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Ying Y, Yang Y, Chen AK. Roles of RNA scaffolding in nanoscale Gag multimerization and selective protein sorting at HIV membranes. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
HIV-1 Gag proteins can multimerize upon the viral genomic RNA or multiple random cellular messenger RNAs to form a virus particle or a virus-like particle, respectively. To date, whether the two types of particles form via the same Gag multimerization process has remained unclarified. Using photoactivated localization microscopy to illuminate Gag organizations and dynamics at the nanoscale, here, we showed that genomic RNA mediates Gag multimerization in a more cluster-centric, cooperative, and spatiotemporally coordinated fashion, with the ability to drive dense Gag clustering dependent on its ability to act as a long-stranded scaffold not easily attainable by cellular messenger RNAs. These differences in Gag multimerization were further shown to affect downstream selective protein sorting into HIV membranes, indicating that the choice of RNA for packaging can modulate viral membrane compositions. These findings should advance the understanding of HIV assembly and further benefit the development of virus-like particle-based therapeutics.
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Affiliation(s)
- Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Peking University, Beijing 100871, China
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2
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Mongkonwattanaporn T, Lertwatcharasarakul P, Rukkwamsuk T. Development of in-house ELISA based on recombinant gag proteins of small ruminant lentiviruses isolated from goats in Thailand. Sci Rep 2024; 14:3636. [PMID: 38351130 PMCID: PMC10864301 DOI: 10.1038/s41598-024-54360-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/12/2024] [Indexed: 02/16/2024] Open
Abstract
Small ruminant lentiviruses (SRLVs), are grouped in Retroviridae family, remain a significant loss in the small ruminant husbandry. As a result of unavailability of vaccine and effective treatment, the diagnosis plays a crucial role for the control of SRLV infection. However, the major challenge of diagnosis of SRLV infection is the genetic and antigenic variability of the viruses that can lead to a failure in serological detection. This study investigated the circulating strains of the viruses in goats in Thailand and an in-house ELISA was developed. The coding sequences for gag protein were optimized, synthesized, and expressed in Escherichia coli for increasing the sensitivity of ELISA test. A total of 365 serum samples were examined against the recombinant protein in an in-house ELISA. The results showed that the recombinant gag achieves 96.67% sensitivity and 93.18% specificity as compared with the commercially available ELISA test kit.
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Affiliation(s)
- Tatchapon Mongkonwattanaporn
- Department of Large Animal and Wildlife Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Malaiman Road, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
| | - Preeda Lertwatcharasarakul
- Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Malaiman Road, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
| | - Theera Rukkwamsuk
- Department of Large Animal and Wildlife Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Malaiman Road, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand.
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3
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Banerjee P, Voth GA. Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding. Biophys J 2024; 123:42-56. [PMID: 37978800 PMCID: PMC10808027 DOI: 10.1016/j.bpj.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/25/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-genomic RNA (gRNA) interactions play a crucial role in the multimerization process, which is yet to be fully understood. We performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to affect mainly the SP1 domain of the 18-mer and the matrix-capsid linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the nucleocapsid domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, and also regulates the dynamic organization of the local membrane region itself.
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Affiliation(s)
- Puja Banerjee
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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Al Othman A, Bagrov D, Rozenberg JM, Glazova O, Skryabin G, Tchevkina E, Mezentsev A, Durymanov M. Retrovirus-like gag protein Arc/Arg3.1 is involved in extracellular-vesicle-mediated mRNA transfer between glioma cells. Biochim Biophys Acta Gen Subj 2024; 1868:130522. [PMID: 37995879 DOI: 10.1016/j.bbagen.2023.130522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/29/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Activity-regulated cytoskeleton-associated (Arc) protein is predominantly expressed in excitatory glutamatergic neurons of vertebrates, where it plays a pivotal role in regulation of synaptic plasticity. Arc protein forms capsid-like particles, which can encapsulate and transfer mRNA in extracellular vesicles (EVs) between hippocampal neurons. Once glioma cell networks actively interact with neurons via paracrine signaling and formation of neurogliomal glutamatergic synapses, we predicted the involvement of Arc in a process of EV-mediated mRNA transfer between glioma cells. MATERIALS AND METHODS Arc expression in three human glioma cell lines was evaluated by WB and immunocytochemistry. The properties of Arc protein/mRNA-containing EVs produced by glioma cells were analyzed by RT-PCR, TEM, and WB. Flow cytometry, RT-PCR, and fluorescent microscopy were used to show the involvement of Arc in EV-mediated mRNA transfer between glioma cells. RESULTS It was found that human glioma cells can produce EVs containing Arc/Arg3.1 protein and Arc mRNA (or "Arc EVs"). Arc EVs from U87 glioma cells internalize and deliver Arc mRNA to recipient U87 cells, where it is translated into a protein. Arc overexpression significantly increases EV production, alters EV morphology, and enhances intercellular transfer of highly expressed mRNA in glioma cell culture. CONCLUSION These findings indicate involvement of Arc EVs into mRNA transfer between glioma cells that could contribute to tumor progression and affect synaptic plasticity in cancer patients.
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Affiliation(s)
- Aya Al Othman
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Dmitry Bagrov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia; Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow, Russia
| | - Julian M Rozenberg
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Olga Glazova
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Gleb Skryabin
- Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Elena Tchevkina
- Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Alexandre Mezentsev
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Mikhail Durymanov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; Department of Radiochemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia.
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Pluta A, Taxis TM, van der Meer F, Shrestha S, Qualley D, Coussens P, Rola-Łuszczak M, Ryło A, Sakhawat A, Mamanova S, Kuźmak J. An immunoinformatics study reveals a new BoLA-DR-restricted CD4+ T cell epitopes on the Gag protein of bovine leukemia virus. Sci Rep 2023; 13:22356. [PMID: 38102157 PMCID: PMC10724172 DOI: 10.1038/s41598-023-48899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leucosis (EBL), which has been reported worldwide. The expression of viral structural proteins: surface glycoprotein (gp51) and three core proteins - p15 (matrix), p24 (capsid), and p12 (nucleocapsid) induce a strong humoral and cellular immune response at first step of infection. CD4+ T-cell activation is generally induced by bovine leukocyte antigen (BoLA) region- positive antigen-presenting cells (APC) after processing of an exogenous viral antigen. Limited data are available on the BLV epitopes from the core proteins recognized by CD4+ T-cells. Thus, immunoinformatic analysis of Gag sequences obtained from 125 BLV isolates from Poland, Canada, Pakistan, Kazakhstan, Moldova and United States was performed to identify the presence of BoLA-DRB3 restricted CD4+ T-cell epitopes. The 379 15-mer overlapping peptides spanning the entire Gag sequence were run in BoLA-DRB3 allele-binding regions using a BoLA-DRB- peptide binding affinity prediction algorithm. The analysis identified 22 CD4+ T-cell peptide epitopes of variable length ranging from 17 to 22 amino acids. The predicted epitopes interacted with 73 different BoLA-DRB3 alleles found in BLV-infected cattle. Importantly, two epitopes were found to be linked with high proviral load in PBMC. A majority of dominant and subdominant epitopes showed high conservation across different viral strains, and therefore could be attractive targets for vaccine development.
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Affiliation(s)
- Aneta Pluta
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland.
| | - Tasia Marie Taxis
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
| | - Frank van der Meer
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sulav Shrestha
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Dominic Qualley
- Department of Chemistry and Biochemistry, and Center for One Health Studies, Berry College, Mt. Berry, GA, 30149, USA
| | - Paul Coussens
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
| | - Marzena Rola-Łuszczak
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland
| | - Anna Ryło
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland
| | - Ali Sakhawat
- Animal Quarantine Department, Ministry of National Food Security and Research, Peshawar, 25000, Pakistan
| | - Saltanat Mamanova
- Laboratory of Virology, Kazakh Scientific Research Veterinary Institute, LLP, 223 Raiymbek Avenue, 050000, Almaty, Republic of Kazakhstan
| | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland
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Kruglova NA, Komkov DS, Mazurov DV, Shepelev MV. The RRE-Rev Module Has No Effect on the Packaging Efficiency of Cas9 and Gag Proteins into NanoMEDIC Virus-like Particles. Dokl Biol Sci 2023; 513:S45-S50. [PMID: 38472686 DOI: 10.1134/s0012496623700886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 03/14/2024]
Abstract
Delivery of ribonucleoprotein complexes of Cas9 nuclease and guide RNA into target cells with virus-like particles (VLP) is one of the novel methods of genome editing and is suitable for gene therapy of human diseases in the future. The efficiency of genome editing with VLPs depends on the Cas9 packaging into VLPs, the process mediated by the viral Gag protein. To improve the packaging of Cas9 into NanoMEDIC VLPs, plasmid constructs for Cas9 and Gag expression were modified by adding the HIV Rev response element (RRE), which was expected to increase the nuclear export of RRE-containing transcripts into the cytosol via the Rev accessory protein, as described for a Vpr-Cas9-based VLP system. The Cas9 and Gag protein levels in cell lysates were found to increase upon cotransfection with either the Rev-expressing plasmid or the empty control plasmid. The effect was independent of the presence of RRE in the transcript. Moreover, AP21967-induced dimerization of FRB and FKBP12, but not plasmid modification with RRE and/or cotransfection with the Rev-expressing plasmid, was shown to play the major role in Cas9 packaging into NanoMEDIC VLPs. The data indicated that it is impractical to use the RRE-Rev module to enhance the packaging of Cas9 nuclease into VLPs.
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Affiliation(s)
- N A Kruglova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - D S Komkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Current address: Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'erSheva, Israel
| | - D V Mazurov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Current address: Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, USA
| | - M V Shepelev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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Maeda Y, Monde K, Terasawa H, Tanaka Y, Sawa T. Interaction of TSG101 with the PTAP Motif in Distinct Locations of Gag Determines the Incorporation of HTLV-1 Env into the Retroviral Virion. Int J Mol Sci 2023; 24:16520. [PMID: 38003710 PMCID: PMC10671467 DOI: 10.3390/ijms242216520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Human T-cell tropic virus type 1 (HTLV-1) is known to be mainly transmitted by cell-to-cell contact due to the lower infectivity of the cell-free virion. However, the reasons why cell-free HTLV-1 infection is poor remain unknown. In this study, we found that the retrovirus pseudotyped with HTLV-1 viral envelope glycoprotein (Env) was infectious when human immunodeficiency virus type 1 (HIV-1) was used to produce the virus. We found that the incorporation of HTLV-1 Env into virus-like particles (VLPs) was low when HTLV-1 Gag was used to produce VLPs, whereas VLPs produced using HIV-1 Gag efficiently incorporated HTLV-1 Env. The production of VLPs using Gag chimeras between HTLV-1 and HIV-1 Gag and deletion mutants of HIV-1 Gag showed that the p6 domain of HIV-1 Gag was responsible for the efficient incorporation of HTLV-1 Env into the VLPs. Further mutagenic analyses of the p6 domain of HIV-1 Gag revealed that the PTAP motif in the p6 domain of HIV-1 Gag facilitates the incorporation of HTLV-1 Env into VLPs. Since the PTAP motif is known to interact with tumor susceptibility gene 101 (TSG101) during the budding process, we evaluated the effect of TSG101 knockdown on the incorporation of HTLV-1 Env into VLPs. We found that TSG101 knockdown suppressed the incorporation of HTLV-1 Env into VLPs and decreased the infectivity of cell-free HIV-1 pseudotyped with HTLV-1 Env. Our results suggest that the interaction of TSG101 with the PTAP motif of the retroviral L domain is involved not only in the budding process but also in the efficient incorporation of HTLV-1 Env into the cell-free virus.
