1
|
Yi B, Tanaka YL, Cornish D, Kosako H, Butlertanaka EP, Sengupta P, Lippincott-Schwartz J, Hultquist JF, Saito A, Yoshimura SH. Host ZCCHC3 blocks HIV-1 infection and production through a dual mechanism. iScience 2024; 27:109107. [PMID: 38384847 PMCID: PMC10879702 DOI: 10.1016/j.isci.2024.109107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/12/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Most mammalian cells prevent viral infection and proliferation by expressing various restriction factors and sensors that activate the immune system. Several host restriction factors that inhibit human immunodeficiency virus type 1 (HIV-1) have been identified, but most of them are antagonized by viral proteins. Here, we describe CCHC-type zinc-finger-containing protein 3 (ZCCHC3) as a novel HIV-1 restriction factor that suppresses the production of HIV-1 and other retroviruses, but does not appear to be directly antagonized by viral proteins. It acts by binding to Gag nucleocapsid (GagNC) via zinc-finger motifs, which inhibits viral genome recruitment and results in genome-deficient virion production. ZCCHC3 also binds to the long terminal repeat on the viral genome via the middle-folded domain, sequestering the viral genome to P-bodies, which leads to decreased viral replication and production. This distinct, dual-acting antiviral mechanism makes upregulation of ZCCHC3 a novel potential therapeutic strategy.
Collapse
Affiliation(s)
- Binbin Yi
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuri L. Tanaka
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Daphne Cornish
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Erika P. Butlertanaka
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Prabuddha Sengupta
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | | | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki, Miyazaki 889-1692, Japan
| | - Shige H. Yoshimura
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto 606-8501, Japan
- Center for Living Systems Information Science (CeLiSIS), Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Guo S, Saha I, Saffarian S, Johnson ME. Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions. eLife 2023; 12:e84881. [PMID: 37435945 PMCID: PMC10361719 DOI: 10.7554/elife.84881] [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: 11/12/2022] [Accepted: 07/12/2023] [Indexed: 07/13/2023] Open
Abstract
For HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However, only 5% of the Gag polyproteins, termed Gag-Pol, carry this protease domain, and they are embedded within the structured lattice. The mechanism of Gag-Pol dimerization is unknown. Here, we use spatial stochastic computer simulations of the immature Gag lattice as derived from experimental structures, showing that dynamics of the lattice on the membrane is unavoidable due to the missing 1/3 of the spherical protein coat. These dynamics allow for Gag-Pol molecules carrying the protease domains to detach and reattach at new places within the lattice. Surprisingly, dimerization timescales of minutes or less are achievable for realistic binding energies and rates despite retaining most of the large-scale lattice structure. We derive a formula allowing extrapolation of timescales as a function of interaction free energy and binding rate, thus predicting how additional stabilization of the lattice would impact dimerization times. We further show that during assembly, dimerization of Gag-Pol is highly likely and therefore must be actively suppressed to prevent early activation. By direct comparison to recent biochemical measurements within budded virions, we find that only moderately stable hexamer contacts (-12kBT<∆G<-8kBT) retain both the dynamics and lattice structures that are consistent with experiment. These dynamics are likely essential for proper maturation, and our models quantify and predict lattice dynamics and protease dimerization timescales that define a key step in understanding formation of infectious viruses.
Collapse
Affiliation(s)
- Sikao Guo
- TC Jenkins Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Ipsita Saha
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of HealthFrederickUnited States
| | - Saveez Saffarian
- Center for Cell and Genome Science, University of UtahSalt Lake CityUnited States
- Department of Physics and Astronomy, University of UtahSalt Lake CityUnited States
- School of Biological Sciences, University of UtahSalt Lake CityUnited States
| | - Margaret E Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| |
Collapse
|
6
|
Mazurov D, Ramadan L, Kruglova N. Packaging and Uncoating of CRISPR/Cas Ribonucleoproteins for Efficient Gene Editing with Viral and Non-Viral Extracellular Nanoparticles. Viruses 2023; 15:v15030690. [PMID: 36992399 PMCID: PMC10056905 DOI: 10.3390/v15030690] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Rapid progress in gene editing based on clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) has revolutionized functional genomic studies and genetic disease correction. While numerous gene editing applications have been easily adapted by experimental science, the clinical utility of CRISPR/Cas remains very limited due to difficulty in delivery to primary cells and possible off-target effects. The use of CRISPR in the form of a ribonucleoprotein (RNP) complex substantially reduces the time of DNA exposure to the effector nuclease and minimizes its off-target activity. The traditional electroporation and lipofection methods lack the cell-type specificity of RNP delivery, can be toxic for cells, and are less efficient when compared to nanoparticle transporters. This review focuses on CRISPR/Cas RNP packaging and delivery using retro/lentiviral particles and exosomes. First, we briefly describe the natural stages of viral and exosomal particle formation, release and entry into the target cells. This helps us understand the mechanisms of CRISPR/Cas RNP packaging and uncoating utilized by the current delivery systems, which we discuss afterward. Much attention is given to the exosomes released during viral particle production that can be passively loaded with RNPs as well as the mechanisms necessary for particle fusion, RNP release, and transportation inside the target cells. Collectively, together with specific packaging mechanisms, all these factors can substantially influence the editing efficiency of the system. Finally, we discuss ways to improve CRISPR/Cas RNP delivery using extracellular nanoparticles.
Collapse
Affiliation(s)
- Dmitriy Mazurov
- Cell and Gene Technology Group, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia
- Correspondence: or
| | - Lama Ramadan
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Natalia Kruglova
- Cell and Gene Technology Group, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia
| |
Collapse
|
7
|
Galuppo C, Gomes de Oliveira Junior A, Dos Santos Oliveira L, de Souza Guarda PH, Buffon R, Abbehausen C. Reactivity of Ni II, Pd II and Pt II complexes bearing phosphine ligands towards Zn II displacement and hydrolysis in Cis 2His 2 and Cis 3His zinc-fingers domains. J Inorg Biochem 2023; 240:112117. [PMID: 36635196 DOI: 10.1016/j.jinorgbio.2022.112117] [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: 08/18/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023]
Abstract
A systematic study of the effect of phosphine and bis-phosphine ligands in the interaction of NiII, PdII, and PtII complexes with two classes of zinc fingers was performed. The Cys2His2, finger 3 of specific protein-1, and the Cys2HisCys C-terminal zinc finger of nucleocapsid protein 7 of the HIV-1 were used as models of the respective class. In general, phosphine ligands favor the metal binding to the peptide, although the bis-phosphine ligands produce more specific binding than the monodentate. In the case of nickel complexes, the interaction of NiII ions with the sequence SKH, present in Cys2His2, results in hydrolysis, contrasting to the preferred zinc ejection produced by the NiII complexes with chelating phosphines, producing Ni(bis-phosphine) fingers. In the absence of the SKH sequence, zinc ejection is observed with the formation of nickel fingers, with reactivity dependent on the phosphine. On the other hand, Pd(phosphines) produces Pd2 fingers in the case of triphenylphosphine with the phosphine coordinated as intermediate species. The bis-phosphine ligands produce very clean spectra and a stable signal Pd(bis-phosphine)finger. Interestingly, phosphines produce very reactive platinum complexes, which eject zinc and promote peptide hydrolysis. The results reported here are relevant to the understanding of the mechanism of these interactions and how to modulate metallocompounds for zinc finger interference.
Collapse
Affiliation(s)
- Carolina Galuppo
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, CEP 13083-970, Campinas, São Paulo, Brazil
| | | | - Laiane Dos Santos Oliveira
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, CEP 13083-970, Campinas, São Paulo, Brazil
| | | | - Regina Buffon
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Camilla Abbehausen
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, CEP 13083-970, Campinas, São Paulo, Brazil.
| |
Collapse
|
8
|
Eriksen MS, Bramham CR. Molecular physiology of Arc/Arg3.1: The oligomeric state hypothesis of synaptic plasticity. Acta Physiol (Oxf) 2022; 236:e13886. [PMID: 36073248 PMCID: PMC9787330 DOI: 10.1111/apha.13886] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
The immediate early gene, Arc, is a pivotal regulator of synaptic plasticity, memory, and cognitive flexibility. But what is Arc protein? How does it work? Inside the neuron, Arc is a protein interaction hub and dynamic regulator of intra-cellular signaling in synaptic plasticity. In remarkable contrast, Arc can also self-assemble into retrovirus-like capsids that are released in extracellular vesicles and capable of intercellular transfer of RNA. Elucidation of the molecular basis of Arc hub and capsid functions, and the relationship between them, is vital for progress. Here, we discuss recent findings on Arc structure-function and regulation of oligomerization that are giving insight into the molecular physiology of Arc. The unique features of mammalian Arc are emphasized, while drawing comparisons with Drosophila Arc and retroviral Gag. The Arc N-terminal domain, found only in mammals, is proposed to play a key role in regulating Arc hub signaling, oligomerization, and formation of capsids. Bringing together several lines of evidence, we hypothesize that Arc function in synaptic plasticity-long-term potentiation (LTP) and long-term depression (LTD)-are dictated by different oligomeric forms of Arc. Specifically, monomer/dimer function in LTP, tetramer function in basic LTD, and 32-unit oligomer function in enhanced LTD. The role of mammalian Arc capsids is unclear but likely depends on the cross-section of captured neuronal activity-induced RNAs. As the functional states of Arc are revealed, it may be possible to selectively manipulate specific forms of Arc-dependent plasticity and intercellular communication involved in brain function and dysfunction.
