1
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Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley D, Mansky LM, Dick RA, Schur FKM. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nat Struct Mol Biol 2024:10.1038/s41594-024-01390-8. [PMID: 39242978 DOI: 10.1038/s41594-024-01390-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/14/2024] [Indexed: 09/09/2024]
Abstract
Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Material and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, Eindhoven, Netherlands
| | - Mathias Percipalle
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Darya Chernikova
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Andreas Thader
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Gergely Pinke
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Dario Porley
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Emory University School of Medicine, Atlanta, GA, USA
| | - Florian K M Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
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2
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Chang NC, Wells JN, Wang AY, Schofield P, Huang YC, Truong VH, Simoes-Costa M, Feschotte C. Gag proteins encoded by endogenous retroviruses are required for zebrafish development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586437. [PMID: 38585793 PMCID: PMC10996621 DOI: 10.1101/2024.03.25.586437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. The process by which TEs become coopted remains obscure because most cases involve ancient, transpositionally inactive elements. Reports of active TEs serving beneficial functions are scarce and often contentious due to difficulties in manipulating repetitive sequences. Here we show that recently active TEs in zebrafish encode products critical for embryonic development. Knockdown and rescue experiments demonstrate that the endogenous retrovirus family BHIKHARI-1 (Bik-1) encodes a Gag protein essential for mesoderm development. Mechanistically, Bik-1 Gag associates with the cell membrane and its ectopic expression in chicken embryos alters cell migration. Similarly, depletion of BHIKHARI-2 Gag, a relative of Bik-1, causes defects in neural crest development in zebrafish. We propose an "addiction" model to explain how active TEs can be integrated into conserved developmental processes.
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Affiliation(s)
- Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Andrew Y Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Phillip Schofield
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Yi-Chia Huang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vinh H Truong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Marcos Simoes-Costa
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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3
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Krebs AS, Liu HF, Zhou Y, Rey JS, Levintov L, Shen J, Howe A, Perilla JR, Bartesaghi A, Zhang P. Molecular architecture and conservation of an immature human endogenous retrovirus. Nat Commun 2023; 14:5149. [PMID: 37620323 PMCID: PMC10449913 DOI: 10.1038/s41467-023-40786-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
The human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus in the human genome and is activated and expressed in many cancers and amyotrophic lateral sclerosis. We present the immature HERV-K capsid structure at 3.2 Å resolution determined from native virus-like particles using cryo-electron tomography and subtomogram averaging. The structure shows a hexamer unit oligomerized through a 6-helix bundle, which is stabilized by a small molecule analogous to IP6 in immature HIV-1 capsid. The HERV-K immature lattice is assembled via highly conserved dimer and trimer interfaces, as detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the linker between the N-terminal and the C-terminal domains of CA occurs during HERV-K maturation. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.
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Affiliation(s)
- Anna-Sophia Krebs
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hsuan-Fu Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, 27708, USA
| | - Juan S Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew Howe
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Computer Science, Duke University, Durham, NC, 27708, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA.
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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4
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Kaddis Maldonado R, Lambert GS, Rice BL, Sudol M, Flanagan JM, Parent LJ. The Rous sarcoma virus Gag Polyprotein Forms Biomolecular Condensates Driven by Intrinsically-disordered Regions. J Mol Biol 2023; 435:168182. [PMID: 37328094 PMCID: PMC10527454 DOI: 10.1016/j.jmb.2023.168182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Biomolecular condensates (BMCs) play important roles incellular structures includingtranscription factories, splicing speckles, and nucleoli. BMCs bring together proteins and other macromolecules, selectively concentrating them so that specific reactions can occur without interference from the surrounding environment. BMCs are often made up of proteins that contain intrinsically disordered regions (IDRs), form phase-separated spherical puncta, form liquid-like droplets that undergo fusion and fission, contain molecules that are mobile, and are disrupted with phase-dissolving drugs such as 1,6-hexanediol. In addition to cellular proteins, many viruses, including influenza A, SARS-CoV-2, and human immunodeficiency virus type 1 (HIV-1) encode proteins that undergo phase separation and rely on BMC formation for replication. In prior studies of the retrovirus Rous sarcoma virus (RSV), we observed that the Gag protein forms discrete spherical puncta in the nucleus, cytoplasm, and at the plasma membrane that co-localize with viral RNA and host factors, raising the possibility that RSV Gag forms BMCs that participate in the intracellular phase of the virion assembly pathway. In our current studies, we found that Gag contains IDRs in the N-terminal (MAp2p10) and C-terminal (NC) regions of the protein and fulfills many criteria of BMCs. Although the role of BMC formation in RSV assembly requires further study, our results suggest the biophysical properties of condensates are required for the formation of Gag complexes in the nucleus and the cohesion of these complexes as they traffic through the nuclear pore, into the cytoplasm, and to the plasma membrane, where the final assembly and release of virus particles occurs.