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Affiliation(s)
- Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
| | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
| | - Hiromi Terasawa
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
| | - Yuetsu Tanaka
- Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan;
| | - Tomohiro Sawa
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
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Koçkaya ES, Can H, Yaman Y, Ün C. In silico discovery of epitopes of gag and env proteins for the development of a multi-epitope vaccine candidate against Maedi Visna Virus using reverse vaccinology approach. Biologicals 2023; 84:101715. [PMID: 37793308 DOI: 10.1016/j.biologicals.2023.101715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/28/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Maedi Visna Virus (MVV) causes a chronic viral disease in sheep. Since there is no specific therapeutic drug that targets MVV, development of a vaccine against the MVV is inevitable. This study aimed to analyze the gag and env proteins as vaccine candidate proteins and to identify epitopes in these proteins. In addition, it was aimed to construct a multi-epitope vaccine candidate. According to the obtained results, the gag protein was detected to be more conserved and had a higher antigenicity value. Also, the number of alpha helix in the secondary structure was higher and transmembrane helices were not detected. Although many B cell and MHC-I/II epitopes were predicted, only 19 of them were detected to have the properties of antigenic, non-allergenic, non-toxic, soluble, and non-hemolytic. Of these epitopes, five were remarkable due to having the highest antigenicity value. However, the final multi-epitope vaccine was constructed with 19 epitopes. A strong affinity was shown between the final multi-epitope vaccine and TLR-2/4. In conclusion, the gag protein was a better antigen. However, both proteins had epitopes with high antigenicity value. Also, the final multi-epitope vaccine construct had a potential to be used as a peptide vaccine due to its immuno-informatics results.
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Affiliation(s)
- Ecem Su Koçkaya
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye
| | - Hüseyin Can
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye
| | - Yalçın Yaman
- Siirt University Faculty of Veterinary Medicine, Department of Genetics, Siirt, Türkiye
| | - Cemal Ün
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye.
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Beckwith SL, Nomberg EJ, Newman AC, Taylor JV, Guerrero-Ferreira RC, Garfinkel DJ. An interchangeable prion-like domain is required for Ty1 retrotransposition. Proc Natl Acad Sci U S A 2023; 120:e2303358120. [PMID: 37459521 PMCID: PMC10372613 DOI: 10.1073/pnas.2303358120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Retrotransposons and retroviruses shape genome evolution and can negatively impact genome function. Saccharomyces cerevisiae and its close relatives harbor several families of LTR-retrotransposons, the most abundant being Ty1 in several laboratory strains. The cytosolic foci that nucleate Ty1 virus-like particle (VLP) assembly are not well understood. These foci, termed retrosomes or T-bodies, contain Ty1 Gag and likely Gag-Pol and the Ty1 mRNA destined for reverse transcription. Here, we report an intrinsically disordered N-terminal prion-like domain (PrLD) within Gag that is required for transposition. This domain contains amino acid composition similar to known yeast prions and is sufficient to nucleate prionogenesis in an established cell-based prion reporter system. Deleting the Ty1 PrLD results in dramatic VLP assembly and retrotransposition defects but does not affect Gag protein level. Ty1 Gag chimeras in which the PrLD is replaced with other sequences, including yeast and mammalian prionogenic domains, display a range of retrotransposition phenotypes from wild type to null. We examine these chimeras throughout the Ty1 replication cycle and find that some support retrosome formation, VLP assembly, and retrotransposition, including the yeast Sup35 prion and the mouse PrP prion. Our interchangeable Ty1 system provides a useful, genetically tractable in vivo platform for studying PrLDs, complete with a suite of robust and sensitive assays. Our work also invites study into the prevalence of PrLDs in additional mobile elements.
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Affiliation(s)
- Sean L. Beckwith
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
| | - Emily J. Nomberg
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
| | - Abigail C. Newman
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
| | - Jeannette V. Taylor
- Robert P. Apkarian Integrated Electron Microscopy Core at Emory University, Atlanta, GA30322
| | | | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
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Hudait A, Hurley JH, Voth GA. Dynamics of upstream ESCRT organization at the HIV-1 budding site. Biophys J 2023; 122:2655-2674. [PMID: 37218128 PMCID: PMC10397573 DOI: 10.1016/j.bpj.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
In the late stages of the HIV-1 life cycle, membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. Release of the virion requires direct interaction between immature Gag lattice and upstream ESCRT machinery at the viral budding site, followed by assembly of downstream ESCRT-III factors, culminating in membrane scission. However, molecular details of upstream ESCRT assembly dynamics at the viral budding site remain unclear. In this work, using coarse-grained (CG) molecular dynamics (MD) simulations, we investigated the interactions between Gag, ESCRT-I, ESCRT-II, and membrane to delineate the dynamical mechanisms by which upstream ESCRTs assemble templated by late-stage immature Gag lattice. We first systematically derived "bottom-up" CG molecular models and interactions of upstream ESCRT proteins from experimental structural data and extensive all-atom MD simulations. Using these molecular models, we performed CG MD simulations of ESCRT-I oligomerization and ESCRT-I/II supercomplex formation at the neck of the budding virion. Our simulations demonstrate that ESCRT-I can effectively oligomerize to higher-order complexes templated by the immature Gag lattice both in the absence of ESCRT-II and when multiple copies of ESCRT-II are localized at the bud neck. The ESCRT-I/II supercomplexes formed in our simulations exhibit predominantly columnar structures, which has important implications for the nucleation pathway of downstream ESCRT-III polymers. Importantly, ESCRT-I/II supercomplexes bound to Gag initiate membrane neck constriction by pulling the inner edge of the bud neck closer to the ESCRT-I headpiece ring. Our findings serve to elucidate a network of interactions between upstream ESCRT machinery, immature Gag lattice, and membrane neck that regulate protein assembly dynamics at the HIV-1 budding site.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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Tariq U, Nazziwa J, Sasinovich S, Shah SA, Naeem S, Abidi SH, Esbjörnsson J. Phylogenetic Characterization of HIV-1 Sub-Subtype A1 in Karachi, Pakistan. Viruses 2022; 14:v14102307. [PMID: 36298862 PMCID: PMC9611109 DOI: 10.3390/v14102307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022] Open
Abstract
(1) Background: HIV-1 sub-subtype A1 is common in parts of Africa, Russia, former Soviet Union countries, and Eastern Europe. In Pakistan, sub-subtype A1 is the predominant HIV-1 subtype. Preliminary evidence suggests that distinct strains of HIV-1 sub-subtype A1 are circulating in Pakistan; however, an in-depth molecular phylogenetic characterization of HIV-1 sub-subtype A1 strains in Pakistan have not been presented. We performed a detailed characterization of the HIV-1 sub-subtype A1 epidemic in Pakistan using state-of-the-art molecular epidemiology and phylodynamics. (2) Methods: A total of 143 HIV-1 sub-subtype A1 gag sequences, including 61 sequences generated specifically for this study from PLHIVs part of our cohort, representing all sub-subtype A1 gag sequences from Pakistan, were analyzed. Maximum-likelihood phylogenetic cluster analysis was used to determine the relationship between Pakistani sub-subtype A1 strains and pandemic sub-subtype A1 strains. Furthermore, we used signature variation, charge distribution, selection pressures, and epitope prediction analyses to characterize variations unique to Pakistani HIV-1 strains and establish the association between signature variations and Gag epitope profile. (3) Results: The HIV-1 sub-subtype A1 sequences from Pakistan formed three main clusters: two that clustered with Kenyan sequences (7 and 10 sequences, respectively) and one that formed a Pakistan-specific cluster of 123 sequences that were much less related to other sub-subtype A1 sequences available in the database. The sequences in the Pakistan-specific cluster and the Kenyan reference strains exhibited several signature variations, especially at amino acid positions 312, 319, 331, 372, 373, 383, and 402. Structural protein modeling suggested that amino acid changes in these positions result in alterations of the Gag protein structure as well as in Gag-specific T-cell epitopes. (4) Conclusions: Our results suggest that the majority of the Pakistan HIV-1 sub-subtype A1 strains were unique to Pakistan and with a specific mutation pattern in Gag.
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Affiliation(s)
- Uroosa Tariq
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
- Department of Biochemistry, University of Karachi, Karachi 75270, Pakistan
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, SE-221 00 Lund, Sweden
| | | | | | - Sadaf Naeem
- Department of Biochemistry, University of Karachi, Karachi 75270, Pakistan
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan
- Correspondence: (S.H.A.); (J.E.)
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, SE-221 00 Lund, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Correspondence: (S.H.A.); (J.E.)
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12
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Herrmann D, Hanson HM, Zhou LW, Addabbo R, Willkomm NA, Angert I, Mueller JD, Mansky LM, Saad JS. Molecular Determinants of Human T-cell Leukemia Virus Type 1 Gag Targeting to the Plasma Membrane for Assembly. J Mol Biol 2022; 434:167609. [PMID: 35490898 PMCID: PMC10557380 DOI: 10.1016/j.jmb.2022.167609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/20/2022] [Accepted: 04/23/2022] [Indexed: 01/10/2023]
Abstract
Assembly of human T-cell leukemia virus type 1 (HTLV-1) particles is initiated by the trafficking of virally encoded Gag polyproteins to the inner leaflet of the plasma membrane (PM). Gag-PM interactions are mediated by the matrix (MA) domain, which contains a myristoyl group (myr) and a basic patch formed by lysine and arginine residues. For many retroviruses, Gag-PM interactions are mediated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]; however, previous studies suggested that HTLV-1 Gag-PM interactions and therefore virus assembly are less dependent on PI(4,5)P2. We have recently shown that PI(4,5)P2 binds directly to HTLV-1 unmyristoylated MA [myr(-)MA] and that myr(-)MA binding to membranes is significantly enhanced by inclusion of phosphatidylserine (PS) and PI(4,5)P2. Herein, we employed structural, biophysical, biochemical, mutagenesis, and cell-based assays to identify residues involved in MA-membrane interactions. Our data revealed that the lysine-rich motif (Lys47, Lys48, and Lys51) constitutes the primary PI(4,5)P2-binding site. Furthermore, we show that arginine residues 3, 7, 14 and 17 located in the unstructured N-terminus are essential for MA binding to membranes containing PS and/or PI(4,5)P2. Substitution of lysine and arginine residues severely attenuated virus-like particle production, but only the lysine residues could be clearly correlated with reduced PM binding. These results support a mechanism by which HTLV-1 Gag targeting to the PM is mediated by a trio engagement of the myr group, Arg-rich and Lys-rich motifs. These findings advance our understanding of a key step in retroviral particle assembly.
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Affiliation(s)
- Dominik Herrmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Heather M Hanson
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States
| | - Lynne W Zhou
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Rayna Addabbo
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Nora A Willkomm
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States
| | - Isaac Angert
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Joachim D Mueller
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States.
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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13
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Yadav M, Atala A, Lu B. Developing all-in-one virus-like particles for Cas9 mRNA/single guide RNA co-delivery and aptamer-containing lentiviral vectors for improved gene expression. Int J Biol Macromol 2022; 209:1260-1270. [PMID: 35461863 DOI: 10.1016/j.ijbiomac.2022.04.114] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/10/2023]
Abstract
Lentiviral vectors (LVs) are widely used for delivering foreign genes for long-term expression. Recently, virus-like particles (VLPs) were developed for mRNA or ribonucleoprotein (RNP) delivery for short-term endonuclease expression. Generating large amount of LVs or VLPs is challenging. On the other hand, methods for using VLPs to co-deliver Cas9 mRNA and single guide RNA (sgRNA) are limited. Fusing aptamer-binding protein (ABP) to the N-terminus of HIV Gag protein is currently the successful way to develop hybrid particles for co-delivering Cas9 mRNA and sgRNA. The effects of modifying Gag protein this way on particle assembly are unknown. Previously we found that adding an ABP after the second zinc finger domain of nucleocapsid (NC) protein had minimal effects on particle assembly. Based on these observations, here we developed hybrid particles for Cas9 mRNA and sgRNA co-delivery with normal capsid assembly efficiency. We further improved LVs for integrated gene expression by including an aptamer sequence in lentiviral genomic RNA, which improved lentiviral particle production and enhanced LV genomic RNA packaging. In summary, here we describe the development of new all-in-one VLPs for co-delivery of Cas9 mRNA and sgRNA, and new LVs for enhanced vector production and gene expression.
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Affiliation(s)
- Manish Yadav
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Baisong Lu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA.