Collapse
Affiliation(s)
| | - Clive R. Bramham
- Department of BiomedicineUniversity of BergenBergenNorway,Mohn Research Center for the BrainUniversity of BergenBergenNorway
| |
Collapse
|
9
|
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.
Collapse
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:
| |
Collapse
|
10
|
Baron Y, Sens J, Lange L, Nassauer L, Klatt D, Hoffmann D, Kleppa MJ, Barbosa PV, Keisker M, Steinberg V, Suerth JD, Vondran FW, Meyer J, Morgan M, Schambach A, Galla M. Improved alpharetrovirus-based Gag.MS2 particles for efficient and transient delivery of CRISPR-Cas9 into target cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:810-823. [PMID: 35141043 PMCID: PMC8801357 DOI: 10.1016/j.omtn.2021.12.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/29/2021] [Indexed: 12/12/2022]
Abstract
DNA-modifying technologies, such as the CRISPR-Cas9 system, are promising tools in the field of gene and cell therapies. However, high and prolonged expression of DNA-modifying enzymes may cause cytotoxic and genotoxic side effects and is therefore unwanted in therapeutic approaches. Consequently, development of new and potent short-term delivery methods is of utmost importance. Recently, we developed non-integrating gammaretrovirus- and MS2 bacteriophage-based Gag.MS2 (g.Gag.MS2) particles for transient transfer of non-retroviral CRISPR-Cas9 RNA into target cells. In the present study, we further improved the technique by transferring the system to the alpharetroviral vector platform (a.Gag.MS2), which significantly increased CRISPR-Cas9 delivery into target cells and allowed efficient targeted knockout of endogenous TP53/Trp53 genes in primary murine fibroblasts as well as primary human fibroblasts, hepatocytes, and cord-blood-derived CD34+ stem and progenitor cells. Strikingly, co-packaging of Cas9 mRNA and multiple single guide RNAs (sgRNAs) into a.Gag.MS2 chimera displayed efficient targeted knockout of up to three genes. Co-transfection of single-stranded DNA donor oligonucleotides during CRISPR-Cas9 particle production generated all-in-one particles, which mediated up to 12.5% of homology-directed repair in primary cell cultures. In summary, optimized a.Gag.MS2 particles represent a versatile tool for short-term delivery of DNA-modifying enzymes into a variety of target cells, including primary murine and human cells.
Collapse
Affiliation(s)
- Yvonne Baron
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Johanna Sens
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Lucas Lange
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Larissa Nassauer
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Denise Klatt
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Marc-Jens Kleppa
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover 30625, Germany
| | - Maximilian Keisker
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Viviane Steinberg
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Julia D. Suerth
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Florian W.R. Vondran
- ReMediES, Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover 30625, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover Medical School, Hannover 30625, Germany
| | - Johann Meyer
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| |
Collapse
|
11
|
Lerner G, Weaver N, Anokhin B, Spearman P. Advances in HIV-1 Assembly. Viruses 2022; 14:v14030478. [PMID: 35336885 PMCID: PMC8952333 DOI: 10.3390/v14030478] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/10/2022] Open
Abstract
The assembly of HIV-1 particles is a concerted and dynamic process that takes place on the plasma membrane of infected cells. An abundance of recent discoveries has advanced our understanding of the complex sequence of events leading to HIV-1 particle assembly, budding, and release. Structural studies have illuminated key features of assembly and maturation, including the dramatic structural transition that occurs between the immature Gag lattice and the formation of the mature viral capsid core. The critical role of inositol hexakisphosphate (IP6) in the assembly of both the immature and mature Gag lattice has been elucidated. The structural basis for selective packaging of genomic RNA into virions has been revealed. This review will provide an overview of the HIV-1 assembly process, with a focus on recent advances in the field, and will point out areas where questions remain that can benefit from future investigation.
Collapse
|
12
|
Qu N, Ying Y, Qin J, Chen AK. Rational design of self-assembled RNA nanostructures for HIV-1 virus assembly blockade. Nucleic Acids Res 2021; 50:e44. [PMID: 34967412 PMCID: PMC9071489 DOI: 10.1093/nar/gkab1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/16/2021] [Accepted: 12/15/2021] [Indexed: 11/14/2022] Open
Abstract
Many pathological processes are driven by RNA-protein interactions, making such interactions promising targets for molecular interventions. HIV-1 assembly is one such process, in which the viral genomic RNA interacts with the viral Gag protein and serves as a scaffold to drive Gag multimerization that ultimately leads to formation of a virus particle. Here, we develop self-assembled RNA nanostructures that can inhibit HIV-1 virus assembly, achieved through hybridization of multiple artificial small RNAs with a stem-loop structure (STL) that we identify as a prominent ligand of Gag that can inhibit virus particle production via STL-Gag interactions. The resulting STL-decorated nanostructures (double and triple stem-loop structures denoted as Dumbbell and Tribell, respectively) can elicit more pronounced viral blockade than their building blocks, with the inhibition arising as a result of nanostructures interfering with Gag multimerization. These findings could open up new avenues for RNA-based therapy.
Collapse
Affiliation(s)
- Na Qu
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Jinshan Qin
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, 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
| |
Collapse
|
13
|
A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions. J Mol Biol 2021; 433:167293. [PMID: 34624298 DOI: 10.1016/j.jmb.2021.167293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/22/2022]
Abstract
Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5' leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.
Collapse
|
14
|
A Comprehensive Analysis of Human Endogenous Retroviruses HERV-K (HML.2) from Teratocarcinoma Cell Lines and Detection of Viral Cargo in Microvesicles. Int J Mol Sci 2021; 22:ijms222212398. [PMID: 34830279 PMCID: PMC8619701 DOI: 10.3390/ijms222212398] [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: 10/15/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
About 8% of our genome is composed of sequences from Human Endogenous Retroviruses (HERVs). The HERV-K (HML.2) family, here abbreviated HML.2, is able to produce virus particles that were detected in cell lines, malignant tumors and in autoimmune diseases. Parameters and properties of HML.2 released from teratocarcinoma cell lines GH and Tera-1 were investigated in detail. In most experiments, analyzed viruses were purified by density gradient centrifugation. HML.2 structural proteins, reverse transcriptase (RT) activity, viral RNA (vRNA) and particle morphology were analyzed. The HML.2 markers were predominantly detected in fractions with a buoyant density of 1.16 g/cm3. Deglycosylation of TM revealed truncated forms of transmembrane (TM) protein. Free virions and extracellular vesicles (presumably microvesicles—MVs) with HML.2 elements, including budding intermediates, were detected by electron microscopy. Viral elements and assembled virions captured and exported by MVs can boost specific immune responses and trigger immunomodulation in recipient cells. Sequencing of cDNA clones demonstrated exclusive presence of HERV-K108 env in HML.2 from Tera-1 cells. Not counting two recombinant variants, four known env sequences were found in HML.2 from GH cells. Obtained results shed light on parameters and morphology of HML.2. A possible mechanism of HML.2-induced diseases is discussed.
Collapse
|
15
|
Saha I, Preece B, Peterson A, Durden H, MacArthur B, Lowe J, Belnap D, Vershinin M, Saffarian S. Gag-Gag Interactions Are Insufficient to Fully Stabilize and Order the Immature HIV Gag Lattice. Viruses 2021; 13:1946. [PMID: 34696376 PMCID: PMC8540168 DOI: 10.3390/v13101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Immature HIV virions harbor a lattice of Gag molecules with significant ordering in CA-NTD, CA-CTD and SP1 regions. This ordering plays a major role during HIV maturation. To test the condition in which the Gag lattice forms in vivo, we assembled virus like particles (VLPs) by expressing only HIV Gag in mammalian cells. Here we show that these VLPs incorporate a similar number of Gag molecules compared to immature HIV virions. However, within these VLPs, Gag molecules diffuse with a pseudo-diffusion rate of 10 nm2/s, this pseudo-diffusion is abrogated in the presence of melittin and is sensitive to mutations within the SP1 region. Using cryotomography, we show that unlike immature HIV virions, in the Gag lattice of VLPs the CA-CTD and SP1 regions are significantly less ordered. Our observations suggest that within immature HIV virions, other viral factors in addition to Gag, contribute to ordering in the CA-CTD and SP1 regions.
Collapse
Affiliation(s)
- Ipsita Saha
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA;
| | - Benjamin Preece
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Abby Peterson
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Haley Durden
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Brian MacArthur
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Jake Lowe
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| | - David Belnap
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Vershinin
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| | - Saveez Saffarian
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| |
Collapse
|
16
|
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.
Collapse
|
17
|
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.
Collapse
|
18
|
Gumna J, Andrzejewska-Romanowska A, Garfinkel DJ, Pachulska-Wieczorek K. RNA Binding Properties of the Ty1 LTR-Retrotransposon Gag Protein. Int J Mol Sci 2021; 22:ijms22169103. [PMID: 34445809 PMCID: PMC8396678 DOI: 10.3390/ijms22169103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 11/16/2022] Open
Abstract
A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. The Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. In addition to capsid assembly functions, Ty1 Gag promotes Ty1 RNA dimerization and cyclization and initiation of reverse transcription. Direct interactions between Gag and retrotransposon genomic RNA (gRNA) are needed for Ty1 replication, and mutations in the RNA-binding domain disrupt nucleation of retrosomes and assembly of functional virus-like particles (VLPs). Unlike retroviral Gag, the specificity of Ty1 Gag-RNA interactions remain poorly understood. Here we use microscale thermophoresis (MST) and electrophoretic mobility shift assays (EMSA) to analyze interactions of immature and mature Ty1 Gag with RNAs. The salt-dependent experiments showed that Ty1 Gag binds with high and similar affinity to different RNAs. However, we observed a preferential interaction between Ty1 Gag and Ty1 RNA containing a packaging signal (Psi) in RNA competition analyses. We also uncover a relationship between Ty1 RNA structure and Gag binding involving the pseudoknot present on Ty1 gRNA. In all likelihood, the differences in Gag binding affinity detected in vitro only partially explain selective Ty1 RNA packaging into VLPs in vivo.