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Affiliation(s)
- Rebecca Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Department of Microbiology & Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Gregory S Lambert
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Breanna L Rice
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Malgorzata Sudol
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - John M Flanagan
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Leslie J Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Department of Microbiology & Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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5
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Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley D, Mansky LM, Dick RA, Schur FKM. Unconventional stabilization of the human T-cell leukemia virus type 1 immature Gag lattice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.548988. [PMID: 37546793 PMCID: PMC10402013 DOI: 10.1101/2023.07.24.548988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) has an atypical immature particle morphology compared to other retroviruses. This indicates that these particles are formed in a way that is unique. Here we report the results of cryo-electron tomography (cryo-ET) studies of HTLV-1 virus-like particles (VLPs) assembled in vitro, as well as derived from cells. This work shows that HTLV-1 employs an unconventional mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature CA tubular arrays reveals that the primary stabilizing component in HTLV-1 is CA-NTD. Mutagenesis and biophysical analysis support this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the CA-CTD. These results are the first to provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus, and this helps explain why HTLV-1 particles are morphologically distinct.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Mathias Percipalle
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Darya Chernikova
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Andreas Thader
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Gergely Pinke
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Dario Porley
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Florian KM Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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6
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Krebs AS, Liu HF, Zhou Y, Rey JS, Levintov L, Shen J, Howe A, Perilla JR, Bartesaghi A, Zhang P. Molecular architecture and conservation of an immature human endogenous retrovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544027. [PMID: 37333227 PMCID: PMC10274761 DOI: 10.1101/2023.06.07.544027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A significant part of the human genome consists of endogenous retroviruses sequences. Human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus, is activated and expressed in many cancers and amyotrophic lateral sclerosis and possibly contributes to the aging process. To understand the molecular architecture of endogenous retroviruses, we determined the structure of immature HERV-K from native virus-like particles (VLPs) using cryo-electron tomography and subtomogram averaging (cryoET STA). The HERV-K VLPs show a greater distance between the viral membrane and immature capsid lattice, correlating with the presence of additional peptides, SP1 and p15, between the capsid (CA) and matrix (MA) proteins compared to the other retroviruses. The resulting cryoET STA map of the immature HERV-K capsid at 3.2 Å resolution shows a hexamer unit oligomerized through a 6-helix bundle which is further stabilized by a small molecule in the same way as the IP6 in immature HIV-1 capsid. The HERV-K immature CA hexamer assembles into the immature lattice via highly conserved dimmer and trimer interfaces, whose interactions were further detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the flexible linker between the N-terminal and the C-terminal domains of CA occurs between the immature and the mature HERV-K capsid protein, analogous to HIV-1. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.
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Affiliation(s)
- Anna-Sophia Krebs
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hsuan-Fu Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Juan S. Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew Howe
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK
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7
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Maldonado RK, Rice BL, Lambert GS, Sudol M, Flanagan JM, Parent LJ. The Rous sarcoma virus Gag polyprotein forms biomolecular condensates driven by intrinsically-disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536043. [PMID: 37066255 PMCID: PMC10104128 DOI: 10.1101/2023.04.07.536043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Biomolecular condensates (BMCs) play important roles in cellular structures including transcription factories, splicing speckles, and nucleoli. BMCs bring together proteins and other macromolecules, selectively concentrating them so that specific reactions can occur without interference from the surrounding environment. BMCs are often made up of proteins that contain intrinsically disordered regions (IDRs), form phase-separated spherical puncta, form liquid-like droplets that undergo fusion and fission, contain molecules that are mobile, and are disrupted with phase-dissolving drugs such as 1,6-hexanediol. In addition to cellular proteins, many viruses, including influenza A, SARS-CoV-2, and human immunodeficiency virus type 1 (HIV-1) encode proteins that undergo phase separation and rely on BMC formation for replication. In prior studies of the retrovirus Rous sarcoma virus (RSV), we observed that the Gag protein forms discrete spherical puncta in the nucleus, cytoplasm, and at the plasma membrane that co-localize with viral RNA and host factors, raising the possibility that RSV Gag forms BMCs that participate in the virion intracellular assembly pathway. In our current studies, we found that Gag contains IDRs in the N-terminal (MAp2p10) and C-terminal (NC) regions of the protein and fulfills many criteria of BMCs. Although the role of BMC formation in RSV assembly requires further study, our results suggest the biophysical properties of condensates are required for the formation of Gag complexes in the nucleus and the cohesion of these complexes as they traffic through the nuclear pore, into the cytoplasm, and to the plasma membrane, where the final assembly and release of virus particles occurs.
