as part of Gag, performs such different RNA binding functions in the viral life cycle. By combining single-molecule optical tweezers measurements with a quantitative mfold-based model, we characterize the equilibrium stability and unfolding barrier for TAR RNA. Comparing measured results with a model of discrete protein binding allows us to localize affected binding sites, in addition to quantifying hairpin stability. We find that, while both NCp7 and Gag∆p6 destabilize the TAR hairpin, Gag∆p6 binding is localized to two sites in the stem, while NCp7 targets sites near the top loop. Unlike Gag∆p6, NCp7 destabilizes this loop, shifting the location of the reaction barrier toward the folded state and increasing the natural rate of hairpin opening by ~104. Thus, our results explain why Gag cleavage and NC release is an essential prerequisite for reverse transcription within the virion.
Collapse
|
10
|
Lin C, Mendoza-Espinosa P, Rouzina I, Guzmán O, Moreno-Razo JA, Francisco JS, Bruinsma R. Specific inter-domain interactions stabilize a compact HIV-1 Gag conformation. PLoS One 2019; 14:e0221256. [PMID: 31437199 PMCID: PMC6705756 DOI: 10.1371/journal.pone.0221256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/04/2019] [Indexed: 01/01/2023] Open
Abstract
HIV-1 Gag is a large multidomain poly-protein with flexible unstructured linkers connecting its globular subdomains. It is compact when in solution but assumes an extended conformation when assembled within the immature HIV-1 virion. Here, we use molecular dynamics (MD) simulations to quantitatively characterize the intra-domain interactions of HIV-1 Gag. We find that the matrix (MA) domain and the C-terminal subdomain CActd of the CA capsid domain can form a bound state. The bound state, which is held together primarily by interactions between complementary charged and polar residues, stabilizes the compact state of HIV-1 Gag. We calculate the depth of the attractive free energy potential between the MA/ CActd sites and find it to be about three times larger than the dimerization interaction between the CActd domains. Sequence analysis shows high conservation within the newly-found intra-Gag MA/CActd binding site, as well as its spatial proximity to other well known elements of Gag -such as CActd's SP1 helix region, its inositol hexaphosphate (IP6) binding site and major homology region (MHR), as well as the MA trimerization site. Our results point to a high, but yet undetermined, functional significance of the intra-Gag binding site. Recent biophysical experiments that address the binding specificity of Gag are interpreted in the context of the MA/CActd bound state, suggesting an important role in selective packaging of genomic RNA by Gag.
Collapse
Affiliation(s)
- Chen Lin
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Paola Mendoza-Espinosa
- Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, Ciudad de México, México
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States of America
| | - Orlando Guzmán
- Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, Ciudad de México, México
| | - José Antonio Moreno-Razo
- Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, Ciudad de México, México
| | - Joseph S. Francisco
- Department of Chemistry, The University of Pennsylvania, Philadelphia, PA, United States of America
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA, United States of America
| |
Collapse
|
11
|
René B, Mauffret O, Fossé P. Retroviral nucleocapsid proteins and DNA strand transfers. BIOCHIMIE OPEN 2018; 7:10-25. [PMID: 30109196 PMCID: PMC6088434 DOI: 10.1016/j.biopen.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022]
Abstract
An infectious retroviral particle contains 1000-1500 molecules of the nucleocapsid protein (NC) that cover the diploid RNA genome. NC is a small zinc finger protein that possesses nucleic acid chaperone activity that enables NC to rearrange DNA and RNA molecules into the most thermodynamically stable structures usually those containing the maximum number of base pairs. Thanks to the chaperone activity, NC plays an essential role in reverse transcription of the retroviral genome by facilitating the strand transfer reactions of this process. In addition, these reactions are involved in recombination events that can generate multiple drug resistance mutations in the presence of anti-HIV-1 drugs. The strand transfer reactions rely on base pairing of folded DNA/RNA structures. The molecular mechanisms responsible for NC-mediated strand transfer reactions are presented and discussed in this review. Antiretroviral strategies targeting the NC-mediated strand transfer events are also discussed.
Collapse
Affiliation(s)
- Brigitte René
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Olivier Mauffret
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Philippe Fossé
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| |
Collapse
|
12
|
Post K, Olson ED, Naufer MN, Gorelick RJ, Rouzina I, Williams MC, Musier-Forsyth K, Levin JG. Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition. Retrovirology 2016; 13:89. [PMID: 28034301 PMCID: PMC5198506 DOI: 10.1186/s12977-016-0322-5] [Citation(s) in RCA: 10] [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: 08/23/2016] [Accepted: 11/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nucleocapsid (NC) domain of HIV-1 Gag is responsible for specific recognition and packaging of genomic RNA (gRNA) into new viral particles. This occurs through specific interactions between the Gag NC domain and the Psi packaging signal in gRNA. In addition to this critical function, NC proteins are also nucleic acid (NA) chaperone proteins that facilitate NA rearrangements during reverse transcription. Although the interaction with Psi and chaperone activity of HIV-1 NC have been well characterized in vitro, little is known about simian immunodeficiency virus (SIV) NC. Non-human primates are frequently used as a platform to study retroviral infection in vivo; thus, it is important to understand underlying mechanistic differences between HIV-1 and SIV NC. RESULTS Here, we characterize SIV NC chaperone activity for the first time. Only modest differences are observed in the ability of SIV NC to facilitate reactions that mimic the minus-strand annealing and transfer steps of reverse transcription relative to HIV-1 NC, with the latter displaying slightly higher strand transfer and annealing rates. Quantitative single molecule DNA stretching studies and dynamic light scattering experiments reveal that these differences are due to significantly increased DNA compaction energy and higher aggregation capability of HIV-1 NC relative to the SIV protein. Using salt-titration binding assays, we find that both proteins are strikingly similar in their ability to specifically interact with HIV-1 Psi RNA. In contrast, they do not demonstrate specific binding to an RNA derived from the putative SIV packaging signal. CONCLUSIONS Based on these studies, we conclude that (1) HIV-1 NC is a slightly more efficient NA chaperone protein than SIV NC, (2) mechanistic differences between the NA interactions of highly similar retroviral NC proteins are revealed by quantitative single molecule DNA stretching, and (3) SIV NC demonstrates cross-species recognition of the HIV-1 Psi RNA packaging signal.
Collapse
Affiliation(s)
- Klara Post
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - M. Nabuan Naufer
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201 USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Judith G. Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
| |
Collapse
|
13
|
The Life-Cycle of the HIV-1 Gag-RNA Complex. Viruses 2016; 8:v8090248. [PMID: 27626439 PMCID: PMC5035962 DOI: 10.3390/v8090248] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/16/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) replication is a highly regulated process requiring the recruitment of viral and cellular components to the plasma membrane for assembly into infectious particles. This review highlights the recent process of understanding the selection of the genomic RNA (gRNA) by the viral Pr55Gag precursor polyprotein, and the processes leading to its incorporation into viral particles.
Collapse
|