Collapse
Affiliation(s)
- Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (J.G.); (A.A.-R.)
| | - Angelika Andrzejewska-Romanowska
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (J.G.); (A.A.-R.)
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA;
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (J.G.); (A.A.-R.)
- Correspondence: ; Tel.: +48-61-852-85-03; Fax: +48-61-852-05-32
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Eriksen MS, Nikolaienko O, Hallin EI, Grødem S, Bustad HJ, Flydal MI, Merski I, Hosokawa T, Lascu D, Akerkar S, Cuéllar J, Chambers JJ, O'Connell R, Muruganandam G, Loris R, Touma C, Kanhema T, Hayashi Y, Stratton MM, Valpuesta JM, Kursula P, Martinez A, Bramham CR. Arc self-association and formation of virus-like capsids are mediated by an N-terminal helical coil motif. FEBS J 2020; 288:2930-2955. [PMID: 33175445 DOI: 10.1111/febs.15618] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022]
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a protein interaction hub with diverse roles in intracellular neuronal signaling, and important functions in neuronal synaptic plasticity, memory, and postnatal cortical development. Arc has homology to retroviral Gag protein and is capable of self-assembly into virus-like capsids implicated in the intercellular transfer of RNA. However, the molecular basis of Arc self-association and capsid formation is largely unknown. Here, we identified a 28-amino-acid stretch in the mammalian Arc N-terminal (NT) domain that is necessary and sufficient for self-association. Within this region, we identified a 7-residue oligomerization motif, critical for the formation of virus-like capsids. Purified wild-type Arc formed capsids as shown by transmission and cryo-electron microscopy, whereas mutant Arc with disruption of the oligomerization motif formed homogenous dimers. An atomic-resolution crystal structure of the oligomerization region peptide demonstrated an antiparallel coiled-coil interface, strongly supporting NT-NT domain interactions in Arc oligomerization. The NT coil-coil interaction was also validated in live neurons using fluorescence lifetime FRET imaging, and mutation of the oligomerization motif disrupted Arc-facilitated endocytosis. Furthermore, using single-molecule photobleaching, we show that Arc mRNA greatly enhances higher-order oligomerization in a manner dependent on the oligomerization motif. In conclusion, a helical coil in the Arc NT domain supports self-association above the dimer stage, mRNA-induced oligomerization, and formation of virus-like capsids. DATABASE: The coordinates and structure factors for crystallographic analysis of the oligomerization region were deposited at the Protein Data Bank with the entry code 6YTU.
Collapse
Affiliation(s)
- Maria S Eriksen
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Oleksii Nikolaienko
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Norway
| | - Sverre Grødem
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Helene J Bustad
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Marte I Flydal
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Ian Merski
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | - Tomohisa Hosokawa
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Daniela Lascu
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Shreeram Akerkar
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Jorge Cuéllar
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts Amherst, MA, USA
| | - Rory O'Connell
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Christine Touma
- Faculty of Biochemistry and Molecular Biology & Biocenter Oulu, University of Oulu, Finland
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway.,Faculty of Biochemistry and Molecular Biology & Biocenter Oulu, University of Oulu, Finland
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| |
Collapse
|
21
|
Lavado-García J, González-Domínguez I, Cervera L, Jorge I, Vázquez J, Gòdia F. Molecular Characterization of the Coproduced Extracellular Vesicles in HEK293 during Virus-Like Particle Production. J Proteome Res 2020; 19:4516-4532. [PMID: 32975947 PMCID: PMC7640977 DOI: 10.1021/acs.jproteome.0c00581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 12/22/2022]
Abstract
Vaccine therapies based on virus-like particles (VLPs) are currently in the spotlight due to their potential for generating high immunogenic responses while presenting fewer side effects than conventional vaccines. These self-assembled nanostructures resemble the native conformation of the virus but lack genetic material. They are becoming a promising platform for vaccine candidates against several diseases due to the ability of modifying their membrane with antigens from different viruses. The coproduction of extracellular vesicles (EVs) when producing VLPs is a key phenomenon currently still under study. In order to characterize this extracellular environment, a quantitative proteomics approach has been carried out. Three conditions were studied: non-transfected, transfected with an empty plasmid as control, and transfected with a plasmid coding for HIV-1 Gag polyprotein. A shift in EV biogenesis has been detected upon transfection, changing the production from large to small EVs. Another remarkable trait found was the presence of DNA being secreted within vesicles smaller than 200 nm. Studying the protein profile of these biological nanocarriers, it was observed that EVs were reflecting an overall energy homeostasis disruption via mitochondrial protein deregulation. Also, immunomodulatory proteins like ITGB1, ENO3, and PRDX5 were identified and quantified in VLP and EV fractions. These findings provide insight on the nature of the VLP extracellular environment defining the characteristics and protein profile of EVs, with potential to develop new downstream separation strategies or using them as adjuvants in viral therapies.
Collapse
Affiliation(s)
- Jesús Lavado-García
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
| | - Irene González-Domínguez
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
| | - Laura Cervera
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
| | - Inmaculada Jorge
- Laboratory
of Cardiovascular Proteomics, Centro Nacional
Investigaciones Cardiovasculares (CNIC), C/Melchor Fernández Almagro 3, Madrid 28029, Spain
- Centro
de Investigación Biomédica en Red Enfermedades Cardiovasculares
(CIBERCV), Madrid, Spain
| | - Jesús Vázquez
- Laboratory
of Cardiovascular Proteomics, Centro Nacional
Investigaciones Cardiovasculares (CNIC), C/Melchor Fernández Almagro 3, Madrid 28029, Spain
- Centro
de Investigación Biomédica en Red Enfermedades Cardiovasculares
(CIBERCV), Madrid, Spain
| | - Francesc Gòdia
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
| |
Collapse
|
22
|
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
|
23
|
Zhao H, Datta SAK, Kim SH, To SC, Chaturvedi SK, Rein A, Schuck P. Nucleic acid-induced dimerization of HIV-1 Gag protein. J Biol Chem 2019; 294:16480-16493. [PMID: 31570521 PMCID: PMC6851336 DOI: 10.1074/jbc.ra119.010580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/20/2019] [Indexed: 01/09/2023] Open
Abstract
HIV-1 Gag is a highly flexible multidomain protein that forms the protein lattice of the immature HIV-1 virion. In vitro, it reversibly dimerizes, but in the presence of nucleic acids (NAs), it spontaneously assembles into virus-like particles (VLPs). High-resolution structures have revealed intricate details of the interactions of the capsid (CA) domain of Gag and the flanking spacer peptide SP1 that stabilize VLPs, but much less is known about the assembly pathway and the interactions of the highly flexible NA-binding nucleocapsid (NC) domain. Here, using a novel hybrid fluorescence proximity/sedimentation velocity method in combination with calorimetric analyses, we studied initial binding events by monitoring the sizes and conformations of complexes of Gag with very short oligonucleotides. We observed that high-affinity binding of oligonucleotides induces conformational changes in Gag accompanied by the formation of complexes with a 2:1 Gag/NA stoichiometry. This NA-liganded dimerization mode is distinct from the widely studied dimer interface in the CA domain and from protein interactions arising in the SP1 region and may be mediated by protein-protein interactions localized in the NC domain. The formation of the liganded dimer is strongly enthalpically driven, resulting in higher dimerization affinity than the CA-domain dimer. Both detailed energetic and conformational analyses of different Gag constructs revealed modulatory contributions to NA-induced dimerization from both matrix and CA domains. We hypothesize that allosterically controlled self-association represents the first step of VLP assembly and, in concert with scaffolding along the NA, can seed the formation of two-dimensional arrays near the NA.
Collapse
Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892
| | - Siddhartha A K Datta
- HIV Dynamics and Replication Program, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702
| | - Sung H Kim
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892
| | - Samuel C To
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892
| | - Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892
| |
Collapse
|
24
|
Floderer C, Masson JB, Boilley E, Georgeault S, Merida P, El Beheiry M, Dahan M, Roingeard P, Sibarita JB, Favard C, Muriaux D. Single molecule localisation microscopy reveals how HIV-1 Gag proteins sense membrane virus assembly sites in living host CD4 T cells. Sci Rep 2018; 8:16283. [PMID: 30389967 PMCID: PMC6214999 DOI: 10.1038/s41598-018-34536-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Monitoring virus assembly at the nanoscale in host cells remains a major challenge. Human immunodeficiency virus type 1 (HIV-1) components are addressed to the plasma membrane where they assemble to form spherical particles of 100 nm in diameter. Interestingly, HIV-1 Gag protein expression alone is sufficient to produce virus-like particles (VLPs) that resemble the immature virus. Here, we monitored VLP formation at the plasma membrane of host CD4+ T cells using a newly developed workflow allowing the analysis of long duration recordings of single-molecule Gag protein localisation and movement. Comparison of Gag assembling platforms in CD4+ T cells expressing wild type or assembly-defective Gag mutant proteins showed that VLP formation lasts roughly 15 minutes with an assembly time of 5 minutes. Trapping energy maps, built from membrane associated Gag protein movements, showed that one third of the assembling energy is due to direct Gag capsid-capsid interaction while the remaining two thirds require the nucleocapsid-RNA interactions. Finally, we show that the viral RNA genome does not increase the attraction of Gag at the membrane towards the assembling site but rather acts as a spatiotemporal coordinator of the membrane assembly process.