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8
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Markússon S, Hallin EI, Bustad HJ, Raasakka A, Xu J, Muruganandam G, Loris R, Martinez A, Bramham CR, Kursula P. High-affinity anti-Arc nanobodies provide tools for structural and functional studies. PLoS One 2022; 17:e0269281. [PMID: 35671319 PMCID: PMC9173642 DOI: 10.1371/journal.pone.0269281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022] Open
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a multidomain protein of retroviral origin with a vital role in the regulation of synaptic plasticity and memory formation in mammals. However, the mechanistic and structural basis of Arc function is poorly understood. Arc has an N-terminal domain (NTD) involved in membrane binding and a C-terminal domain (CTD) that binds postsynaptic protein ligands. In addition, the NTD and CTD both function in Arc oligomerisation, including assembly of retrovirus-like capsids involved in intercellular signalling. To obtain new tools for studies on Arc structure and function, we produced and characterised six high-affinity anti-Arc nanobodies (Nb). The CTD of rat and human Arc were both crystallised in ternary complexes with two Nbs. One Nb bound deep into the stargazin-binding pocket of Arc CTD and suggested competitive binding with Arc ligand peptides. The crystallisation of the human Arc CTD in two different conformations, accompanied by SAXS data and molecular dynamics simulations, paints a dynamic picture of the mammalian Arc CTD. The collapsed conformation closely resembles Drosophila Arc in capsids, suggesting that we have trapped a capsid-like conformation of the human Arc CTD. Our data obtained with the help of anti-Arc Nbs suggest that structural dynamics of the CTD and dimerisation of the NTD may promote the formation of capsids. Taken together, the recombinant high-affinity anti-Arc Nbs are versatile tools that can be further developed for studying mammalian Arc structure and function, as well as mechanisms of Arc capsid formation, both in vitro and in vivo. For example, the Nbs could serve as a genetically encoded tools for inhibition of endogenous Arc interactions in the study of neuronal function and plasticity.
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Affiliation(s)
| | - Erik I. Hallin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ju Xu
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- * E-mail:
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9
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Wang Z, Patwardhan A, Kleywegt GJ. Validation analysis of EMDB entries. Acta Crystallogr D Struct Biol 2022; 78:542-552. [PMID: 35503203 PMCID: PMC9063848 DOI: 10.1107/s205979832200328x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
The Electron Microscopy Data Bank (EMDB) is the central archive of the electron cryo-microscopy (cryo-EM) community for storing and disseminating volume maps and tomograms. With input from the community, EMDB has developed new resources for the validation of cryo-EM structures, focusing on the quality of the volume data alone and that of the fit of any models, themselves archived in the Protein Data Bank (PDB), to the volume data. Based on recommendations from community experts, the validation resources are developed in a three-tiered system. Tier 1 covers an extensive and evolving set of validation metrics, including tried and tested metrics as well as more experimental ones, which are calculated for all EMDB entries and presented in the Validation Analysis (VA) web resource. This system is particularly useful for cryo-EM experts, both to validate individual structures and to assess the utility of new validation metrics. Tier 2 comprises a subset of the validation metrics covered by the VA resource that have been subjected to extensive testing and are considered to be useful for specialists as well as nonspecialists. These metrics are presented on the entry-specific web pages for the entire archive on the EMDB website. As more experience is gained with the metrics included in the VA resource, it is expected that consensus will emerge in the community regarding a subset that is suitable for inclusion in the tier 2 system. Tier 3, finally, consists of the validation reports and servers that are produced by the Worldwide Protein Data Bank (wwPDB) Consortium. Successful metrics from tier 2 will be proposed for inclusion in the wwPDB validation pipeline and reports. The details of the new resource are described, with an emphasis on the tier 1 system. The output of all three tiers is publicly available, either through the EMDB website (tiers 1 and 2) or through the wwPDB ftp sites (tier 3), although the content of all three will evolve over time (fastest for tier 1 and slowest for tier 3). It is our hope that these validation resources will help the cryo-EM community to obtain a better understanding of the quality and of the best ways to assess the quality of cryo-EM structures in EMDB and PDB.