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14
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Bernacchi S. Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview. Viruses 2022; 14:v14020324. [PMID: 35215917 PMCID: PMC8876502 DOI: 10.3390/v14020324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
Retroviruses must selectively recognize their unspliced RNA genome (gRNA) among abundant cellular and spliced viral RNAs to assemble into newly formed viral particles. Retroviral gRNA packaging is governed by Gag precursors that also orchestrate all the aspects of viral assembly. Retroviral life cycles, and especially the HIV-1 one, have been previously extensively analyzed by several methods, most of them based on molecular biology and biochemistry approaches. Despite these efforts, the spatio-temporal mechanisms leading to gRNA packaging and viral assembly are only partially understood. Nevertheless, in these last decades, progress in novel bioimaging microscopic approaches (as FFS, FRAP, TIRF, and wide-field microscopy) have allowed for the tracking of retroviral Gag and gRNA in living cells, thus providing important insights at high spatial and temporal resolution of the events regulating the late phases of the retroviral life cycle. Here, the implementation of these recent bioimaging tools based on highly performing strategies to label fluorescent macromolecules is described. This report also summarizes recent gains in the current understanding of the mechanisms employed by retroviral Gag polyproteins to regulate molecular mechanisms enabling gRNA packaging and the formation of retroviral particles, highlighting variations and similarities among the different retroviruses.
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Affiliation(s)
- Serena Bernacchi
- Architecture et Réactivité de l'ARN-UPR 9002, IBMC, CNRS, Université de Strasbourg, F-67000 Strasbourg, France
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15
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Zurowska K, Alam A, Ganser-Pornillos BK, Pornillos O. Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins. Proteins 2022; 90:309-313. [PMID: 34357660 PMCID: PMC8671222 DOI: 10.1002/prot.26204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 01/03/2023]
Abstract
The Gag proteins of retroviruses play an essential role in virus particle assembly by forming a protein shell or capsid and thus generating the virion compartment. A variety of human proteins have now been identified with structural similarity to one or more of the major Gag domains. These human proteins are thought to have been evolved or "domesticated" from ancient integrations due to retroviral infections or retrotransposons. Here, we report that X-ray crystal structures of stably folded domains of MOAP1 (modulator of apoptosis 1) and PEG10 (paternally expressed gene 10) are highly similar to the C-terminal capsid (CA) domains of cognate Gag proteins. The structures confirm classification of MOAP1 and PEG10 as domesticated Gags, and suggest that these proteins may have preserved some of the key interactions that facilitated assembly of their ancestral Gags into capsids.
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Affiliation(s)
- Katarzyna Zurowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ayaan Alam
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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16
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Durand S, Seigneuret F, Burlaud-Gaillard J, Lemoine R, Tassi MF, Moreau A, Mougel M, Roingeard P, Tauber C, de Rocquigny H. Quantitative analysis of the formation of nucleoprotein complexes between HIV-1 Gag protein and genomic RNA using transmission electron microscopy. J Biol Chem 2022; 298:101500. [PMID: 34929171 PMCID: PMC8760521 DOI: 10.1016/j.jbc.2021.101500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 01/06/2023] Open
Abstract
In HIV, the polyprotein precursor Gag orchestrates the formation of the viral capsid. In the current view of this viral assembly, Gag forms low-order oligomers that bind to the viral genomic RNA triggering the formation of high-ordered ribonucleoprotein complexes. However, this assembly model was established using biochemical or imaging methods that do not describe the cellular location hosting Gag-gRNA complex nor distinguish gRNA packaging in single particles. Here, we studied the intracellular localization of these complexes by electron microscopy and monitored the distances between the two partners by morphometric analysis of gold beads specifically labeling Gag and gRNA. We found that formation of these viral clusters occurred shortly after the nuclear export of the gRNA. During their transport to the plasma membrane, the distance between Gag and gRNA decreases together with an increase of gRNA packaging. Point mutations in the zinc finger patterns of the nucleocapsid domain of Gag caused an increase in the distance between Gag and gRNA as well as a sharp decrease of gRNA packaged into virions. Finally, we show that removal of stem loop 1 of the 5'-untranslated region does not interfere with gRNA packaging, whereas combined with the removal of stem loop 3 is sufficient to decrease but not abolish Gag-gRNA cluster formation and gRNA packaging. In conclusion, this morphometric analysis of Gag-gRNA cluster formation sheds new light on HIV-1 assembly that can be used to describe at nanoscale resolution other viral assembly steps involving RNA or protein-protein interactions.
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Affiliation(s)
- Stéphanie Durand
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Florian Seigneuret
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Julien Burlaud-Gaillard
- Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Roxane Lemoine
- B Cell Ressources Platform, EA4245 "Transplantation, Immunology and Inflammation", University of Tours, Tours Cedex 1, France
| | - Marc-Florent Tassi
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Alain Moreau
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Marylène Mougel
- Équipe R2D2 Retroviral RNA Dynamics and Delivery, IRIM, CNRS UMR9004, University of Montpellier, Montpellier, France
| | - Philippe Roingeard
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France; Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Clovis Tauber
- UMR U1253 iBrain, Inserm, University of Tours, Tours Cedex 1, France
| | - Hugues de Rocquigny
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France.
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17
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Balakrishnan K, Jaguva Vasudevan AA, Mohareer K, Luedde T, Münk C, Banerjee S. Encapsidation of Staufen-2 Enhances Infectivity of HIV-1. Viruses 2021; 13:v13122459. [PMID: 34960728 PMCID: PMC8703407 DOI: 10.3390/v13122459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
Staufen, the RNA-binding family of proteins, affects various steps in the Human Immuno-Deficiency Virus (HIV-1) replication cycle. While our previous study established Staufen-2–HIV-1 Rev interaction and its role in augmenting nucleocytoplasmic export of RRE-containing viral RNA, viral incorporation of Staufen-2 and its effect on viral propagation were unknown. Here, we report that Staufen-2 interacts with HIV-1 Gag and is incorporated into virions and that encapsidated Staufen-2 boosted viral infectivity. Further, Staufen-2 gets co-packaged into virions, possibly by interacting with host factors Staufen-1 or antiviral protein APOBEC3G, which resulted in different outcomes on the infectivity of Staufen-2-encapsidated virions. These observations suggest that encapsidated host factors influence viral population dynamics and infectivity. With the explicit identification of the incorporation of Staufen proteins into HIV-1 and other retroviruses, such as Simian Immunodeficiency Virus (SIV), we propose that packaging of RNA binding proteins, such as Staufen, in budding virions of retroviruses is probably a general phenomenon that can drive or impact the viral population dynamics, infectivity, and evolution.
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Affiliation(s)
- Kannan Balakrishnan
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India; (K.B.); (K.M.)
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
| | - Ananda Ayyappan Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
| | - Krishnaveni Mohareer
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India; (K.B.); (K.M.)
| | - Tom Luedde
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
- Correspondence: (C.M.); (S.B.); Tel.: +49-021-1811-0887 (C.M.); +91-40-2313-4573 (S.B.)
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India; (K.B.); (K.M.)
- Correspondence: (C.M.); (S.B.); Tel.: +49-021-1811-0887 (C.M.); +91-40-2313-4573 (S.B.)
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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19
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Chameettachal A, Vivet-Boudou V, Pitchai F, Pillai V, Ali L, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi T. A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag. Nucleic Acids Res 2021; 49:4668-4688. [PMID: 33836091 PMCID: PMC8096270 DOI: 10.1093/nar/gkab223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 12/22/2022] Open
Abstract
Retroviral RNA genome (gRNA) harbors cis-acting sequences that facilitate its specific packaging from a pool of other viral and cellular RNAs by binding with high-affinity to the viral Gag protein during virus assembly. However, the molecular intricacies involved during selective gRNA packaging are poorly understood. Binding and footprinting assays on mouse mammary tumor virus (MMTV) gRNA with purified Pr77Gag along with in cell gRNA packaging study identified two Pr77Gag binding sites constituting critical, non-redundant packaging signals. These included: a purine loop in a bifurcated stem-loop containing the gRNA dimerization initiation site, and the primer binding site (PBS). Despite these sites being present on both unspliced and spliced RNAs, Pr77Gag specifically bound to unspliced RNA, since only that could adopt the native bifurcated stem-loop structure containing looped purines. These results map minimum structural elements required to initiate MMTV gRNA packaging, distinguishing features that are conserved amongst divergent retroviruses from those perhaps unique to MMTV. Unlike purine-rich motifs frequently associated with packaging signals, direct involvement of PBS in gRNA packaging has not been documented in retroviruses. These results enhance our understanding of retroviral gRNA packaging/assembly, making it not only a target for novel therapeutic interventions, but also development of safer gene therapy vectors.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Anjana Krishnan
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
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20
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Hantak MP, Einstein J, Kearns RB, Shepherd JD. Intercellular Communication in the Nervous System Goes Viral. Trends Neurosci 2021; 44:248-259. [PMID: 33485691 PMCID: PMC8041237 DOI: 10.1016/j.tins.2020.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/19/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022]
Abstract
Viruses and transposable elements are major drivers of evolution and make up over half the sequences in the human genome. In some cases, these elements are co-opted to perform biological functions for the host. Recent studies made the surprising observation that the neuronal gene Arc forms virus-like protein capsids that can transfer RNA between neurons to mediate a novel intercellular communication pathway. Phylogenetic analyses showed that mammalian Arc is derived from an ancient retrotransposon of the Ty3/gypsy family and contains homology to the retroviral Gag polyproteins. The Drosophila Arc homologs, which are independently derived from the same family of retrotransposons, also mediate cell-to-cell signaling of RNA at the neuromuscular junction; a striking example of convergent evolution. Here we propose an Arc 'life cycle', based on what is known about retroviral Gag, and discuss how elucidating these biological processes may lead to novel insights into brain plasticity and memory.
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Affiliation(s)
- Michael P Hantak
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, USA
| | - Jenifer Einstein
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, USA
| | - Rachel B Kearns
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, USA
| | - Jason D Shepherd
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, USA.
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21
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Xiao P, Dienger-Stambaugh K, Chen X, Wei H, Phan S, Beavis AC, Singh K, Adhikary NRD, Tiwari P, Villinger F, He B, Spearman P. Parainfluenza Virus 5 Priming Followed by SIV/HIV Virus-Like-Particle Boosting Induces Potent and Durable Immune Responses in Nonhuman Primates. Front Immunol 2021; 12:623996. [PMID: 33717130 PMCID: PMC7946978 DOI: 10.3389/fimmu.2021.623996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022] Open
Abstract
The search for a preventive vaccine against HIV infection remains an ongoing challenge, indicating the need for novel approaches. Parainfluenza virus 5 (PIV5) is a paramyxovirus replicating in the upper airways that is not associated with any animal or human pathology. In animal models, PIV5-vectored vaccines have shown protection against influenza, RSV, and other human pathogens. Here, we generated PIV5 vaccines expressing HIV envelope (Env) and SIV Gag and administered them intranasally to macaques, followed by boosting with virus-like particles (VLPs) containing trimeric HIV Env. Moreover, we compared the immune responses generated by PIV5-SHIV prime/VLPs boost regimen in naïve vs a control group in which pre-existing immunity to the PIV5 vector was established. We demonstrate for the first time that intranasal administration of PIV5-based HIV vaccines is safe, well-tolerated and immunogenic, and that boosting with adjuvanted trimeric Env VLPs enhances humoral and cellular immune responses. The PIV5 prime/VLPs boost regimen induced robust and durable systemic and mucosal Env-specific antibody titers with functional activities including ADCC and neutralization. This regimen also induced highly polyfunctional antigen-specific T cell responses. Importantly, we show that diminished responses due to PIV5 pre-existing immunity can be overcome in part with VLP protein boosts. Overall, these results establish that PIV5-based HIV vaccine candidates are promising and warrant further investigation including moving on to primate challenge studies.