Collapse
Affiliation(s)
- Charlotte Floderer
- Infectious Disease Research Institute of Montpellier (IRIM), UMR9004 CNRS, University of Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, UMR 3571 CNRS, Pasteur Institute, Paris, France
| | - Elise Boilley
- Infectious Disease Research Institute of Montpellier (IRIM), UMR9004 CNRS, University of Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Sonia Georgeault
- INSERM U966 and IBiSA EM Facility, University of Tours, Tours, France
| | - Peggy Merida
- Infectious Disease Research Institute of Montpellier (IRIM), UMR9004 CNRS, University of Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Mohamed El Beheiry
- Light and Optical Control of Cellular Organization, Curie Institute, UMR, 168 CNRS, Paris, France
| | - Maxime Dahan
- Light and Optical Control of Cellular Organization, Curie Institute, UMR, 168 CNRS, Paris, France
| | | | - Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, UMR 5297 CNRS, University of Bordeaux, Bordeaux, France
| | - Cyril Favard
- Infectious Disease Research Institute of Montpellier (IRIM), UMR9004 CNRS, University of Montpellier, 1919 route de Mende, 34293, Montpellier, France.
| | - Delphine Muriaux
- Infectious Disease Research Institute of Montpellier (IRIM), UMR9004 CNRS, University of Montpellier, 1919 route de Mende, 34293, Montpellier, France.
| |
Collapse
|
25
|
Dubois N, Khoo KK, Ghossein S, Seissler T, Wolff P, McKinstry WJ, Mak J, Paillart JC, Marquet R, Bernacchi S. The C-terminal p6 domain of the HIV-1 Pr55 Gag precursor is required for specific binding to the genomic RNA. RNA Biol 2018; 15:923-936. [PMID: 29954247 DOI: 10.1080/15476286.2018.1481696] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The Pr55Gag precursor specifically selects the HIV-1 genomic RNA (gRNA) from a large excess of cellular and partially or fully spliced viral RNAs and drives the virus assembly at the plasma membrane. During these processes, the NC domain of Pr55Gag interacts with the gRNA, while its C-terminal p6 domain binds cellular and viral factors and orchestrates viral particle release. Gag∆p6 is a truncated form of Pr55Gag lacking the p6 domain usually used as a default surrogate for wild type Pr55Gag for in vitro analysis. With recent advance in production of full-length recombinant Pr55Gag, here, we tested whether the p6 domain also contributes to the RNA binding specificity of Pr55Gag by systematically comparing binding of Pr55Gag and Gag∆p6 to a panel of viral and cellular RNAs. Unexpectedly, our fluorescence data reveal that the p6 domain is absolutely required for specific binding of Pr55Gag to the HIV-1 gRNA. Its deletion resulted not only in a decreased affinity for gRNA, but also in an increased affinity for spliced viral and cellular RNAs. In contrast Gag∆p6 displayed a similar affinity for all tested RNAs. Removal of the C-terminal His-tag from Pr55Gag and Gag∆p6 uniformly increased the Kd values of the RNA-protein complexes by ~ 2.5 fold but did not affect the binding specificities of these proteins. Altogether, our results demonstrate a novel role of the p6 domain in the specificity of Pr55Gag-RNA interactions, and strongly suggest that the p6 domain contributes to the discrimination of HIV-1 gRNA from cellular and spliced viral mRNAs, which is necessary for its selective encapsidation.
Collapse
Affiliation(s)
- Noé Dubois
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Keith K Khoo
- b School of Medicine , Deakin University , Geelong , Australia.,c CSIRO Manufacturing , Parkville , Australia
| | - Shannon Ghossein
- b School of Medicine , Deakin University , Geelong , Australia.,c CSIRO Manufacturing , Parkville , Australia
| | - Tanja Seissler
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Philippe Wolff
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France.,d Plateforme protéomique Strasbourg-Esplanade, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | | | - Johnson Mak
- b School of Medicine , Deakin University , Geelong , Australia.,e Institute for Glycomics, Griffith University , Southport , Australia
| | - Jean-Christophe Paillart
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Roland Marquet
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Serena Bernacchi
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| |
Collapse
|
26
|
Kaposi's Sarcoma-Associated Herpesvirus mRNA Accumulation in Nuclear Foci Is Influenced by Viral DNA Replication and Viral Noncoding Polyadenylated Nuclear RNA. J Virol 2018; 92:JVI.00220-18. [PMID: 29643239 DOI: 10.1128/jvi.00220-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV), like other herpesviruses, replicates within the nuclei of its human cell host and hijacks host machinery for expression of its genes. The activities that culminate in viral DNA synthesis and assembly of viral proteins into capsids physically concentrate in nuclear areas termed viral replication compartments. We sought to better understand the spatiotemporal regulation of viral RNAs during the KSHV lytic phase by examining and quantifying the subcellular localization of select viral transcripts. We found that viral mRNAs, as expected, localized to the cytoplasm throughout the lytic phase. However, dependent on active viral DNA replication, viral transcripts also accumulated in the nucleus, often in foci in and around replication compartments, independent of the host shutoff effect. Our data point to involvement of the viral long noncoding polyadenylated nuclear (PAN) RNA in the localization of an early, intronless viral mRNA encoding ORF59-58 to nuclear foci that are associated with replication compartments.IMPORTANCE Late in the lytic phase, mRNAs from Kaposi's sarcoma-associated herpesvirus accumulate in the host cell nucleus near viral replication compartments, centers of viral DNA synthesis and virion production. This work contributes spatiotemporal data on herpesviral mRNAs within the lytic host cell and suggests a mechanism for viral RNA accumulation. Our findings indicate that the mechanism is independent of the host shutoff effect and splicing but dependent on active viral DNA synthesis and in part on the viral noncoding RNA, PAN RNA. PAN RNA is essential for the viral life cycle, and its contribution to the nuclear accumulation of viral messages may facilitate propagation of the virus.
Collapse
|
27
|
Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy. Proc Natl Acad Sci U S A 2018; 115:6721-6726. [PMID: 29891653 PMCID: PMC6042153 DOI: 10.1073/pnas.1805728115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During HIV-1 assembly, the retroviral structural protein Gag forms an immature capsid, containing thousands of Gag molecules, at the plasma membrane (PM). Interactions between Gag nucleocapsid (NC) and viral RNA (vRNA) are thought to drive assembly, but the exact roles of these interactions have remained poorly understood. Since previous studies have shown that Gag dimer- or trimer-forming mutants (GagZiL) lacking an NC domain can form immature capsids independent of RNA binding, it is often hypothesized that vRNA drives Gag assembly by inducing Gag to form low-ordered multimers, but is dispensable for subsequent assembly. In this study, we examined the role of vRNA in HIV-1 assembly by characterizing the distribution and mobility of Gag and Gag NC mutants at the PM using photoactivated localization microscopy (PALM) and single-particle tracking PALM (spt-PALM). We showed that both Gag and GagZiL assembly involve a similar basic assembly unit, as expected. Unexpectedly, the two proteins underwent different subsequent assembly pathways, with Gag cluster density increasing asymptotically, while GagZiL cluster density increased linearly. Additionally, the directed movement of Gag, but not GagZiL, was maintained at a constant speed, suggesting that the two proteins experience different external driving forces. Assembly was abolished when Gag was rendered monomeric by NC deletion. Collectively, these results suggest that, beyond inducing Gag to form low-ordered multimer basic assembly units, vRNA is essential in scaffolding and maintaining the stability of the subsequent assembly process. This finding should advance the current understanding of HIV-1 and, potentially, other retroviruses.
Collapse
|
28
|
Properties and Functions of Feline Immunodeficiency Virus Gag Domains in Virion Assembly and Budding. Viruses 2018; 10:v10050261. [PMID: 29772651 PMCID: PMC5977254 DOI: 10.3390/v10050261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 01/11/2023] Open
Abstract
Feline immunodeficiency virus (FIV) is an important cat pathogen worldwide whose biological and pathophysiological properties resemble those of human immunodeficiency virus type 1 (HIV-1). Therefore, the study of FIV not only benefits its natural host but is also useful for the development of antiviral strategies directed against HIV-1 infections in humans. FIV assembly results from the multimerization of a single but complex viral polypeptide, the Gag precursor. In this review, we will first give an overview of the current knowledge of the proteins encoded by the FIV pol, env, rev, vif, and orf-A genes, and then we will describe and discuss in detail the critical roles that each of the FIV Gag domains plays in virion morphogenesis. Since retroviral assembly is an attractive target for therapeutic interventions, gaining a better understanding of this process is highly desirable.