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Affiliation(s)
- Zhe Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Gerard J. Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
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10
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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; 14:324. [PMID: 35215917 PMCID: PMC8876502 DOI: 10.3390/v14020324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [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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11
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [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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12
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Perspective: Emerging strategies for determining atomic-resolution structures of macromolecular complexes within cells. J Struct Biol 2021; 214:107827. [PMID: 34915129 PMCID: PMC8978977 DOI: 10.1016/j.jsb.2021.107827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/28/2022]
Abstract
In principle, electron cryo-tomography (cryo-ET) of thin portions of cells provides high-resolution images of the three-dimensional spatial arrangement of all members of the proteome. In practice, however, radiation damage creates a tension between recording images at many different tilt angles, but at correspondingly reduced exposure levels, versus limiting the number of tilt angles in order to improve the signal-to-noise ratio (SNR). Either way, it is challenging to read the available information out at the level of atomic structure. Here, we first review work that explores the optimal strategy for data collection, which currently seems to favor the use of a limited angular range for tilting the sample or even the use of a single image to record the high-resolution information. Looking then to the future, we point to the alternative of so-called “deconvolution microscopy”, which may be applied to tilt-series or optically-sectioned, focal series data. Recording data as a focal series has the advantage that little or no translational alignment of frames might be needed, and a three-dimensional reconstruction might require only 2/3 the number of images as does standard tomography. We also point to the unexploited potential of phase plates to increase the contrast, and thus to reduce the electron exposure levels while retaining the ability align and merge the data. In turn, using much lower exposures per image could have the advantage that high-resolution information is retained throughout the full data-set, whether recorded as a tilt series or a focal series of images.
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A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly. Viruses 2021; 13:v13091853. [PMID: 34578434 PMCID: PMC8473085 DOI: 10.3390/v13091853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 11/17/2022] Open
Abstract
The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.
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14
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Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nat Commun 2021; 12:3226. [PMID: 34050170 PMCID: PMC8163826 DOI: 10.1038/s41467-021-23506-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/03/2021] [Indexed: 02/08/2023] Open
Abstract
Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.
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15
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Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation. Proc Natl Acad Sci U S A 2021; 118:2020054118. [PMID: 33397805 PMCID: PMC7826355 DOI: 10.1073/pnas.2020054118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 particle assembly is driven by the viral Gag protein, which oligomerizes into a hexameric array on the inner surface of the viral envelope, forming a truncated spherical lattice containing large and small gaps. Gag is then cut by the viral protease, disassembles, and rearranges to form the mature, infectious virus. Here, we present structures and molecular dynamics simulations of the edges of the immature Gag lattice. Our analysis shows that Gag dimers are the basic assembly unit of the HIV-1 particle, lattice edges are partial hexamers, and partial hexamers are prone to structural changes allowing protease to cut Gag. These findings provide insights into assembly of the immature virus, its structure, and how it disassembles during maturation. The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by incorporating small lattice defects and a large gap at the site of budding. This lattice is stabilized by intrahexameric and interhexameric CA-CA interactions, which are important in regulating viral assembly and maturation. We applied subtomogram averaging and classification to determine the oligomerization state of CA at lattice edges and found that CA forms partial hexamers. These structures reveal the network of interactions formed by CA-SP1 at the lattice edge. We also performed atomistic molecular dynamics simulations of CA-CA interactions stabilizing the immature lattice and partial CA-SP1 helical bundles. Free energy calculations reveal increased propensity for helix-to-coil transitions in partial hexamers compared to complete six-helix bundles. Taken together, these results suggest that the CA dimer is the basic unit of lattice assembly, partial hexamers exist at lattice edges, these are in a helix-coil dynamic equilibrium, and partial helical bundles are more likely to unfold, representing potential sites for HIV-1 maturation initiation.