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MESH Headings
- AIDS Vaccines/administration & dosage
- AIDS Vaccines/genetics
- AIDS Vaccines/immunology
- Administration, Intranasal
- Animals
- Antibodies, Viral/blood
- Cattle
- Cell Line
- Gene Products, gag/administration & dosage
- Gene Products, gag/genetics
- Gene Products, gag/immunology
- HIV-1/genetics
- HIV-1/immunology
- Host-Pathogen Interactions
- Immunity, Cellular
- Immunity, Humoral
- Immunity, Mucosal
- Immunogenicity, Vaccine
- Macaca mulatta
- Male
- Nasal Mucosa/immunology
- Nasal Mucosa/virology
- Parainfluenza Virus 5/genetics
- Parainfluenza Virus 5/immunology
- Simian Immunodeficiency Virus/genetics
- Simian Immunodeficiency Virus/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/virology
- Vaccination
- Vaccines, DNA/administration & dosage
- Vaccines, DNA/immunology
- Virion/genetics
- Virion/immunology
- env Gene Products, Human Immunodeficiency Virus/administration & dosage
- env Gene Products, Human Immunodeficiency Virus/genetics
- env Gene Products, Human Immunodeficiency Virus/immunology
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Affiliation(s)
- Peng Xiao
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, United States
| | - Krista Dienger-Stambaugh
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and University of Cincinnati, Cincinnati, OH, United States
| | - Xuemin Chen
- Division of Infectious Diseases, Emory University, Atlanta, GA, United States
| | - Huiling Wei
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Shannon Phan
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Ashley C. Beavis
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Karnail Singh
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and University of Cincinnati, Cincinnati, OH, United States
| | - Nihar R. Deb Adhikary
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, United States
| | - Pooja Tiwari
- Wallace H Coulter Department of Bioengineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Francois Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, United States
| | - Biao He
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Paul Spearman
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and University of Cincinnati, Cincinnati, OH, United States
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22
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Sumner RP, Harrison L, Touizer E, Peacock TP, Spencer M, Zuliani‐Alvarez L, Towers GJ. Disrupting HIV-1 capsid formation causes cGAS sensing of viral DNA. EMBO J 2020; 39:e103958. [PMID: 32852081 PMCID: PMC7560218 DOI: 10.15252/embj.2019103958] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 01/28/2023] Open
Abstract
Detection of viral DNA by cyclic GMP-AMP synthase (cGAS) is a first line of defence leading to the production of type I interferon (IFN). As HIV-1 replication is not a strong inducer of IFN, we hypothesised that an intact capsid physically cloaks viral DNA from cGAS. To test this, we generated defective viral particles by treatment with HIV-1 protease inhibitors or by genetic manipulation of gag. These viruses had defective Gag cleavage, reduced infectivity and diminished capacity to saturate TRIM5α. Importantly, unlike wild-type HIV-1, infection with cleavage defective HIV-1 triggered an IFN response in THP-1 cells that was dependent on viral DNA and cGAS. An IFN response was also observed in primary human macrophages infected with cleavage defective viruses. Infection in the presence of the capsid destabilising small molecule PF-74 also induced a cGAS-dependent IFN response. These data demonstrate a protective role for capsid and suggest that antiviral activity of capsid- and protease-targeting antivirals may benefit from enhanced innate and adaptive immunity in vivo.
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Affiliation(s)
- Rebecca P Sumner
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Lauren Harrison
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Emma Touizer
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Thomas P Peacock
- Division of Infection and ImmunityUniversity College LondonLondonUK
- Present address:
Department of MedicineImperial College LondonLondonUK
| | - Matthew Spencer
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | | | - Greg J Towers
- Division of Infection and ImmunityUniversity College LondonLondonUK
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23
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Donhauser N, Socher E, Millen S, Heym S, Sticht H, Thoma-Kress AK. Transfer of HTLV-1 p8 and Gag to target T-cells depends on VASP, a novel interaction partner of p8. PLoS Pathog 2020; 16:e1008879. [PMID: 32997728 PMCID: PMC7526893 DOI: 10.1371/journal.ppat.1008879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
The Human T-cell leukemia virus type 1 (HTLV-1) orf I-encoded accessory protein p8 is cleaved from its precursor p12, and both proteins contribute to viral persistence. p8 induces cellular protrusions, which are thought to facilitate transfer of p8 to target cells and virus transmission. Host factors interacting with p8 and mediating p8 transfer are unknown. Here, we report that vasodilator-stimulated phosphoprotein (VASP), which promotes actin filament elongation, is a novel interaction partner of p8 and important for p8 and HTLV-1 Gag cell-to-cell transfer. VASP contains an Ena/VASP homology 1 (EVH1) domain that targets the protein to focal adhesions. Bioinformatics identified a short stretch in p8 (amino acids (aa) 24–45) which may mediate interactions with the EVH1 domain of VASP. Co-immunoprecipitations confirmed interactions of VASP:p8 in 293T, Jurkat and HTLV-1-infected MT-2 cells. Co-precipitation of VASP:p8 could be significantly blocked by peptides mimicking aa 26–37 of p8. Mutational studies revealed that the EVH1-domain of VASP is necessary, but not sufficient for the interaction with p8. Further, deletion of the VASP G- and F-actin binding domains significantly diminished co-precipitation of p8. Imaging identified areas of partial co-localization of VASP with p8 at the plasma membrane and in protrusive structures, which was confirmed by proximity ligation assays. Co-culture experiments revealed that p8 is transferred between Jurkat T-cells via VASP-containing conduits. Imaging and flow cytometry revealed that repression of both endogenous and overexpressed VASP by RNA interference or by CRISPR/Cas9 reduced p8 transfer to the cell surface and to target Jurkat T-cells. Stable repression of VASP by RNA interference in chronically infected MT-2 cells impaired both p8 and HTLV-1 Gag transfer to target Jurkat T-cells, while virus release was unaffected. Thus, we identified VASP as a novel interaction partner of p8, which is important for transfer of HTLV-1 p8 and Gag to target T-cells. The delta-retrovirus Human T-cell leukemia virus type 1 encodes the accessory protein p8, which is generated by proteolytic cleavage from p12. Earlier work has shown that p8 enhances the formation of cellular conduits between T-cells, is transferred through these conduits to target T-cells and increases HTLV-1 transmission. It was suggested that p8 dampens T-cell responses in target T-cells, thus facilitating HTLV-1 infection. Our work sheds light on the mechanism of p8 transfer to target T-cells. We show that vasodilator-stimulated phosphoprotein (VASP), a novel interaction partner of p8, contributes to transfer of p8 to target T-cells. Mechanistically, VASP is crucial for recruitment of p8 to the cell surface. Since VASP is known to promote elongation of actin filaments by preventing them from capping, interactions of p8 with VASP are an elegant strategy to exploit the host cell machinery for being transported to the cell surface, and as a consequence, to other cells. Given that VASP is also important for cell-to-cell transfer of the HTLV-1 Gag protein, our work proposes that VASP is a new cellular target to counteract HTLV-1 cell-to-cell transmission.
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Affiliation(s)
- Norbert Donhauser
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Eileen Socher
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sebastian Millen
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Stefanie Heym
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andrea K. Thoma-Kress
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- * E-mail:
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24
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Brown JB, Summers HR, Brown LA, Marchant J, Canova PN, O'Hern CT, Abbott ST, Nyaunu C, Maxwell S, Johnson T, Moser MB, Ablan SD, Carter H, Freed EO, Summers MF. Structural and Mechanistic Studies of the Rare Myristoylation Signal of the Feline Immunodeficiency Virus. J Mol Biol 2020; 432:4076-4091. [PMID: 32442659 PMCID: PMC7316625 DOI: 10.1016/j.jmb.2020.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
All retroviruses encode a Gag polyprotein containing an N-terminal matrix domain (MA) that anchors Gag to the plasma membrane and recruits envelope glycoproteins to virus assembly sites. Membrane binding by the Gag protein of HIV-1 and most other lentiviruses is dependent on N-terminal myristoylation of MA by host N-myristoyltransferase enzymes (NMTs), which recognize a six-residue "myristoylation signal" with consensus sequence: M1GXXX[ST]. For unknown reasons, the feline immunodeficiency virus (FIV), which infects both domestic and wild cats, encodes a non-consensus myristoylation sequence not utilized by its host or by other mammals (most commonly: M1GNGQG). To explore the evolutionary basis for this sequence, we compared the structure, dynamics, and myristoylation properties of native FIV MA with a mutant protein containing a consensus feline myristoylation motif (MANOS) and examined the impact of MA mutations on virus assembly and ability to support spreading infection. Unexpectedly, myristoylation efficiency of MANOS in Escherichia coli by co-expressed mammalian NMT was reduced by ~70% compared to the wild-type protein. NMR studies revealed that residues of the N-terminal myristoylation signal are fully exposed and mobile in the native protein but partially sequestered in the MANOS chimera, suggesting that the unusual FIV sequence is conserved to promote exposure and efficient myristoylation of the MA N terminus. In contrast, virus assembly studies indicate that the MANOS mutation does not affect virus assembly, but does prevent virus spread, in feline kidney cells. Our findings indicate that residues of the FIV myristoylation sequence play roles in replication beyond NMT recognition and Gag-membrane binding.
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Affiliation(s)
- Janae B Brown
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Holly R Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Lola A Brown
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Jan Marchant
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Paige N Canova
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Colin T O'Hern
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Sophia T Abbott
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Constance Nyaunu
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Simon Maxwell
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Talayah Johnson
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Morgan B Moser
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Sherimay D Ablan
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, National Cancer Institute at Fredrick, Fredrick, MD 21702-1201, USA
| | - Hannah Carter
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, National Cancer Institute at Fredrick, Fredrick, MD 21702-1201, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, National Cancer Institute at Fredrick, Fredrick, MD 21702-1201, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
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25
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Arunachalam PS, Charles TP, Joag V, Bollimpelli VS, Scott MKD, Wimmers F, Burton SL, Labranche CC, Petitdemange C, Gangadhara S, Styles TM, Quarnstrom CF, Walter KA, Ketas TJ, Legere T, Jagadeesh Reddy PB, Kasturi SP, Tsai A, Yeung BZ, Gupta S, Tomai M, Vasilakos J, Shaw GM, Kang CY, Moore JP, Subramaniam S, Khatri P, Montefiori D, Kozlowski PA, Derdeyn CA, Hunter E, Masopust D, Amara RR, Pulendran B. T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers. Nat Med 2020; 26:932-940. [PMID: 32393800 PMCID: PMC7303014 DOI: 10.1038/s41591-020-0858-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/27/2020] [Indexed: 01/05/2023]
Abstract
Recent efforts toward an HIV vaccine focus on inducing broadly neutralizing antibodies, but eliciting both neutralizing antibodies (nAbs) and cellular responses may be superior. Here, we immunized macaques with an HIV envelope trimer, either alone to induce nAbs, or together with a heterologous viral vector regimen to elicit nAbs and cellular immunity, including CD8+ tissue-resident memory T cells. After ten vaginal challenges with autologous virus, protection was observed in both vaccine groups at 53.3% and 66.7%, respectively. A nAb titer >300 was generally associated with protection but in the heterologous viral vector + nAb group, titers <300 were sufficient. In this group, protection was durable as the animals resisted six more challenges 5 months later. Antigen stimulation of T cells in ex vivo vaginal tissue cultures triggered antiviral responses in myeloid and CD4+ T cells. We propose that cellular immune responses reduce the threshold of nAbs required to confer superior and durable protection.
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MESH Headings
- Animals
- Antibodies, Neutralizing/drug effects
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/drug effects
- Antibodies, Viral/immunology
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- Female
- Gene Products, gag/genetics
- Gene Products, gag/immunology
- Genetic Vectors
- Immunity, Cellular/drug effects
- Immunity, Cellular/immunology
- Immunity, Heterologous
- Immunogenicity, Vaccine
- Immunologic Memory/immunology
- Macaca mulatta
- Mucous Membrane
- SAIDS Vaccines/pharmacology
- Simian Acquired Immunodeficiency Syndrome/prevention & control
- Simian Immunodeficiency Virus/immunology
- Vagina
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Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Tysheena P Charles
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Vineet Joag
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Venkata S Bollimpelli
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Madeleine K D Scott
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Samantha L Burton
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Celia C Labranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Caroline Petitdemange
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
- HIV Inflammation and Persistence Unit, Institut Pasteur, Paris, France
| | - Sailaja Gangadhara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Tiffany M Styles
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Clare F Quarnstrom
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Korey A Walter
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Traci Legere
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Pradeep Babu Jagadeesh Reddy
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
- Pfizer, Andover, MA, USA
| | - Sudhir Pai Kasturi
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | | | | | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Mark Tomai
- 3M Corporate Research and Materials Lab, Saint Paul, MN, USA
| | | | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chil-Yong Kang
- Department of Microbiology and Immunology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Cynthia A Derdeyn
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA.
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA.
| | - David Masopust
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA.
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA.