Collapse
|
29
|
HIV-1 Matrix Protein Interactions with tRNA: Implications for Membrane Targeting. J Mol Biol 2018; 430:2113-2127. [PMID: 29752967 DOI: 10.1016/j.jmb.2018.04.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 12/31/2022]
Abstract
The N-terminally myristoylated matrix (MA) domain of the HIV-1 Gag polyprotein promotes virus assembly by targeting Gag to the inner leaflet of the plasma membrane. Recent studies indicate that, prior to membrane binding, MA associates with cytoplasmic tRNAs (including tRNALys3), and in vitro studies of tRNA-dependent MA interactions with model membranes have led to proposals that competitive tRNA interactions contribute to membrane discrimination. We have characterized interactions between native, mutant, and unmyristylated (myr-) MA proteins and recombinant tRNALys3 by NMR spectroscopy and isothermal titration calorimetry. NMR experiments confirm that tRNALys3 interacts with a patch of basic residues that are also important for binding to the plasma membrane marker, phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. Unexpectedly, the affinity of MA for tRNALys3 (Kd = 0.63 ± 0.03 μM) is approximately 1 order of magnitude greater than its affinity for PI(4,5)P2-enriched liposomes (Kd(apparent) = 10.2 ± 2.1 μM), and NMR studies indicate that tRNALys3 binding blocks MA association with liposomes, including those enriched with PI(4,5)P2, phosphatidylserine, and cholesterol. However, the affinity of MA for tRNALys3 is diminished by mutations or sample conditions that promote myristate exposure. Since Gag-Gag interactions are known to promote myristate exposure, our findings support virus assembly models in which membrane targeting and genome binding are mechanistically coupled.
Collapse
|
30
|
Bieniasz PD, Kutluay SB. CLIP-related methodologies and their application to retrovirology. Retrovirology 2018; 15:35. [PMID: 29716635 PMCID: PMC5930818 DOI: 10.1186/s12977-018-0417-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/17/2018] [Indexed: 01/28/2023] Open
Abstract
Virtually every step of HIV-1 replication and numerous cellular antiviral defense mechanisms are regulated by the binding of a viral or cellular RNA-binding protein (RBP) to distinct sequence or structural elements on HIV-1 RNAs. Until recently, these protein-RNA interactions were studied largely by in vitro binding assays complemented with genetics approaches. However, these methods are highly limited in the identification of the relevant targets of RBPs in physiologically relevant settings. Development of crosslinking-immunoprecipitation sequencing (CLIP) methodology has revolutionized the analysis of protein-nucleic acid complexes. CLIP combines immunoprecipitation of covalently crosslinked protein-RNA complexes with high-throughput sequencing, providing a global account of RNA sequences bound by a RBP of interest in cells (or virions) at near-nucleotide resolution. Numerous variants of the CLIP protocol have recently been developed, some with major improvements over the original. Herein, we briefly review these methodologies and give examples of how CLIP has been successfully applied to retrovirology research.
Collapse
Affiliation(s)
- Paul D. Bieniasz
- Howard Hughes Medical Institute and Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065 USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110 USA
| |
Collapse
|
31
|
Mutations in the Basic Region of the Mason-Pfizer Monkey Virus Nucleocapsid Protein Affect Reverse Transcription, Genomic RNA Packaging, and the Virus Assembly Site. J Virol 2018; 92:JVI.00106-18. [PMID: 29491167 DOI: 10.1128/jvi.00106-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/20/2018] [Indexed: 12/19/2022] Open
Abstract
In addition to specific RNA-binding zinc finger domains, the retroviral Gag polyprotein contains clusters of basic amino acid residues that are thought to support Gag-viral genomic RNA (gRNA) interactions. One of these clusters is the basic K16NK18EK20 region, located upstream of the first zinc finger of the Mason-Pfizer monkey virus (M-PMV) nucleocapsid (NC) protein. To investigate the role of this basic region in the M-PMV life cycle, we used a combination of in vivo and in vitro methods to study a series of mutants in which the overall charge of this region was more positive (RNRER), more negative (AEAEA), or neutral (AAAAA). The mutations markedly affected gRNA incorporation and the onset of reverse transcription. The introduction of a more negative charge (AEAEA) significantly reduced the incorporation of M-PMV gRNA into nascent particles. Moreover, the assembly of immature particles of the AEAEA Gag mutant was relocated from the perinuclear region to the plasma membrane. In contrast, an enhancement of the basicity of this region of M-PMV NC (RNRER) caused a substantially more efficient incorporation of gRNA, subsequently resulting in an increase in M-PMV RNRER infectivity. Nevertheless, despite the larger amount of gRNA packaged by the RNRER mutant, the onset of reverse transcription was delayed in comparison to that of the wild type. Our data clearly show the requirement for certain positively charged amino acid residues upstream of the first zinc finger for proper gRNA incorporation, assembly of immature particles, and proceeding of reverse transcription.IMPORTANCE We identified a short sequence within the Gag polyprotein that, together with the zinc finger domains and the previously identified RKK motif, contributes to the packaging of genomic RNA (gRNA) of Mason-Pfizer monkey virus (M-PMV). Importantly, in addition to gRNA incorporation, this basic region (KNKEK) at the N terminus of the nucleocapsid protein is crucial for the onset of reverse transcription. Mutations that change the positive charge of the region to a negative one significantly reduced specific gRNA packaging. The assembly of immature particles of this mutant was reoriented from the perinuclear region to the plasma membrane. On the contrary, an enhancement of the basic character of this region increased both the efficiency of gRNA packaging and the infectivity of the virus. However, the onset of reverse transcription was delayed even in this mutant. In summary, the basic region in M-PMV Gag plays a key role in the packaging of genomic RNA and, consequently, in assembly and reverse transcription.
Collapse
|
32
|
Olson ED, Musier-Forsyth K. Retroviral Gag protein-RNA interactions: Implications for specific genomic RNA packaging and virion assembly. Semin Cell Dev Biol 2018; 86:129-139. [PMID: 29580971 DOI: 10.1016/j.semcdb.2018.03.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/09/2018] [Accepted: 03/22/2018] [Indexed: 02/04/2023]
Abstract
Retroviral Gag proteins are responsible for coordinating many aspects of virion assembly. Gag possesses two distinct nucleic acid binding domains, matrix (MA) and nucleocapsid (NC). One of the critical functions of Gag is to specifically recognize, bind, and package the retroviral genomic RNA (gRNA) into assembling virions. Gag interactions with cellular RNAs have also been shown to regulate aspects of assembly. Recent results have shed light on the role of MA and NC domain interactions with nucleic acids, and how they jointly function to ensure packaging of the retroviral gRNA. Here, we will review the literature regarding RNA interactions with NC, MA, as well as overall mechanisms employed by Gag to interact with RNA. The discussion focuses on human immunodeficiency virus type-1, but other retroviruses will also be discussed. A model is presented combining all of the available data summarizing the various factors and layers of selection Gag employs to ensure specific gRNA packaging and correct virion assembly.
Collapse
Affiliation(s)
- Erik D Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH, 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
33
|
Fang PY, Bowman JC, Gómez Ramos L, Hsiao C, Williams LD. RNA: packaged and protected by VLPs. RSC Adv 2018; 8:21399-21406. [PMID: 35539947 PMCID: PMC9080931 DOI: 10.1039/c8ra02084a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023] Open
Abstract
VLP packaging is most efficient for compact RNA, and protects RNA against assault by small diffusible damaging agents.
Collapse
Affiliation(s)
- Po-Yu Fang
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Lizzette M. Gómez Ramos
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemical and Biomolecular Engineering
| | - Chiaolong Hsiao
- Institute of Biochemical Sciences
- National Taiwan University
- Taipei 10617
- Republic of China
| | - Loren Dean Williams
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| |
Collapse
|
34
|
Qu N, Ma Z, Zhang M, Rushdi MN, Krueger CJ, Chen AK. Inhibition of retroviral Gag assembly by non-silencing miRNAs promotes autophagic viral degradation. Protein Cell 2017; 9:640-651. [PMID: 28884441 PMCID: PMC6019656 DOI: 10.1007/s13238-017-0461-z] [Citation(s) in RCA: 7] [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: 06/30/2017] [Accepted: 08/07/2017] [Indexed: 12/29/2022] Open
Abstract
We recently reported an unconventional mechanism by which miRNAs inhibit HIV-1 viral production. This occurs when miRNAs bind nonspecifically to the viral structural protein Gag, interfering with viral RNA-mediated Gag assembly at the plasma membrane. Consequently, misassembled viral complexes are redirected into the endocytic pathway where they are delivered to lysosomes for degradation. In this study, we demonstrate that autophagy is a critical mediator of the viral degradation pathway and that this pathway is not HIV-1 specific. Misassembled viral complexes were found to colocalize extensively with LC3 and p62 in late endosomes/lysosomes, demonstrating a convergence of autophagy with functional degradative compartments. Knocking down autophagosome formation machineries reduced this convergence, while treatment with autophagy-inducer rapamycin enhanced the convergence. Furthermore, similar autophagy-dependent nonspecific miRNA inhibition of murine leukemia virus (MLV) assembly was shown. Overall, these results reveal autophagy as a crucial regulator of the retroviral degradation pathway in host cells initiated by nonspecific miRNA-Gag interactions. These findings could have significant implications for understanding how cells may regulate retroviral complex assembly by miRNA expression and autophagy, and raise the possibility that similar regulations can occur in other biological contexts.