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16
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Effect of Small Polyanions on In Vitro Assembly of Selected Members of Alpha-, Beta- and Gammaretroviruses. Viruses 2021; 13:v13010129. [PMID: 33477490 PMCID: PMC7831069 DOI: 10.3390/v13010129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
The assembly of a hexameric lattice of retroviral immature particles requires the involvement of cell factors such as proteins and small molecules. A small, negatively charged polyanionic molecule, myo-inositol hexaphosphate (IP6), was identified to stimulate the assembly of immature particles of HIV-1 and other lentiviruses. Interestingly, cryo-electron tomography analysis of the immature particles of two lentiviruses, HIV-1 and equine infectious anemia virus (EIAV), revealed that the IP6 binding site is similar. Based on this amino acid conservation of the IP6 interacting site, it is presumed that the assembly of immature particles of all lentiviruses is stimulated by IP6. Although this specific region for IP6 binding may be unique for lentiviruses, it is plausible that other retroviral species also recruit some small polyanion to facilitate the assembly of their immature particles. To study whether the assembly of retroviruses other than lentiviruses can be stimulated by polyanionic molecules, we measured the effect of various polyanions on the assembly of immature virus-like particles of Rous sarcoma virus (RSV), a member of alpharetroviruses, Mason-Pfizer monkey virus (M-PMV) representative of betaretroviruses, and murine leukemia virus (MLV), a member of gammaretroviruses. RSV, M-PMV and MLV immature virus-like particles were assembled in vitro from truncated Gag molecules and the effect of selected polyanions, myo-inostol hexaphosphate, myo-inositol, glucose-1,6-bisphosphate, myo-inositol hexasulphate, and mellitic acid, on the particles assembly was quantified. Our results suggest that the assembly of immature particles of RSV and MLV was indeed stimulated by the presence of myo-inostol hexaphosphate and myo-inositol, respectively. In contrast, no effect on the assembly of M-PMV as a betaretrovirus member was observed.
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17
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Wen Y, Feigenson GW, Vogt VM, Dick RA. Mechanisms of PI(4,5)P2 Enrichment in HIV-1 Viral Membranes. J Mol Biol 2020; 432:5343-5364. [PMID: 32739462 PMCID: PMC8262684 DOI: 10.1016/j.jmb.2020.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/12/2020] [Accepted: 07/26/2020] [Indexed: 01/10/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) is critical for HIV-1 virus assembly. The viral membrane is enriched in PIP2, suggesting that the virus assembles at PIP2-rich microdomains. We showed previously that in model membranes PIP2 can form nanoscopic clusters bridged by multivalent cations. Here, using purified proteins we quantitated the binding of HIV-1 Gag-related proteins to giant unilamellar vesicles containing either clustered or free PIP2. Myristoylated MA strongly preferred binding to clustered PIP2. By contrast, unmyristoylated HIV-1 MA, RSV MA, and a PH domain all preferred to interact with free PIP2. We also found that HIV-1 Gag multimerization promotes PIP2 clustering. Truncated Gag proteins comprising the MA, CA, and SP domains (MACASP) or the MA and CA domains (MACA) induced self-quenching of acyl chain-labeled fluorescent PIP2 in liposomes, implying clustering. However, HIV-1 MA itself did not induce PIP2 clustering. A CA inter-hexamer dimer interface mutation led to a loss of induced PIP2 clustering in MACA, indicating the importance of protein multimerization. Cryo-electron tomography of liposomes with bound MACA showed an amorphous protein layer on the membrane surface. Thus, it appears that while protein–protein interactions are required for PIP2 clustering, formation of a regular lattice is not. Protein-induced PIP2 clustering and multivalent cation-induced PIP2 clustering are additive. Taken together, these results provide the first evidence that HIV-1 Gag can selectively target pre-existing PIP2-enriched domains of the plasma membrane for viral assembly, and that Gag multimerization can further enrich PIP2 at assembly sites. These effects could explain the observed PIP2 enrichment in HIV-1.
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Affiliation(s)
- Yi Wen
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Gerald W Feigenson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Volker M Vogt
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Robert A Dick
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA.
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18
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PF74 and Its Novel Derivatives Stabilize Hexameric Lattice of HIV-1 Mature-Like Particles. Molecules 2020; 25:molecules25081895. [PMID: 32325987 PMCID: PMC7221806 DOI: 10.3390/molecules25081895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 01/23/2023] Open
Abstract
A major structural retroviral protein, capsid protein (CA), is able to oligomerize into two different hexameric lattices, which makes this protein a key component for both the early and late stages of HIV-1 replication. During the late stage, the CA protein, as part of the Gag polyprotein precursor, facilitates protein–protein interactions that lead to the assembly of immature particles. Following protease activation and Gag polyprotein processing, CA also drives the assembly of the mature viral core. In the early stage of infection, the role of the CA protein is distinct. It controls the disassembly of the mature CA hexameric lattice i.e., uncoating, which is critical for the reverse transcription of the single-stranded RNA genome into double stranded DNA. These properties make CA a very attractive target for small molecule functioning as inhibitors of HIV-1 particle assembly and/or disassembly. Of these, inhibitors containing the PF74 scaffold have been extensively studied. In this study, we reported a series of modifications of the PF74 molecule and its characterization through a combination of biochemical and structural approaches. Our data supported the hypothesis that PF74 stabilizes the mature HIV-1 CA hexameric lattice. We identified derivatives with a higher in vitro stabilization activity in comparison to the original PF74 molecule.