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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26
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Virnik K, Rosati M, Medvedev A, Scanlan A, Walsh G, Dayton F, Broderick KE, Lewis M, Bryson Y, Lifson JD, Ruprecht RM, Felber BK, Berkower I. Immunotherapy with DNA vaccine and live attenuated rubella/SIV gag vectors plus early ART can prevent SIVmac251 viral rebound in acutely infected rhesus macaques. PLoS One 2020; 15:e0228163. [PMID: 32130229 PMCID: PMC7055890 DOI: 10.1371/journal.pone.0228163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 01/29/2023] Open
Abstract
Anti-retroviral therapy (ART) has been highly successful in controlling HIV replication, reducing viral burden, and preventing both progression to AIDS and viral transmission. Yet, ART alone cannot cure the infection. Even after years of successful therapy, ART withdrawal leads inevitably to viral rebound within a few weeks or months. Our hypothesis: effective therapy must control both the replicating virus pool and the reactivatable latent viral reservoir. To do this, we have combined ART and immunotherapy to attack both viral pools simultaneously. The vaccine regimen consisted of DNA vaccine expressing SIV Gag, followed by a boost with live attenuated rubella/gag vectors. The vectors grow well in rhesus macaques, and they are potent immunogens when used in a prime and boost strategy. We infected rhesus macaques by high dose mucosal challenge with virulent SIVmac251 and waited three days to allow viral dissemination and establishment of a reactivatable viral reservoir before starting ART. While on ART, the control group received control DNA and empty rubella vaccine, while the immunotherapy group received DNA/gag prime, followed by boosts with rubella vectors expressing SIV gag over 27 weeks. Both groups had a vaccine "take" to rubella, and the vaccine group developed antibodies and T cells specific for Gag. Five weeks after the last immunization, we stopped ART and monitored virus rebound. All four control animals eventually had a viral rebound, and two were euthanized for AIDS. One control macaque did not rebound until 2 years after ART release. In contrast, there was only one viral rebound in the vaccine group. Three out of four vaccinees had no viral rebound, even after CD8 depletion, and they remain in drug-free viral remission more than 2.5 years later. The strategy of early ART combined with immunotherapy can produce a sustained SIV remission in macaques and may be relevant for immunotherapy of HIV in humans.
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Affiliation(s)
- Konstantin Virnik
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Margherita Rosati
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Alexei Medvedev
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Aaron Scanlan
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Gabrielle Walsh
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Frances Dayton
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Kate E. Broderick
- Inovio Pharmaceuticals, Inc., Plymouth Meeting, Pennsylvania, United States of America
| | - Mark Lewis
- BioQual, Inc., Rockville, Maryland, United States of America
| | - Yvonne Bryson
- Department of Pediatrics, Division of Infectious Disease, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ruth M. Ruprecht
- University of Louisiana at Lafayette, New Iberia Research Center, New Iberia, Louisiana, United States of America
| | - Barbara K. Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Ira Berkower
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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27
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Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FKM. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLoS Pathog 2020; 16:e1008277. [PMID: 31986188 PMCID: PMC7004409 DOI: 10.1371/journal.ppat.1008277] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/06/2020] [Accepted: 12/11/2019] [Indexed: 01/11/2023] Open
Abstract
Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.
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MESH Headings
- Amino Acid Sequence
- Animals
- Electron Microscope Tomography
- Equine Infectious Anemia/metabolism
- Equine Infectious Anemia/virology
- Gene Products, gag/chemistry
- Gene Products, gag/genetics
- Gene Products, gag/metabolism
- HIV Infections/metabolism
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/physiology
- HIV-1/ultrastructure
- Horses
- Host-Pathogen Interactions
- Infectious Anemia Virus, Equine/chemistry
- Infectious Anemia Virus, Equine/genetics
- Infectious Anemia Virus, Equine/physiology
- Infectious Anemia Virus, Equine/ultrastructure
- Phytic Acid/metabolism
- Sequence Alignment
- Virion/genetics
- Virion/physiology
- Virion/ultrastructure
- Virus Assembly
- gag Gene Products, Human Immunodeficiency Virus/chemistry
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Robert A. Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (RAD); (FKMS)
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - Dustin R. Morado
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Clifton L. Ricana
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Terri D. Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Arianna M. Broad
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - J. Ryan Feathers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Marc C. Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Volker M. Vogt
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - John A. G. Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Florian K. M. Schur
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail: (RAD); (FKMS)
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Kodidela S, Wang Y, Patters BJ, Gong Y, Sinha N, Ranjit S, Gerth K, Haque S, Cory T, McArthur C, Kumar A, Wan JY, Kumar S. Proteomic Profiling of Exosomes Derived from Plasma of HIV-Infected Alcohol Drinkers and Cigarette Smokers. J Neuroimmune Pharmacol 2019; 15:501-519. [PMID: 31065972 DOI: 10.1007/s11481-019-09853-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/10/2019] [Indexed: 12/12/2022]
Abstract
Abuse of alcohol and tobacco could exacerbate HIV pathogenesis by transferring materials through exosomes (small nanovesicles). Exosomes present a stable and accessible source of information concerning the health and/or disease status of patients, which can provide diagnostic and prognostic biomarkers for myriad conditions. Therefore, we aimed to study the specific exosomal proteins that are altered in both HIV-infected subjects and alcohol/tobacco users. Exosomes were isolated from plasma of the following subjects: a) HIV-negative subjects (healthy), b) HIV-positive subjects (HIV), c) HIV-negative alcohol drinkers (drinkers), d) HIV-negative tobacco smokers (smokers), e) HIV-positive drinkers (HIV + drinkers), and f) HIV-positive smokers (HIV + smokers). Quantitative proteomic profiling was then performed from these exosomes. Sixteen proteins were significantly altered in the HIV group, ten in drinkers, four in HIV + drinkers, and fifteen in smokers compared to healthy subjects. Only one protein, fibulin-1 (FBLN1), was significantly altered in HIV + smokers. Interestingly, hemopexin was not significantly altered in drinkers or HIV patients but was significantly altered in HIV + drinkers. Further, our study is the first to show properdin expression in plasma exosomes, which was decreased in HIV + smokers and HIV + drinkers compared to HIV patients. The present findings suggest that hemopexin and properdin show potential as markers for physiological effects that may arise in HIV-infected individuals who abuse alcohol and tobacco. Graphical abstract This study presents a proteomic analysis of plasma-derived exosomes from HIV-infected alcohol drinkers and smokers. Among the proteins altered due to drug-abuse, hemopexin and properdin were of highest significance. These proteins can be potential biomarkers for co-morbid conditions associated with drug abuse in HIV-patients.
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Affiliation(s)
- Sunitha Kodidela
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Yujie Wang
- Department of Pharmacy, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mo He Road, Shanghai, 201999, China
| | - Benjamin J Patters
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Yuqing Gong
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Namita Sinha
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Sabina Ranjit
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Kelli Gerth
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Sanjana Haque
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Theodore Cory
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA
| | - Carole McArthur
- Department of Oral and Craniofacial Science, School of Dentistry, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Anil Kumar
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Jim Y Wan
- Division of Biostatistics, Department of Preventive Medicine, University of Tennessee Health Science Center College of Medicine, Memphis, TN, USA
| | - Santosh Kumar
- College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN, 38163, USA.
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Abed M, Verschueren E, Budayeva H, Liu P, Kirkpatrick DS, Reja R, Kummerfeld SK, Webster JD, Gierke S, Reichelt M, Anderson KR, Newman RJ, Roose-Girma M, Modrusan Z, Pektas H, Maltepe E, Newton K, Dixit VM. The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification. PLoS One 2019; 14:e0214110. [PMID: 30951545 PMCID: PMC6450627 DOI: 10.1371/journal.pone.0214110] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023] Open
Abstract
Peg10 (paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotransposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiating TSCs was bound to many cellular RNAs including Hbegf (Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression of Hbegf was reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.
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Affiliation(s)
- Mona Abed
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Erik Verschueren
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Hanna Budayeva
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Peter Liu
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Donald S. Kirkpatrick
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Rohit Reja
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah K. Kummerfeld
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Joshua D. Webster
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah Gierke
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Mike Reichelt
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Keith R. Anderson
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Robert J. Newman
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Merone Roose-Girma
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Zora Modrusan
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Hazal Pektas
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Emin Maltepe
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Kim Newton
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Vishva M. Dixit
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
- * E-mail:
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30
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Colitti B, Coradduzza E, Puggioni G, Capucchio MT, Reina R, Bertolotti L, Rosati S. A new approach for Small Ruminant Lentivirus full genome characterization revealed the circulation of divergent strains. PLoS One 2019; 14:e0212585. [PMID: 30789950 PMCID: PMC6383919 DOI: 10.1371/journal.pone.0212585] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/05/2019] [Indexed: 11/18/2022] Open
Abstract
Small Ruminant Lentiviruses (SRLV) include at least 4 viral highly divergent genotypes. Genotypes A and B are widely distributed and genotypes C and E have been recognized in restricted geographic areas. New phylogroups have been identified targeting conserved regions. However, this approach suffers from the potential risk to misamplify highly divergent strains. Pathogenic strains are easily adapted to fibroblastic cells, but non-pathogenic strains isolation may require a different approach. We developed a fast and effective method for SRLV full genome characterization after cell culture isolation. Spleen samples were collected during regular slaughter from sheep and goats in northwestern Italy. Spleen-derived macrophage cultures were monitored for reverse transcriptase activity and RNA was extracted from the supernatant of positive cultures. Using Illumina MiSeq platform 22 new full genome sequences were obtained. The success of this approach is based on the following features: spleen is one of the main target for SRLV persistence; red pulp is a reserve of resident macrophages, the main target for SRLV replication in vivo; RTA is a sensitive assay for any replicating retrovirus; de novo sequencing do not require genetic knowledge in advance.
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Affiliation(s)
- Barbara Colitti
- University of Turin, Dept. Veterinary Science, Grugliasco, Torino, Italy
| | | | | | | | - Ramsés Reina
- Institute of Agrobiotechnology (CSIC-UPNA-Government of Navarra), Navarra, Spain
| | - Luigi Bertolotti
- University of Turin, Dept. Veterinary Science, Grugliasco, Torino, Italy
- * E-mail:
| | - Sergio Rosati
- University of Turin, Dept. Veterinary Science, Grugliasco, Torino, Italy
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31
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Sakuragi S, Shioda T, Sakuragi JI. Relationship between genome packaging and Gag translation/AUG of primate lentiviruses. Microbes Infect 2018; 21:119-123. [PMID: 30292880 DOI: 10.1016/j.micinf.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 11/30/2022]
Abstract
About the relationship between retroviral genome packaging and translation, three possible modes (random-, trans-, and cis-) of packaging process could be assumed. In this report, we developed an assay system based on the RT-qPCR to measure the packaging efficiency of primate lentiviruses. With this system, we analyzed the genome packaging modes of primate lentiviruses such as HIV-1, 2, SIVmac and SIVagm. The data suggested that the modes of all viruses analyzed were very similar. In addition, we observed that the Gag-AUG sequences of them played important roles for maintaining efficient packaging, other than the initiation of translation.
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Affiliation(s)
- Sayuri Sakuragi
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jun-Ichi Sakuragi
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
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32
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Roychoudhury P, De Silva Feelixge H, Reeves D, Mayer BT, Stone D, Schiffer JT, Jerome KR. Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir. BMC Biol 2018; 16:75. [PMID: 29996827 PMCID: PMC6040082 DOI: 10.1186/s12915-018-0544-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 06/21/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND RNA-guided CRISPR/Cas9 systems can be designed to mutate or excise the integrated HIV genome from latently infected cells and have therefore been proposed as a curative approach for HIV. However, most studies to date have focused on molecular clones with ideal target site recognition and do not account for target site variability observed within and between patients. For clinical success and broad applicability, guide RNA (gRNA) selection must account for circulating strain diversity and incorporate the within-host diversity of HIV. RESULTS We identified a set of gRNAs targeting HIV LTR, gag, and pol using publicly available sequences for these genes and ranked gRNAs according to global conservation across HIV-1 group M and within subtypes A-C. By considering paired and triplet combinations of gRNAs, we found triplet sets of target sites such that at least one of the gRNAs in the set was present in over 98% of all globally available sequences. We then selected 59 gRNAs from our list of highly conserved LTR target sites and evaluated in vitro activity using a loss-of-function LTR-GFP fusion reporter. We achieved efficient GFP knockdown with multiple gRNAs and found clustering of highly active gRNA target sites near the middle of the LTR. Using published deep-sequence data from HIV-infected patients, we found that globally conserved sites also had greater within-host target conservation. Lastly, we developed a mathematical model based on varying distributions of within-host HIV sequence diversity and enzyme efficacy. We used the model to estimate the number of doses required to deplete the latent reservoir and achieve functional cure thresholds. Our modeling results highlight the importance of within-host target site conservation. While increased doses may overcome low target cleavage efficiency, inadequate targeting of rare strains is predicted to lead to rebound upon cART cessation even with many doses. CONCLUSIONS Target site selection must account for global and within host viral genetic diversity. Globally conserved target sites are good starting points for design, but multiplexing is essential for depleting quasispecies and preventing viral load rebound upon therapy cessation.