Collapse
Affiliation(s)
- Na Qu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Mengrao Zhang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Muaz N Rushdi
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
| |
Collapse
|
35
|
Allosteric HIV-1 Integrase Inhibitors Lead to Premature Degradation of the Viral RNA Genome and Integrase in Target Cells. J Virol 2017; 91:JVI.00821-17. [PMID: 28615207 DOI: 10.1128/jvi.00821-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 12/23/2022] Open
Abstract
Recent evidence indicates that inhibition of HIV-1 integrase (IN) binding to the viral RNA genome by allosteric integrase inhibitors (ALLINIs) or through mutations within IN yields aberrant particles in which the viral ribonucleoprotein complexes (vRNPs) are eccentrically localized outside the capsid lattice. These particles are noninfectious and are blocked at an early reverse transcription stage in target cells. However, the basis of this reverse transcription defect is unknown. Here, we show that the viral RNA genome and IN from ALLINI-treated virions are prematurely degraded in target cells, whereas reverse transcriptase remains active and stably associated with the capsid lattice. The aberrantly shaped cores in ALLINI-treated particles can efficiently saturate and be degraded by a restricting TRIM5 protein, indicating that they are still composed of capsid proteins arranged in a hexagonal lattice. Notably, the fates of viral core components follow a similar pattern in cells infected with eccentric particles generated by mutations within IN that inhibit its binding to the viral RNA genome. We propose that IN-RNA interactions allow packaging of both the viral RNA genome and IN within the protective capsid lattice to ensure subsequent reverse transcription and productive infection in target cells. Conversely, disruption of these interactions by ALLINIs or mutations in IN leads to premature degradation of both the viral RNA genome and IN, as well as the spatial separation of reverse transcriptase from the viral genome during early steps of infection.IMPORTANCE Recent evidence indicates that HIV-1 integrase (IN) plays a key role during particle maturation by binding to the viral RNA genome. Inhibition of IN-RNA interactions yields aberrant particles with the viral ribonucleoprotein complexes (vRNPs) eccentrically localized outside the conical capsid lattice. Although these particles contain all of the components necessary for reverse transcription, they are blocked at an early reverse transcription stage in target cells. To explain the basis of this defect, we tracked the fates of multiple viral components in infected cells. Here, we show that the viral RNA genome and IN in eccentric particles are prematurely degraded, whereas reverse transcriptase remains active and stably associated within the capsid lattice. We propose that IN-RNA interactions ensure the packaging of both vRNPs and IN within the protective capsid cores to facilitate subsequent reverse transcription and productive infection in target cells.
Collapse
|
36
|
Interactions between HIV-1 Gag and Viral RNA Genome Enhance Virion Assembly. J Virol 2017; 91:JVI.02319-16. [PMID: 28539452 DOI: 10.1128/jvi.02319-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/11/2017] [Indexed: 01/09/2023] Open
Abstract
Most HIV-1 virions contain two copies of full-length viral RNA, indicating that genome packaging is efficient and tightly regulated. However, the structural protein Gag is the only component required for the assembly of noninfectious viruslike particles, and the viral RNA is dispensable in this process. The mechanism that allows HIV-1 to achieve such high efficiency of genome packaging when a packageable viral RNA is not required for virus assembly is currently unknown. In this report, we examined the role of HIV-1 RNA in virus assembly and found that packageable HIV-1 RNA enhances particle production when Gag is expressed at levels similar to those in cells containing one provirus. However, such enhancement is diminished when Gag is overexpressed, suggesting that the effects of viral RNA can be replaced by increased Gag concentration in cells. We also showed that the specific interactions between Gag and viral RNA are required for the enhancement of particle production. Taken together, these studies are consistent with our previous hypothesis that specific dimeric viral RNA-Gag interactions are the nucleation event of infectious virion assembly, ensuring that one RNA dimer is packaged into each nascent virion. These studies shed light on the mechanism by which HIV-1 achieves efficient genome packaging during virus assembly.IMPORTANCE Retrovirus assembly is a well-choreographed event, during which many viral and cellular components come together to generate infectious virions. The viral RNA genome carries the genetic information to new host cells, providing instructions to generate new virions, and therefore is essential for virion infectivity. In this report, we show that the specific interaction of the viral RNA genome with the structural protein Gag facilitates virion assembly and particle production. These findings resolve the conundrum that HIV-1 RNA is selectively packaged into virions with high efficiency despite being dispensable for virion assembly. Understanding the mechanism used by HIV-1 to ensure genome packaging provides significant insights into viral assembly and replication.
Collapse
|
37
|
Comas-Garcia M, Datta SA, Baker L, Varma R, Gudla PR, Rein A. Dissection of specific binding of HIV-1 Gag to the 'packaging signal' in viral RNA. eLife 2017; 6. [PMID: 28726630 PMCID: PMC5531834 DOI: 10.7554/elife.27055] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/13/2017] [Indexed: 01/26/2023] Open
Abstract
Selective packaging of HIV-1 genomic RNA (gRNA) requires the presence of a cis-acting RNA element called the 'packaging signal' (Ψ). However, the mechanism by which Ψ promotes selective packaging of the gRNA is not well understood. We used fluorescence correlation spectroscopy and quenching data to monitor the binding of recombinant HIV-1 Gag protein to Cy5-tagged 190-base RNAs. At physiological ionic strength, Gag binds with very similar, nanomolar affinities to both Ψ-containing and control RNAs. We challenged these interactions by adding excess competing tRNA; introducing mutations in Gag; or raising the ionic strength. These modifications all revealed high specificity for Ψ. This specificity is evidently obscured in physiological salt by non-specific, predominantly electrostatic interactions. This nonspecific activity was attenuated by mutations in the MA, CA, and NC domains, including CA mutations disrupting Gag-Gag interaction. We propose that gRNA is selectively packaged because binding to Ψ nucleates virion assembly with particular efficiency.
Collapse
Affiliation(s)
- Mauricio Comas-Garcia
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, United States
| | - Siddhartha Ak Datta
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, United States
| | - Laura Baker
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, United States
| | | | - Prabhakar R Gudla
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick, United States
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, United States
| |
Collapse
|
38
|
Mohammad AA, Costa H, Landázuri N, Lui WO, Hultenby K, Rahbar A, Yaiw KC, Söderberg-Nauclér C. Human cytomegalovirus microRNAs are carried by virions and dense bodies and are delivered to target cells. J Gen Virol 2017; 98:1058-1072. [PMID: 28589873 PMCID: PMC5656795 DOI: 10.1099/jgv.0.000736] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human cytomegalovirus (HCMV) infection results in the production of virions, dense bodies (DBs) and non-infectious enveloped particles, all of which incorporate proteins and RNAs that can be transferred to host cells. Here, we investigated whether virions and DBs also carry microRNAs (miRNAs) and assessed their delivery and functionality in cells. Human lung fibroblasts (MRC-5) were infected with the HCMV strain AD169, and conditioned cell culture medium was collected and centrifuged. The pellets were treated with RNase-ONE, and the virions and DBs were purified with a potassium tartrate–glycerol gradient and dialysed. The virions and DBs were incubated with micrococcal nuclease, DNA and RNA were extracted and then analysed with TaqMan PCR assays, while the proteins were examined with Western blots. To assess the delivery of miRNAs to cells and their functionality, virions and DBs were irradiated with UV light. The purity of the virions and DBs was confirmed by typical morphology, the presence of the structural protein pp65 and the HCMV genome, the ability to infect MRC-5 cells and the absence of the host genome. RNA analysis revealed the presence of 14 HCMV-encoded miRNAs (UL22A-5p, US25-1-5p, UL22A-3p, US5-2-3p, UL112-3p, US25-2-3p, US25-2-5p, US33-3p, US5-1, UL36-5p, US4-5p, UL36-3p, UL70-5p and US25-1-3p), HCMV immediate-early mRNA and long non-coding RNA2.7, moreover, two host-encoded miRNAs (hsa-miR-218-5p and hsa-miR-21-5p) and beta-2-microglobulin RNA. UV-irradiated virions and DBs delivered viral miRNAs (US25-1-5p and UL112-3p) to the host cells, and miR-US25-1-5p was functional in a luciferase reporter assay. We conclude that virions and DBs carry miRNAs that are biologically functional and can be delivered to cells, which may affect cellular processes.
Collapse
Affiliation(s)
- Abdul-Aleem Mohammad
- Department of Medicine, Solna, Experimental Cardiovascular Unit, Department of Neurology, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Helena Costa
- Department of Medicine, Solna, Experimental Cardiovascular Unit, Department of Neurology, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Natalia Landázuri
- Department of Medicine, Solna, Experimental Cardiovascular Unit, Department of Neurology, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Kjell Hultenby
- Department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Afsar Rahbar
- Department of Medicine, Solna, Experimental Cardiovascular Unit, Department of Neurology, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Koon-Chu Yaiw
- Department of Medicine, Solna, Experimental Cardiovascular Unit, Department of Neurology, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Cecilia Söderberg-Nauclér
- Department of Medicine, Solna, Experimental Cardiovascular Unit, Department of Neurology, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| |
Collapse
|
39
|
Tanwar HS, Khoo KK, Garvey M, Waddington L, Leis A, Hijnen M, Velkov T, Dumsday GJ, McKinstry WJ, Mak J. The thermodynamics of Pr55Gag-RNA interaction regulate the assembly of HIV. PLoS Pathog 2017; 13:e1006221. [PMID: 28222188 PMCID: PMC5336307 DOI: 10.1371/journal.ppat.1006221] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/03/2017] [Accepted: 02/06/2017] [Indexed: 11/29/2022] Open
Abstract
The interactions that occur during HIV Pr55Gag oligomerization and genomic RNA packaging are essential elements that facilitate HIV assembly. However, mechanistic details of these interactions are not clearly defined. Here, we overcome previous limitations in producing large quantities of full-length recombinant Pr55Gag that is required for isothermal titration calorimetry (ITC) studies, and we have revealed the thermodynamic properties of HIV assembly for the first time. Thermodynamic analysis showed that the binding between RNA and HIV Pr55Gag is an energetically favourable reaction (ΔG<0) that is further enhanced by the oligomerization of Pr55Gag. The change in enthalpy (ΔH) widens sequentially from: (1) Pr55Gag-Psi RNA binding during HIV genome selection; to (2) Pr55Gag-Guanosine Uridine (GU)-containing RNA binding in cytoplasm/plasma membrane; and then to (3) Pr55Gag-Adenosine(A)-containing RNA binding in immature HIV. These data imply the stepwise increments of heat being released during HIV biogenesis may help to facilitate the process of viral assembly. By mimicking the interactions between A-containing RNA and oligomeric Pr55Gag in immature HIV, it was noted that a p6 domain truncated Pr50Gag Δp6 is less efficient than full-length Pr55Gag in this thermodynamic process. These data suggest a potential unknown role of p6 in Pr55Gag-Pr55Gag oligomerization and/or Pr55Gag-RNA interaction during HIV assembly. Our data provide direct evidence on how nucleic acid sequences and the oligomeric state of Pr55Gag regulate HIV assembly. Formation of any virus particle will require energy, yet the precise biophysical properties that drive the formation of HIV particles remain undefined. Isothermal titration calorimetry (ITC) is a biophysical technique that is the gold standard to reveal parameters governing biochemical and biophysical reaction. However, ITC requires large amount of proteins for analysis. As large quantities of full-length recombinant HIV Pr55Gag proteins have not been available in the past 30 years due to technical limitation, a comprehensive thermodynamic analysis of full-length HIV Pr55Gag has not been possible. Here, we have generated sufficient amount of full-length recombinant HIV Pr55Gag protein for isothermal titration calorimetry analysis. Our analyses have shown that the major interactions amongst HIV proteins and RNA sequences during viral assembly are energetically favourable reactions. In other words, HIV Pr55Gag proteins and viral RNA have evolved to overcome the energy barrier for virus formation by utilising energy obtained from protein-RNA interactions in order to facilitate the viral assembly process. Furthermore, HIV also use the oligomeric states of HIV Pr55Gag proteins and the RNA sequences as means to regulate the viral assembly process.