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Affiliation(s)
| | | | - Daniel Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Bryan T Mayer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
- Department of Medicine, University of Washington, Seattle, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
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33
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Paris J, Tobaly-Tapiero J, Giron ML, Burlaud-Gaillard J, Buseyne F, Roingeard P, Lesage P, Zamborlini A, Saïb A. The invariant arginine within the chromatin-binding motif regulates both nucleolar localization and chromatin binding of Foamy virus Gag. Retrovirology 2018; 15:48. [PMID: 29996845 PMCID: PMC6042332 DOI: 10.1186/s12977-018-0428-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/25/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Nuclear localization of Gag is a property shared by many retroviruses and retrotransposons. The importance of this stage for retroviral replication is still unknown, but studies on the Rous Sarcoma virus indicate that Gag might select the viral RNA genome for packaging in the nucleus. In the case of Foamy viruses, genome encapsidation is mediated by Gag C-terminal domain (CTD), which harbors three clusters of glycine and arginine residues named GR boxes (GRI-III). In this study we investigated how PFV Gag subnuclear distribution might be regulated. RESULTS We show that the isolated GRI and GRIII boxes act as nucleolar localization signals. In contrast, both the entire Gag CTD and the isolated GRII box, which contains the chromatin-binding motif, target the nucleolus exclusively upon mutation of the evolutionary conserved arginine residue at position 540 (R540), which is a key determinant of FV Gag chromatin tethering. We also provide evidence that Gag localizes in the nucleolus during FV replication and uncovered that the viral protein interacts with and is methylated by Protein Arginine Methyltransferase 1 (PRMT1) in a manner that depends on the R540 residue. Finally, we show that PRMT1 depletion by RNA interference induces the concentration of Gag C-terminus in nucleoli. CONCLUSION Altogether, our findings suggest that methylation by PRMT1 might finely tune the subnuclear distribution of Gag depending on the stage of the FV replication cycle. The role of this step for viral replication remains an open question.
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Affiliation(s)
- Joris Paris
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Joëlle Tobaly-Tapiero
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Marie-Lou Giron
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Julien Burlaud-Gaillard
- Plateforme IBiSA de Microscopie Electronique, Université François Rabelais and CHRU de Tours, Tours, France
- INSERM U1259, Université François Rabelais and CHRU de Tours, Tours, France
| | - Florence Buseyne
- Institut Pasteur, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
- CNRS UMR3569, Insitut Pasteur, Paris, France
| | - Philippe Roingeard
- Plateforme IBiSA de Microscopie Electronique, Université François Rabelais and CHRU de Tours, Tours, France
- INSERM U1259, Université François Rabelais and CHRU de Tours, Tours, France
| | - Pascale Lesage
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Alessia Zamborlini
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Laboratoire PVM, Conservatoire National des Arts et Métiers (Cnam), Paris, France
| | - Ali Saïb
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Wanaguru M, Barry DJ, Benton DJ, O’Reilly NJ, Bishop KN. Murine leukemia virus p12 tethers the capsid-containing pre-integration complex to chromatin by binding directly to host nucleosomes in mitosis. PLoS Pathog 2018; 14:e1007117. [PMID: 29906285 PMCID: PMC6021111 DOI: 10.1371/journal.ppat.1007117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/27/2018] [Accepted: 05/22/2018] [Indexed: 12/31/2022] Open
Abstract
The murine leukaemia virus (MLV) Gag cleavage product, p12, is essential for both early and late steps in viral replication. The N-terminal domain of p12 binds directly to capsid (CA) and stabilises the mature viral core, whereas defects in the C-terminal domain (CTD) of p12 can be rescued by addition of heterologous chromatin binding sequences (CBSs). We and others hypothesised that p12 tethers the pre-integration complex (PIC) to host chromatin ready for integration. Using confocal microscopy, we have observed for the first time that CA localises to mitotic chromatin in infected cells in a p12-dependent manner. GST-tagged p12 alone, however, did not localise to chromatin and mass-spectrometry analysis of its interactions identified only proteins known to bind the p12 region of Gag. Surprisingly, the ability to interact with chromatin was conferred by a single amino acid change, M63I, in the p12 CTD. Interestingly, GST-p12_M63I showed increased phosphorylation in mitosis relative to interphase, which correlated with an increased interaction with mitotic chromatin. Mass-spectrometry analysis of GST-p12_M63I revealed nucleosomal histones as primary interactants. Direct binding of MLV p12_M63I peptides to histones was confirmed by biolayer-interferometry (BLI) assays using highly-avid recombinant poly-nucleosomal arrays. Excitingly, using this method, we also observed binding between MLV p12_WT and nucleosomes. Nucleosome binding was additionally detected with p12 orthologs from feline and gibbon ape leukemia viruses using both pull-down and BLI assays, indicating that this a common feature of gammaretroviral p12 proteins. Importantly, p12 peptides were able to block the binding of the prototypic foamy virus CBS to nucleosomes and vice versa, implying that their docking sites overlap and suggesting a conserved mode of chromatin tethering for different retroviral genera. We propose that p12 is acting in a similar capacity to CPSF6 in HIV-1 infection by facilitating initial chromatin targeting of CA-containing PICs prior to integration.
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Affiliation(s)
- Madushi Wanaguru
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David J. Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, United Kingdom
| | - Donald J. Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Kate N. Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
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35
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Reed JC, Westergreen N, Barajas BC, Ressler DTB, Phuong DJ, Swain JV, Lingappa VR, Lingappa JR. Formation of RNA Granule-Derived Capsid Assembly Intermediates Appears To Be Conserved between Human Immunodeficiency Virus Type 1 and the Nonprimate Lentivirus Feline Immunodeficiency Virus. J Virol 2018; 92:e01761-17. [PMID: 29467316 PMCID: PMC5899207 DOI: 10.1128/jvi.01761-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/14/2018] [Indexed: 01/18/2023] Open
Abstract
During immature capsid assembly in cells, human immunodeficiency virus type 1 (HIV-1) Gag co-opts a host RNA granule, forming a pathway of intracellular assembly intermediates containing host components, including two cellular facilitators of assembly, ABCE1 and DDX6. A similar assembly pathway has been observed for other primate lentiviruses. Here we asked whether feline immunodeficiency virus (FIV), a nonprimate lentivirus, also forms RNA granule-derived capsid assembly intermediates. First, we showed that the released FIV immature capsid and a large FIV Gag-containing intracellular complex are unstable during analysis, unlike for HIV-1. We identified harvest conditions, including in situ cross-linking, that overcame this problem, revealing a series of FIV Gag-containing complexes corresponding in size to HIV-1 assembly intermediates. Previously, we showed that assembly-defective HIV-1 Gag mutants are arrested at specific assembly intermediates; here we identified four assembly-defective FIV Gag mutants, including three not previously studied, and demonstrated that they appear to be arrested at the same intermediate as the cognate HIV-1 mutants. Further evidence that these FIV Gag-containing complexes correspond to assembly intermediates came from coimmunoprecipitations demonstrating that endogenous ABCE1 and the RNA granule protein DDX6 are associated with FIV Gag, as shown previously for HIV-1 Gag, but are not associated with a ribosomal protein, at steady state. Additionally, we showed that FIV Gag associates with another RNA granule protein, DCP2. Finally, we validated the FIV Gag-ABCE1 and FIV Gag-DCP2 interactions with proximity ligation assays demonstrating colocalization in situ Together, these data support a model in which primate and nonprimate lentiviruses form intracellular capsid assembly intermediates derived from nontranslating host RNA granules.IMPORTANCE Like HIV-1 Gag, FIV Gag assembles into immature capsids; however, it is not known whether FIV Gag progresses through a pathway of immature capsid assembly intermediates derived from host RNA granules, as shown for HIV-1 Gag. Here we showed that FIV Gag forms complexes that resemble HIV-1 capsid assembly intermediates in size and in their association with ABCE1 and DDX6, two host facilitators of HIV-1 immature capsid assembly that are found in HIV-1 assembly intermediates. Our studies also showed that known and novel assembly-defective FIV Gag mutants fail to progress past putative intermediates in a pattern resembling that observed for HIV-1 Gag mutants. Finally, we used imaging to demonstrate colocalization of FIV Gag with ABCE1 and with the RNA granule protein DCP2. Thus, we conclude that formation of assembly intermediates derived from host RNA granules is likely conserved between primate and nonprimate lentiviruses and could provide targets for future antiviral strategies.
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Affiliation(s)
| | | | - Brook C Barajas
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Daryl J Phuong
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - John V Swain
- Prosetta Biosciences, San Francisco, California, USA
| | | | - Jaisri R Lingappa
- Department of Global Health, University of Washington, Seattle, Washington, USA
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Renner TM, Bélanger K, Lam C, Gerpe MCR, McBane JE, Langlois MA. Full-Length Glycosylated Gag of Murine Leukemia Virus Can Associate with the Viral Envelope as a Type I Integral Membrane Protein. J Virol 2018; 92:e01530-17. [PMID: 29298890 PMCID: PMC5827372 DOI: 10.1128/jvi.01530-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/20/2017] [Indexed: 11/20/2022] Open
Abstract
The glycosylated Gag protein (gPr80) of murine leukemia viruses (MLVs) has been shown to exhibit multiple roles in facilitating retrovirus release, infection, and resistance to host-encoded retroviral restriction factors, such as APOBEC3, SERINC3, and SERINC5. One way in which gPr80 helps MLVs to escape host innate immune restriction is by increasing capsid stability, a feature that protects viral replication intermediates from being detected by cytosolic DNA sensors. gPr80 also increases the resistance of MLVs to deamination and restriction by mouse APOBEC3 (mA3). How the gPr80 accessory protein, with its three N-linked glycosylation sites, contributes to these resistance mechanisms is still not fully understood. Here we further characterized the function of gPr80 and, more specifically, revealed that the asparagines targeted for glycosylation in gPr80 also contribute to capsid stability through their parallel involvement in the Pr65 Gag structural polyprotein. In fact, we demonstrate that sensitivity to deamination by the mA3 and human A3 proteins is directly linked to capsid stability. We also show that full-length gPr80 is detected in purified viruses. However, our results suggest that gPr80 is inserted in the NexoCcyto orientation of a type I integral membrane protein. Additionally, our experiments have revealed the existence of a large population of Env-deficient virus-like particles (VLPs) harboring gPr80 inserted in the opposite (NcytoCexo) polarity, which is typical of type II integral membrane proteins. Overall this study provides new insight into the complex nature of the MLV gPr80 accessory protein.IMPORTANCE Viruses have evolved numerous strategies to infect, spread in, and persist in their hosts. Here we analyze the details of how the MLV-encoded glycosylated Gag (gPr80) protein protects the virus from being restricted by host innate immune defenses. gPr80 is a variant of the structural Pr65 Gag protein with an 88-amino-acid extended leader sequence that directs the protein for translation and glycosylation in the endoplasmic reticulum. This study dissects the specific contributions of gPr80 glycans and capsid stability in helping the virus to infect cells, spread, and counteract the effects of the host intrinsic restriction factor APOBEC3. Overall this study provides further insight into the elusive role of the gPr80 protein.