Collapse
Affiliation(s)
- Hanumant S. Tanwar
- School of Medicine, Deakin University, Geelong, Australia
- CSIRO Manufacturing, Parkville, Victoria, Australia
| | - Keith K. Khoo
- School of Medicine, Deakin University, Geelong, Australia
- CSIRO Manufacturing, Parkville, Victoria, Australia
| | - Megan Garvey
- School of Medicine, Deakin University, Geelong, Australia
- CSIRO Australian Animal Health Laboratory, Geelong, Australia
| | | | - Andrew Leis
- CSIRO Australian Animal Health Laboratory, Geelong, Australia
| | | | - Tony Velkov
- Monash Institute of Pharmaceutical Science, Parkville, Victoria, Australia
| | | | | | - Johnson Mak
- School of Medicine, Deakin University, Geelong, Australia
- CSIRO Australian Animal Health Laboratory, Geelong, Australia
- * E-mail:
| |
Collapse
|
40
|
Sette P, O'Connor SK, Yerramilli VS, Dussupt V, Nagashima K, Chutiraka K, Lingappa J, Scarlata S, Bouamr F. HIV-1 Nucleocapsid Mimics the Membrane Adaptor Syntenin PDZ to Gain Access to ESCRTs and Promote Virus Budding. Cell Host Microbe 2016; 19:336-48. [PMID: 26962944 DOI: 10.1016/j.chom.2016.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/07/2016] [Accepted: 02/11/2016] [Indexed: 01/09/2023]
Abstract
HIV-1 recruits cellular endosomal sorting complexes required for transport (ESCRTs) to bud virions from the membrane. Disruption of the viral nucleocapsid (NC) domain integrity affects HIV-1 budding. However, the molecular mechanisms of NC's involvement in HIV budding remain unclear. We find that NC mimics the PDZ domains of syntenin, a membrane-binding adaptor involved in cell-to-cell contact/communication, to capture the Bro1 domain of ALIX, which is an ESCRTs recruiting cellular adaptor. NC binds membranes via basic residues in either the distal or proximal zinc fingers, and NC-membrane binding is essential for Bro1 capture and HIV-1 budding. Removal of RNA enhances NC membrane binding, suggesting a dynamic competition between membrane lipids and RNA for the same binding sites in NC. Remarkably, syntenin PDZ can substitute for NC function in HIV-1 budding. Thus, NC mimics syntenin PDZs to function as a membrane-binding adaptor critical for HIV-1 budding at specific microdomains of the membrane.
Collapse
Affiliation(s)
- Paola Sette
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA
| | - Sarah K O'Connor
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA
| | - V Siddartha Yerramilli
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Vincent Dussupt
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA
| | - Kunio Nagashima
- Electron Microscope Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Kasana Chutiraka
- Department of Global Health, University of Washington, Seattle, WA 98102, USA
| | - Jaisri Lingappa
- Department of Global Health, University of Washington, Seattle, WA 98102, USA
| | - Suzanne Scarlata
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Fadila Bouamr
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA.
| |
Collapse
|
41
|
Saxena P, He L, Malyutin A, Datta SAK, Rein A, Bond KM, Jarrold MF, Spilotros A, Svergun D, Douglas T, Dragnea B. Virus Matryoshka: A Bacteriophage Particle-Guided Molecular Assembly Approach to a Monodisperse Model of the Immature Human Immunodeficiency Virus. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5862-5872. [PMID: 27634413 PMCID: PMC6810630 DOI: 10.1002/smll.201601712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/05/2016] [Indexed: 05/27/2023]
Abstract
Immature human immunodeficiency virus type 1 (HIV-1) is approximately spherical, but is constructed from a hexagonal lattice of the Gag protein. As a hexagonal lattice is necessarily flat, the local symmetry cannot be maintained throughout the structure. This geometrical frustration presumably results in bending stress. In natural particles, the stress is relieved by incorporation of packing defects, but the magnitude of this stress and its significance for the particles is not known. In order to control this stress, we have now assembled the Gag protein on a quasi-spherical template derived from bacteriophage P22. This template is monodisperse in size and electron-transparent, enabling the use of cryo-electron microscopy in structural studies. These templated assemblies are far less polydisperse than any previously described virus-like particles (and, while constructed according to the same lattice as natural particles, contain almost no packing defects). This system gives us the ability to study the relationship between packing defects, curvature and elastic energy, and thermodynamic stability. As Gag is bound to the P22 template by single-stranded DNA, treatment of the particles with DNase enabled us to determine the intrinsic radius of curvature of a Gag lattice, unconstrained by DNA or a template. We found that this intrinsic radius is far larger than that of a virion or P22-templated particle. We conclude that Gag is under elastic strain in a particle; this has important implications for the kinetics of shell growth, the stability of the shell, and the type of defects it will assume as it grows.
Collapse
Affiliation(s)
- Pooja Saxena
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Li He
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Andrey Malyutin
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Siddhartha A K Datta
- National Cancer Institute, P.O. Box B, Building 535, Frederick, MD, 21702-1201, USA
| | - Alan Rein
- National Cancer Institute, P.O. Box B, Building 535, Frederick, MD, 21702-1201, USA
| | - Kevin M Bond
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Alessandro Spilotros
- European Molecular Biology Laboratory-DESY, Notkestrasse 85, Geb. 25a, 22603, Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory-DESY, Notkestrasse 85, Geb. 25a, 22603, Hamburg, Germany
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| |
Collapse
|
42
|
Kutluay SB, Bieniasz PD. Analysis of HIV-1 Gag-RNA Interactions in Cells and Virions by CLIP-seq. Methods Mol Biol 2016; 1354:119-31. [PMID: 26714708 DOI: 10.1007/978-1-4939-3046-3_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Next-generation sequencing-based methodologies have revolutionized the analysis of protein-nucleic acid complexes; yet these novel approaches have rarely been applied in virology. Because it has an RNA genome, RNA-protein interactions play critical roles in human immunodeficiency virus type 1 (HIV-1) replication. In many cases, the binding sites of proteins on HIV-1 RNA molecules in physiologically relevant settings are not known. Cross-linking-immunoprecipitation sequencing (CLIP-seq) methodologies, which combine immunoprecipitation of covalently crosslinked protein-RNA complexes with high-throughput sequencing, is a powerful technique that can be applied to such questions as it provides a global account of RNA sequences bound by a RNA-binding protein of interest in physiological settings at near-nucleotide resolution. Here, we describe the application of the CLIP-seq methodology to identify the RNA molecules that are bound by the HIV-1 Gag protein in cells and in virions. This protocol can easily be applied to other viral and cellular RNA-binding proteins that influence HIV-1 replication.
Collapse
Affiliation(s)
- Sebla B Kutluay
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University, 455 First Avenue, New York, NY, 10016, USA. .,Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO, 63110, USA.
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University, 455 First Avenue, New York, NY, 10016, USA. .,Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center, The Rockefeller University, 455 First Avenue, New York, NY, 10016, USA.
| |
Collapse
|
43
|
Cross- and Co-Packaging of Retroviral RNAs and Their Consequences. Viruses 2016; 8:v8100276. [PMID: 27727192 PMCID: PMC5086612 DOI: 10.3390/v8100276] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 12/23/2022] Open
Abstract
Retroviruses belong to the family Retroviridae and are ribonucleoprotein (RNP) particles that contain a dimeric RNA genome. Retroviral particle assembly is a complex process, and how the virus is able to recognize and specifically capture the genomic RNA (gRNA) among millions of other cellular and spliced retroviral RNAs has been the subject of extensive investigation over the last two decades. The specificity towards RNA packaging requires higher order interactions of the retroviral gRNA with the structural Gag proteins. Moreover, several retroviruses have been shown to have the ability to cross-/co-package gRNA from other retroviruses, despite little sequence homology. This review will compare the determinants of gRNA encapsidation among different retroviruses, followed by an examination of our current understanding of the interaction between diverse viral genomes and heterologous proteins, leading to their cross-/co-packaging. Retroviruses are well-known serious animal and human pathogens, and such a cross-/co-packaging phenomenon could result in the generation of novel viral variants with unknown pathogenic potential. At the same time, however, an enhanced understanding of the molecular mechanisms involved in these specific interactions makes retroviruses an attractive target for anti-viral drugs, vaccines, and vectors for human gene therapy.