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Affiliation(s)
- Tyler Milston Renner
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Kasandra Bélanger
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Cindy Lam
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - María Carla Rosales Gerpe
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Joanne Eileen McBane
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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Barklis E, Staubus AO, Mack A, Harper L, Barklis RL, Alfadhli A. Lipid biosensor interactions with wild type and matrix deletion HIV-1 Gag proteins. Virology 2018; 518:264-271. [PMID: 29549788 DOI: 10.1016/j.virol.2018.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 11/19/2022]
Abstract
The matrix (MA) domain of the HIV-1 precursor Gag protein (PrGag) has been shown interact with the HIV-1 envelope (Env) protein, and to direct PrGag proteins to plasma membrane (PM) assembly sites by virtue of its affinity to phosphatidylinositol-4,5-bisphosphate (PI[4,5]P2). Unexpectedly, HIV-1 viruses with large MA deletions (ΔMA) have been shown to be conditionally infectious as long as they are matched with Env truncation mutant proteins or alternative viral glycoproteins. To characterize the interactions of wild type (WT) and ΔMA Gag proteins with PI(4,5)P2 and other acidic phospholipids, we have employed a set of lipid biosensors as probes. Our investigations showed marked differences in WT and ΔMA Gag colocalization with biosensors, effects on biosensor release, and association of biosensors with virus-like particles. These results demonstrate an alternative approach to the analysis of viral protein-lipid associations, and provide new data as to the lipid compositions of HIV-1 assembly sites.
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Affiliation(s)
- Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97035, United States.
| | - August O Staubus
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97035, United States
| | - Andrew Mack
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97035, United States
| | - Logan Harper
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97035, United States
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97035, United States
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97035, United States
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Olech M, Valas S, Kuźmak J. Epidemiological survey in single-species flocks from Poland reveals expanded genetic and antigenic diversity of small ruminant lentiviruses. PLoS One 2018; 13:e0193892. [PMID: 29505612 PMCID: PMC5837103 DOI: 10.1371/journal.pone.0193892] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/19/2018] [Indexed: 11/18/2022] Open
Abstract
Small ruminant lentivirus (SRLV) infections are widespread in Poland and circulation of subtypes A1, A12, A13, B1 and B2 was detected. The present work aimed at extending previous study based on the analysis of a larger number of animals from single-species flocks. Animals were selected for genetic analysis based on serological reactivity towards a range of recombinant antigens derived from Gag and Env viral proteins. Phylogenetic analysis revealed the existence of subtypes B2 and A12 in both goats and sheep and subtypes A1 and B1 in goats only. In addition, two novel subtypes, A16 and A17, were found in goats. Co-infections with strains belonging to different subtypes within A and B groups were detected in 1 sheep and 4 goats originating from four flocks. Although the reactivity of serum samples towards the recombinant antigens confirmed immunological relatedness between Gag epitopes of different subtypes and the cross-reactive nature of Gag antibodies, eleven serum samples failed to react with antigens representing all subtypes detected up-to-date in Poland, highlighting the limitations of the serological diagnosis. These data showed the complex nature of SRLV subtypes circulating in sheep and goats in Poland and the need for improving SRLV-related diagnostic capacity.
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Affiliation(s)
- Monika Olech
- Department of Biochemistry, National Veterinary Research Institute, Puławy, Poland
- * E-mail:
| | | | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, Puławy, Poland
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Salinero AC, Knoll ER, Zhu ZI, Landsman D, Curcio MJ, Morse RH. The Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters. PLoS Genet 2018; 14:e1007232. [PMID: 29462141 PMCID: PMC5834202 DOI: 10.1371/journal.pgen.1007232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/02/2018] [Accepted: 01/30/2018] [Indexed: 12/24/2022] Open
Abstract
The Ty1 retrotransposons present in the genome of Saccharomyces cerevisiae belong to the large class of mobile genetic elements that replicate via an RNA intermediary and constitute a significant portion of most eukaryotic genomes. The retromobility of Ty1 is regulated by numerous host factors, including several subunits of the Mediator transcriptional co-activator complex. In spite of its known function in the nucleus, previous studies have implicated Mediator in the regulation of post-translational steps in Ty1 retromobility. To resolve this paradox, we systematically examined the effects of deleting non-essential Mediator subunits on the frequency of Ty1 retromobility and levels of retromobility intermediates. Our findings reveal that loss of distinct Mediator subunits alters Ty1 retromobility positively or negatively over a >10,000-fold range by regulating the ratio of an internal transcript, Ty1i, to the genomic Ty1 transcript. Ty1i RNA encodes a dominant negative inhibitor of Ty1 retromobility that blocks virus-like particle maturation and cDNA synthesis. These results resolve the conundrum of Mediator exerting sweeping control of Ty1 retromobility with only minor effects on the levels of Ty1 genomic RNA and the capsid protein, Gag. Since the majority of characterized intrinsic and extrinsic regulators of Ty1 retromobility do not appear to effect genomic Ty1 RNA levels, Mediator could play a central role in integrating signals that influence Ty1i expression to modulate retromobility. Retrotransposons are mobile genetic elements that copy their RNA genomes into DNA and insert the DNA copies into the host genome. These elements contribute to genome instability, control of host gene expression and adaptation to changing environments. Retrotransposons depend on numerous host factors for their own propagation and control. The retrovirus-like retrotransposon, Ty1, in the yeast Saccharomyces cerevisiae has been an invaluable model for retrotransposon research, and hundreds of host factors that regulate Ty1 retrotransposition have been identified. Non-essential subunits of the Mediator transcriptional co-activator complex have been identified as one set of host factors implicated in Ty1 regulation. Here, we report a systematic investigation of the effects of loss of these non-essential subunits of Mediator on Ty1 retrotransposition. Our findings reveal a heretofore unknown mechanism by which Mediator influences the balance between transcription from two promoters in Ty1 to modulate expression of an autoinhibitory transcript known as Ty1i RNA. Our results provide new insights into host control of retrotransposon activity via promoter choice and elucidate a novel mechanism by which the Mediator co-activator governs this choice.
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Affiliation(s)
- Alicia C. Salinero
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
| | - Elisabeth R. Knoll
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
| | - Z. Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, United States of America
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, United States of America
| | - M. Joan Curcio
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail: (MJC); (RHM)
| | - Randall H. Morse
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail: (MJC); (RHM)
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40
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Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, Thomson T. Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons. Cell 2018; 172:262-274.e11. [PMID: 29328915 PMCID: PMC5793882 DOI: 10.1016/j.cell.2017.12.022] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 08/15/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022]
Abstract
Arc/Arg3.1 is required for synaptic plasticity and cognition, and mutations in this gene are linked to autism and schizophrenia. Arc bears a domain resembling retroviral/retrotransposon Gag-like proteins, which multimerize into a capsid that packages viral RNA. The significance of such a domain in a plasticity molecule is uncertain. Here, we report that the Drosophila Arc1 protein forms capsid-like structures that bind darc1 mRNA in neurons and is loaded into extracellular vesicles that are transferred from motorneurons to muscles. This loading and transfer depends on the darc1-mRNA 3' untranslated region, which contains retrotransposon-like sequences. Disrupting transfer blocks synaptic plasticity, suggesting that transfer of dArc1 complexed with its mRNA is required for this function. Notably, cultured cells also release extracellular vesicles containing the Gag region of the Copia retrotransposon complexed with its own mRNA. Taken together, our results point to a trans-synaptic mRNA transport mechanism involving retrovirus-like capsids and extracellular vesicles.
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Affiliation(s)
- James Ashley
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Benjamin Cordy
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diandra Lucia
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lee G Fradkin
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vivian Budnik
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Travis Thomson
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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41
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Pastuzyn ED, Day CE, Kearns RB, Kyrke-Smith M, Taibi AV, McCormick J, Yoder N, Belnap DM, Erlendsson S, Morado DR, Briggs JAG, Feschotte C, Shepherd JD. The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer. Cell 2018; 172:275-288.e18. [PMID: 29328916 PMCID: PMC5884693 DOI: 10.1016/j.cell.2017.12.024] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 08/15/2017] [Accepted: 12/18/2017] [Indexed: 12/25/2022]
Abstract
The neuronal gene Arc is essential for long-lasting information storage in the mammalian brain, mediates various forms of synaptic plasticity, and has been implicated in neurodevelopmental disorders. However, little is known about Arc's molecular function and evolutionary origins. Here, we show that Arc self-assembles into virus-like capsids that encapsulate RNA. Endogenous Arc protein is released from neurons in extracellular vesicles that mediate the transfer of Arc mRNA into new target cells, where it can undergo activity-dependent translation. Purified Arc capsids are endocytosed and are able to transfer Arc mRNA into the cytoplasm of neurons. These results show that Arc exhibits similar molecular properties to retroviral Gag proteins. Evolutionary analysis indicates that Arc is derived from a vertebrate lineage of Ty3/gypsy retrotransposons, which are also ancestors to retroviruses. These findings suggest that Gag retroelements have been repurposed during evolution to mediate intercellular communication in the nervous system.
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Affiliation(s)
- Elissa D Pastuzyn
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Cameron E Day
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Rachel B Kearns
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Madeleine Kyrke-Smith
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - Andrew V Taibi
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - John McCormick
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Nathan Yoder
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA
| | - David M Belnap
- Department of Biochemistry, The University of Utah, Salt Lake City, UT, USA; Department of Biology, The University of Utah, Salt Lake City, UT, USA
| | - Simon Erlendsson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark; MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Cédric Feschotte
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Jason D Shepherd
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT, USA; Department of Biochemistry, The University of Utah, Salt Lake City, UT, USA.
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42
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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: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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Balagopal V, Beemon KL. Rous Sarcoma Virus RNA Stability Element Inhibits Deadenylation of mRNAs with Long 3'UTRs. Viruses 2017; 9:v9080204. [PMID: 28763028 PMCID: PMC5580461 DOI: 10.3390/v9080204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/14/2017] [Accepted: 07/26/2017] [Indexed: 12/15/2022] Open
Abstract
All retroviruses use their full-length primary transcript as the major mRNA for Group-specific antigen (Gag) capsid proteins. This results in a long 3′ untranslated region (UTR) downstream of the termination codon. In the case of Rous sarcoma virus (RSV), there is a 7 kb 3′UTR downstream of the gag terminator, containing the pol, env, and src genes. mRNAs containing long 3′UTRs, like those with premature termination codons, are frequently recognized by the cellular nonsense-mediated mRNA decay (NMD) machinery and targeted for degradation. To prevent this, RSV has evolved an RNA stability element (RSE) in the RNA immediately downstream of the gag termination codon. This 400-nt RNA sequence stabilizes premature termination codons (PTCs) in gag. It also stabilizes globin mRNAs with long 3′UTRs, when placed downstream of the termination codon. It is not clear how the RSE stabilizes the mRNA and prevents decay. We show here that the presence of RSE inhibits deadenylation severely. In addition, the RSE also impairs decapping (DCP2) and 5′-3′ exonucleolytic (XRN1) function in knockdown experiments in human cells.
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Affiliation(s)
- Vidya Balagopal
- Biology Department, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Karen L Beemon
- Biology Department, Johns Hopkins University, Baltimore, MD 21218, USA.
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Kim SH, Kong Y, Bae YA. Recurrent emergence of structural variants of LTR retrotransposon CsRn1 evolving novel expression strategy and their selective expansion in a carcinogenic liver fluke, Clonorchis sinensis. Mol Biochem Parasitol 2017; 214:14-26. [PMID: 28322871 DOI: 10.1016/j.molbiopara.2017.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 11/19/2022]
Abstract
Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups. However, only a few investigations to date have focused on the emergence of retrotransposons evolving novel expression strategy and causal genetic drivers of the structural variants. In this study, the bulk of genomic and transcribed sequences of a Ty3/gypsy-like CsRn1 retrotransposon in Clonorchis sinensis were analyzed for the comprehensive examination of its expression strategy. Our results demonstrated that structural variants with single open reading frame (ORF) have recurrently emerged from precedential CsRn1 copies encoding overlapping gag-pol ORFs by a single-nucleotide insertion in an upstream region of gag stop codon. In the parasite genome, some of the newly evolved variants appeared to undergo proliferative burst as active master lineages together with their ancestral copies. The genetic event was similarly observed in Opisthorchis viverrini, the closest neighbor of C. sinensis, whereas the resulting structural variants might have failed to overcome purifying selection and comprised minor remnant copies in the Opisthorchis genome.
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Affiliation(s)
- Seon-Hee Kim
- Department of Microbiology, College of Medicine, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea
| | - Yoon Kong
- Department of Molecular Parasitology, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Young-An Bae
- Department of Microbiology, College of Medicine, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea.
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Wang J, Wen S, Zhao R, Qi J, Liu Z, Li W, An J, Wood C, Wang Y. Covalent conjugation of the equine infectious anemia virus Gag with SUMO. Biochem Biophys Res Commun 2017; 486:712-719. [PMID: 28342872 DOI: 10.1016/j.bbrc.2017.03.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/21/2017] [Indexed: 02/02/2023]
Abstract
The conjugation of small ubiquitin-like modifier (SUMO) to the target protein, namely, SUMOylation, is involved in the regulation of many important biological events including host-pathogen interaction. Some viruses have evolved to exploit the host SUMOylation machinery to modify their own protein. Retroviral Gag protein plays critical roles in the viral life cycle. The HIV-1 p6 and the Moloney murine leukemia virus CA have been reported to be conjugated with SUMO. In this study, we report for the first time, to our knowledge, the covalent conjugation of equine infectious anemia virus (EIAV) Gag with SUMO. The C-terminal p9 domain of Gag is a main target for SUMOylation and SUMO is attached to multiple sites of p9, including K30 whose mutation abolished p9 SUMOylation completely. The SUMOylation of p9, but not the p9-K30 mutant, was also detected in equine fibroblastic cells ATCC® CCL-57™. Ubc9 and its C93 residue are indispensable for the SUMOylation of p9. Using confocal microscopy, it is found that EIAV Gag localizes primarily, if not exclusively, in the cytoplasm of the cell and the co-localization of EIAV Gag with Ubc9 was observed. Our findings that EIAV Gag is SUMOylated at p9-K30, together with previous findings on the defects of p9-K30 mutant in viral DNA translocation from cytoplasm to the nucleus, suggests that SUMOylation of Gag may be involved in such functions.
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Affiliation(s)
- Jinzhong Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Shuping Wen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Rui Zhao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Jing Qi
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Zhao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Weiwei Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Jing An
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Charles Wood
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska, Lincoln, NE 68583, USA.
| | - Ying Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China.
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46
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Ball NJ, Nicastro G, Dutta M, Pollard DJ, Goldstone DC, Sanz-Ramos M, Ramos A, Müllers E, Stirnnagel K, Stanke N, Lindemann D, Stoye JP, Taylor WR, Rosenthal PB, Taylor IA. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid. PLoS Pathog 2016; 12:e1005981. [PMID: 27829070 PMCID: PMC5102385 DOI: 10.1371/journal.ppat.1005981] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 10/06/2016] [Indexed: 12/26/2022] Open
Abstract
The Spumaretrovirinae, or foamy viruses (FVs) are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV). The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA) and C-terminal domains (CtDCA) of archetypal orthoretroviral capsid protein (CA). Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN—CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold. Foamyviruses (FVs) or Spuma-retroviruses derive their name from the cytopathic effects they cause in cell culture. However, infection in humans is benign and FVs have entered the human population through zoonosis from apes resulting in the emergence of Prototype FV (PFV). Like all retroviruses, FVs contain gag, pol and env structural genes and replicate through reverse-transcription and host genome integration. Gag, the major structural protein, is required for genome packaging, virion assembly, trafficking and egress. However, although functionally equivalent, FV and orthoretroviral Gag share little sequence homology and it is unclear how they perform the same function. Therefore, to understand more about relationship between FV and orthoretroviral replication we have carried out structural studies of PFV-Gag. Here we present the structure of CA domains from a central region PFV-Gag and show that despite little sequence similarity they share the same fold as the CA domains of orthoretroviral Gag. These data provide the first information relating the Spuma and Orthoretrovirinae Gag proteins. We discuss our findings in terms of evolutionary divergence of spuma and orthoretroviral lineages.
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Affiliation(s)
- Neil J. Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Moumita Dutta
- Structural Biology of Cells and Viruses, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Dominic J. Pollard
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - David C. Goldstone
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Marta Sanz-Ramos
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Andres Ramos
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Erik Müllers
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | | | - Nicole Stanke
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - William R. Taylor
- Computational Cell and Molecular Biology Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
- * E-mail:
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Liu Y, Li K, Gao Y, Gao L, Zhong L, Zhang Y, Liu C, Zhang Y, Wang X. Recombinant Marek's Disease Virus as a Vector-Based Vaccine against Avian Leukosis Virus Subgroup J in Chicken. Viruses 2016; 8:v8110301. [PMID: 27827933 PMCID: PMC5127015 DOI: 10.3390/v8110301] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 10/18/2016] [Accepted: 10/26/2016] [Indexed: 11/21/2022] Open
Abstract
Avian leukosis virus subgroup J (ALV-J) is an immunosuppressive virus that causes considerable economic losses to the chicken industry in China. However, there is currently no effective vaccine to prevent ALV-J infection. In order to reduce the losses caused by ALV-J, we constructed two effective ALV-J vaccines by inserting the ALV-J (strain JL093-1) env or gag+env genes into the US2 gene of the Marek’s disease herpesviruses (MDV) by transfection of overlapping fosmid DNAs, creating two recombinant MDVs, rMDV/ALV-gag+env and rMDV/ALV-env. Analysis of cultured chicken embryo fibroblasts infected with the rMDVs revealed that Env and Gag were successfully expressed and that there was no difference in growth kinetics in cells infected with rMDVs compared with that of cells infected with the parent MDV. Chickens vaccinated with either rMDV revealed that positive serum antibodies were induced. Both rMDVs also effectively reduced the rate of positive viremia in chicken flocks challenged with ALV-J. The protective effect provided by rMDV/ALV-env inoculation was slightly stronger than that provided by rMDV/ALV-gag+env. This represents the first study where a potential rMDV vaccine, expressing ALV-J antigenic genes, has been shown to be effective in the prevention of ALV-J. Our study also opens new avenues for the control of MDV and ALV-J co-infection.
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Affiliation(s)
- Yongzhen Liu
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Kai Li
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Yulong Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Li Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Li Zhong
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Yao Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Changjun Liu
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Yanping Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Xiaomei Wang
- Avian Immunosuppressive Diseases Division, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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48
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Chutiwitoonchai N, Siarot L, Takeda E, Shioda T, Ueda M, Aida Y. HIV-1 Vpr Abrogates the Effect of TSG101 Overexpression to Support Virus Release. PLoS One 2016; 11:e0163100. [PMID: 27648839 PMCID: PMC5029901 DOI: 10.1371/journal.pone.0163100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 09/02/2016] [Indexed: 11/18/2022] Open
Abstract
HIV-1 budding requires interaction between Gag and cellular TSG101 to initiate viral particle assembly and release via the endosomal sorting complexes required for transport (ESCRT) pathway. However, some reports show that overexpression of TSG101 inhibits virus release by disruption of Gag targeting process. Since a HIV-1 accessory protein, Vpr binds to Gag p6 domain at the position close to the binding site for TSG101, whether Vpr implicates TSG101 overexpression effect has not been investigated. Here, we found that Vpr abrogates TSG101 overexpression effect to rescue viral production. Co-transfection of TSG101 and Gag with Vpr prevented TSG101-induced Gag accumulation in endosomes and lysosomes. In addition, Vpr rescued virus-like particle (VLP) production in a similar manner as a lysosomal inhibitor, Bafilomycin A1 indicating that Vpr inhibits TSG101-induced Gag downregulation via lysosomal pathway. Vpr and Gag interaction is required to counteract TSG101 overexpression effect since Vpr A30F mutant which is unable to interact with Gag and incorporate into virions, reduced ability to prevent Gag accumulation and to rescue VLP production. In addition, GST pull-down assays and Biacore analysis revealed that Vpr competed with TSG101 for Gag binding. These results indicate that Vpr overcomes the effects of TSG101 overexpression to support viral production by competing with TSG101 to bind Gag.
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Affiliation(s)
- Nopporn Chutiwitoonchai
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
- Japan Foundation for AIDS Prevention, Chiyoda-ku, Tokyo, Japan
| | - Lowela Siarot
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Eri Takeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Motoki Ueda
- Nano Medical Engineering Laboratory, RIKEN, Wako, Saitama, Japan
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
- * E-mail:
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49
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Rousvoal S, Bouyer B, López-Cristoffanini C, Boyen C, Collén J. Mutant swarms of a totivirus-like entities are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome. J Phycol 2016; 52:493-504. [PMID: 27151076 DOI: 10.1111/jpy.12427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
Chondrus crispus Stackhouse (Gigartinales) is a red seaweed found on North Atlantic rocky shores. Electrophoresis of RNA extracts showed a prominent band with a size of around 6,000 bp. Sequencing of the band revealed several sequences with similarity to totiviruses, double-stranded RNA viruses that normally infect fungi. This virus-like entity was named C. crispus virus (CcV). It should probably be regarded as an extreme viral quasispecies or a mutant swarm since low identity (<65%) was found between sequences. Totiviruses typically code for two genes: one capsid gene (gag) and one RNA-dependent RNA polymerase gene (pol) with a pseudoknot structure between the genes. Both the genes and the intergenic structures were found in the CcV sequences. A nonidentical gag gene was also found in the nuclear genome of C. crispus, with associated expressed sequence tags (EST) and upstream regulatory features. The gene was presumably horizontally transferred from the virus to the alga. Similar dsRNA bands were seen in extracts from different life cycle stages of C. crispus and from all geographic locations tested. In addition, similar bands were also observed in RNA extractions from other red algae; however, the significance of this apparently widespread phenomenon is unknown. Neither phenotype caused by the infection nor any virus particles or capsid proteins were identified; thus, the presence of viral particles has not been validated. These findings increase the known host range of totiviruses to include marine red algae.
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Affiliation(s)
- Sylvie Rousvoal
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Betty Bouyer
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Camilo López-Cristoffanini
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Catherine Boyen
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Jonas Collén
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
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50
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Deere JD, Chang WLW, Castillo LD, Schmidt KA, Kieu HT, Renzette N, Kowalik T, Barthold SW, Shacklett BL, Barry PA, Sparger EE. Utilizing a TLR5-Adjuvanted Cytomegalovirus as a Lentiviral Vaccine in the Nonhuman Primate Model for AIDS. PLoS One 2016; 11:e0155629. [PMID: 27182601 PMCID: PMC4868283 DOI: 10.1371/journal.pone.0155629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/01/2016] [Indexed: 01/09/2023] Open
Abstract
Despite tremendous progress in our understanding of human immunodeficiency virus (HIV) natural history and advances in HIV treatment, there is neither an approved vaccine nor a cure for infection. Here, we describe the development and characterization of a novel replicating vaccine vector utilizing Cytomegalovirus (CMV) and a TLR5 adjuvant. After partial truncation of the central, immunodominant hypervariable domain, flagellin (fliC) from Salmonella was cloned downstream of a codon optimized gag gene from simian immunodeficiency virus (SIV) and transiently expressed in telomerized rhesus fibroblast (TeloRF) cells in culture. Lysates generated from these transfected cells induced the tumor necrosis factor alpha (TNF-α), in a mouse macrophage cell line, in a TLR5-dependent manner. The Gag/FliC expression construct was cloned into a bacterial artificial chromosome encoding the rhesus CMV (RhCMV) genome, and infectious RhCMV was generated following transfection of TeloRF cells. This virus stably expressed an SIV Gag/FliC fusion protein through four serial passages. Lysates generated from infected cells induced TNF-α in a TLR5-dependent manner. Western blot analysis of infected cell lysates verified expression of a Gag/FliC fusion protein using a SIV p27 capsid monoclonal antibody. Lastly, rhesus macaques inoculated with this novel RhCMV virus demonstrated increased inflammatory responses at the site of inoculation seven days post-infection when compared to the parental RhCMV. These results demonstrate that an artificially constructed replicating RhCMV expressing an SIV Gag/FliC fusion protein is capable of activating TLR5 in a macrophage cell line in vitro and induction of an altered inflammatory response in vivo. Ongoing animals studies are aimed at determining vaccine efficacy, including subsequent challenge with pathogenic SIV.
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Affiliation(s)
- Jesse D. Deere
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - W. L. William Chang
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Luis D. Castillo
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Kim A. Schmidt
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Hung T. Kieu
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Nicholas Renzette
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Timothy Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Stephen W. Barthold
- Department of Veterinary Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Barbara L. Shacklett
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Peter A. Barry
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
- * E-mail: (PAB); (EES)
| | - Ellen E. Sparger
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- * E-mail: (PAB); (EES)
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