Collapse
|
44
|
Comas-Garcia M, Davis SR, Rein A. On the Selective Packaging of Genomic RNA by HIV-1. Viruses 2016; 8:v8090246. [PMID: 27626441 PMCID: PMC5035960 DOI: 10.3390/v8090246] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/16/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022] Open
Abstract
Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. However, in the absence of the gRNA, cellular messenger RNAs (mRNAs) are packaged. While the gRNA is selected because of its cis-acting packaging signal, the mechanism of this selection is not understood. The affinity of Gag (the viral structural protein) for cellular RNAs at physiological ionic strength is not much higher than that for the gRNA. However, binding to the gRNA is more salt-resistant, implying that it has a higher non-electrostatic component. We have previously studied the spacer 1 (SP1) region of Gag and showed that it can undergo a concentration-dependent conformational transition. We proposed that this transition represents the first step in assembly, i.e., the conversion of Gag to an assembly-ready state. To explain selective packaging of gRNA, we suggest here that binding of Gag to gRNA, with its high non-electrostatic component, triggers this conversion more readily than binding to other RNAs; thus we predict that a Gag-gRNA complex will nucleate particle assembly more efficiently than other Gag-RNA complexes. New data shows that among cellular mRNAs, those with long 3'-untranslated regions (UTR) are selectively packaged. It seems plausible that the 3'-UTR, a stretch of RNA not occupied by ribosomes, offers a favorable binding site for Gag.
Collapse
Affiliation(s)
- Mauricio Comas-Garcia
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Sean R Davis
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| |
Collapse
|
45
|
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
|
46
|
Hamann MV, Lindemann D. Foamy Virus Protein-Nucleic Acid Interactions during Particle Morphogenesis. Viruses 2016; 8:v8090243. [PMID: 27589786 PMCID: PMC5035957 DOI: 10.3390/v8090243] [Citation(s) in RCA: 8] [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: 06/29/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 12/24/2022] Open
Abstract
Compared with orthoretroviruses, our understanding of the molecular and cellular replication mechanism of foamy viruses (FVs), a subfamily of retroviruses, is less advanced. The FV replication cycle differs in several key aspects from orthoretroviruses, which leaves established retroviral models debatable for FVs. Here, we review the general aspect of the FV protein-nucleic acid interactions during virus morphogenesis. We provide a summary of the current knowledge of the FV genome structure and essential sequence motifs required for RNA encapsidation as well as Gag and Pol binding in combination with details about the Gag and Pol biosynthesis. This leads us to address open questions in FV RNA engagement, binding and packaging. Based on recent findings, we propose to shift the point of view from individual glycine-arginine-rich motifs having functions in RNA interactions towards envisioning the FV Gag C-terminus as a general RNA binding protein module. We encourage further investigating a potential new retroviral RNA packaging mechanism, which seems more complex in terms of the components that need to be gathered to form an infectious particle. Additional molecular insights into retroviral protein-nucleic acid interactions help us to develop safer, more specific and more efficient vectors in an era of booming genome engineering and gene therapy approaches.
Collapse
Affiliation(s)
- Martin V Hamann
- Institute of Virology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany.
- CRTD/DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Dirk Lindemann
- Institute of Virology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany.
- CRTD/DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany.
| |
Collapse
|
47
|
Telesnitsky A, Wolin SL. The Host RNAs in Retroviral Particles. Viruses 2016; 8:v8080235. [PMID: 27548206 PMCID: PMC4997597 DOI: 10.3390/v8080235] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 12/15/2022] Open
Abstract
As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs' packaging determinants differ from the viral genome's, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs-if any-have remained elusive.
Collapse
Affiliation(s)
- Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06536, USA.
| |
Collapse
|
48
|
Mekdad HE, Boutant E, Karnib H, Biedma ME, Sharma KK, Malytska I, Laumond G, Roy M, Réal E, Paillart JC, Moog C, Darlix JL, Mély Y, de Rocquigny H. Characterization of the interaction between the HIV-1 Gag structural polyprotein and the cellular ribosomal protein L7 and its implication in viral nucleic acid remodeling. Retrovirology 2016; 13:54. [PMID: 27515235 PMCID: PMC4982112 DOI: 10.1186/s12977-016-0287-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Abstract
Background In HIV-1 infected cells, the integrated viral DNA is transcribed by the host cell machinery to generate the full length HIV-1 RNA (FL RNA) that serves as mRNA encoding for the Gag and GagPol precursors. Virion formation is orchestrated by Gag, and the current view is that a specific interaction between newly made Gag molecules and FL RNA initiates the process. This in turn would cause FL RNA dimerization by the NC domain of Gag (GagNC). However the RNA chaperoning activity of unprocessed Gag is low as compared to the mature NC protein. This prompted us to search for GagNC co-factors. Results Here we report that RPL7, a major ribosomal protein involved in translation regulation, is a partner of Gag via its interaction with the NC domain. This interaction is mediated by the NC zinc fingers and the N- and C-termini of RPL7, respectively, but seems independent of RNA binding, Gag oligomerization and its interaction with the plasma membrane. Interestingly, RPL7 is shown for the first time to exhibit a potent DNA/RNA chaperone activity higher than that of Gag. In addition, Gag and RPL7 can function in concert to drive rapid nucleic acid hybridization. Conclusions Our results show that GagNC interacts with the ribosomal protein RPL7 endowed with nucleic acid chaperone activity, favoring the notion that RPL7 could be a Gag helper chaperoning factor possibly contributing to the start of Gag assembly. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0287-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hala El Mekdad
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Emmanuel Boutant
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Hassan Karnib
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Marina E Biedma
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), INSERM U1109, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg Cedex, France
| | - Kamal Kant Sharma
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Iuliia Malytska
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Géraldine Laumond
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), INSERM U1109, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg Cedex, France
| | - Marion Roy
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg Cedex, France
| | - Eléonore Réal
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg Cedex, France
| | - Christiane Moog
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), INSERM U1109, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg Cedex, France
| | - Jean Luc Darlix
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Hugues de Rocquigny
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France.
| |
Collapse
|
49
|
Eckwahl MJ, Arnion H, Kharytonchyk S, Zang T, Bieniasz PD, Telesnitsky A, Wolin SL. Analysis of the human immunodeficiency virus-1 RNA packageome. RNA (NEW YORK, N.Y.) 2016; 22:1228-38. [PMID: 27247436 PMCID: PMC4931115 DOI: 10.1261/rna.057299.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 05/15/2016] [Indexed: 05/16/2023]
Abstract
All retroviruses package cellular RNAs into virions. Studies of murine leukemia virus (MLV) revealed that the major host cell RNAs encapsidated by this simple retrovirus were LTR retrotransposons and noncoding RNAs (ncRNAs). Several classes of ncRNAs appeared to be packaged by MLV shortly after synthesis, as precursors to tRNAs, small nuclear RNAs, and small nucleolar RNAs were all enriched in virions. To determine the extent to which the human immunodeficiency virus (HIV-1) packages similar RNAs, we used high-throughput sequencing to characterize the RNAs within infectious HIV-1 virions produced in CEM-SS T lymphoblastoid cells. We report that the most abundant cellular RNAs in HIV-1 virions are 7SL RNA and transcripts from numerous divergent and truncated members of the long interspersed element (LINE) and short interspersed element (SINE) families of retrotransposons. We also detected precursors to several tRNAs and small nuclear RNAs as well as transcripts derived from the ribosomal DNA (rDNA) intergenic spacers. We show that packaging of a pre-tRNA requires the nuclear export receptor Exportin 5, indicating that HIV-1 recruits at least some newly made ncRNAs in the cytoplasm. Together, our work identifies the set of RNAs packaged by HIV-1 and reveals that early steps in HIV-1 assembly intersect with host cell ncRNA biogenesis pathways.
Collapse
Affiliation(s)
- Matthew J Eckwahl
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06536, USA
| | - Helene Arnion
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06536, USA
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Trinity Zang
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10016, USA Laboratory of Retrovirology, The Rockefeller University, New York, New York 10016, USA Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10016, USA
| | - Paul D Bieniasz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10016, USA Laboratory of Retrovirology, The Rockefeller University, New York, New York 10016, USA Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10016, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06536, USA Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06536, USA Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
| |
Collapse
|
50
|
Hellmund C, Lever AML. Coordination of Genomic RNA Packaging with Viral Assembly in HIV-1. Viruses 2016; 8:E192. [PMID: 27428992 PMCID: PMC4974527 DOI: 10.3390/v8070192] [Citation(s) in RCA: 8] [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: 06/16/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 12/15/2022] Open
Abstract
The tremendous progress made in unraveling the complexities of human immunodeficiency virus (HIV) replication has resulted in a library of drugs to target key aspects of the replication cycle of the virus. Yet, despite this accumulated wealth of knowledge, we still have much to learn about certain viral processes. One of these is virus assembly, where the viral genome and proteins come together to form infectious progeny. Here we review this topic from the perspective of how the route to production of an infectious virion is orchestrated by the viral genome, and we compare and contrast aspects of the assembly mechanisms employed by HIV-1 with those of other RNA viruses.
Collapse
Affiliation(s)
- Chris Hellmund
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
| |
Collapse
|