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19
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Biochemical Reconstitution of HIV-1 Assembly and Maturation. J Virol 2020; 94:JVI.01844-19. [PMID: 31801870 DOI: 10.1128/jvi.01844-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/28/2019] [Indexed: 12/18/2022] Open
Abstract
The assembly of an orthoretrovirus such as HIV-1 requires the coordinated functioning of multiple biochemical activities of the viral Gag protein. These activities include membrane targeting, lattice formation, packaging of the RNA genome, and recruitment of cellular cofactors that modulate assembly. In most previous studies, these Gag activities have been investigated individually, which provided somewhat limited insight into how they functionally integrate during the assembly process. Here, we report the development of a biochemical reconstitution system that allowed us to investigate how Gag lattice formation, RNA binding, and the assembly cofactor inositol hexakisphosphate (IP6) synergize to generate immature virus particles in vitro The results identify an important rate-limiting step in assembly and reveal new insights into how RNA and IP6 promote immature Gag lattice formation. The immature virus-like particles can be converted into mature capsid-like particles by the simple addition of viral protease, suggesting that it is possible in principle to fully biochemically reconstitute the sequential processes of HIV-1 assembly and maturation from purified components.IMPORTANCE Assembly and maturation are essential steps in the replication of orthoretroviruses such as HIV-1 and are proven therapeutic targets. These processes require the coordinated functioning of the viral Gag protein's multiple biochemical activities. We describe here the development of an experimental system that allows an integrative analysis of how Gag's multiple functionalities cooperate to generate a retrovirus particle. Our current studies help to illuminate how Gag synergizes the formation of the virus compartment with RNA binding and how these activities are modulated by the small molecule IP6. Further development and use of this system should lead to a more comprehensive understanding of the molecular mechanisms of HIV-1 assembly and maturation and may provide new insights for the development of antiretroviral drugs.
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20
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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] [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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21
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Zhang P. Advances in cryo-electron tomography and subtomogram averaging and classification. Curr Opin Struct Biol 2019; 58:249-258. [PMID: 31280905 PMCID: PMC6863431 DOI: 10.1016/j.sbi.2019.05.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/20/2022]
Abstract
Cryo-electron tomography (cryoET) can provide 3D reconstructions, or tomograms, of pleomorphic objects such as organelles or cells in their close-to-native states. Subtomograms that contain repetitive structures can be further extracted and subjected to averaging and classification to improve resolution, and this process has become an emerging structural biology method referred to as cryoET subtomogram averaging and classification (cryoSTAC). Recent technical advances in cryoSTAC have had a profound impact on many fields in biology. Here, I review recent exciting work on several macromolecular assemblies demonstrating the power of cryoSTAC for in situ structure analysis and discuss challenges and future directions.
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Affiliation(s)
- Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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22
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Obr M, Schur FKM. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. Adv Virus Res 2019; 105:117-159. [PMID: 31522703 DOI: 10.1016/bs.aivir.2019.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Florian K M Schur
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.
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23
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Pornillos O, Ganser-Pornillos BK. Maturation of retroviruses. Curr Opin Virol 2019; 36:47-55. [PMID: 31185449 PMCID: PMC6730672 DOI: 10.1016/j.coviro.2019.05.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 01/10/2023]
Abstract
During retrovirus maturation, cleavage of the precursor structural Gag polyprotein by the viral protease induces architectural rearrangement of the virus particle from an immature into a mature, infectious form. The structural rearrangement encapsidates the viral RNA genome in a fullerene capsid, producing a diffusible viral core that can initiate infection upon entry into the cytoplasm of a host cell. Maturation is an important therapeutic window against HIV-1. In this review, we highlight recent breakthroughs in understanding of the structures of retroviral immature and mature capsid lattices that define the boundary conditions of maturation and provide novel insights on capsid transformation. We also discuss emerging insights on encapsidation of the viral genome in the mature capsid, as well as remaining questions for further study.
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Affiliation(s)
- Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
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24
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Dodonova SO, Prinz S, Bilanchone V, Sandmeyer S, Briggs JAG. Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses. Proc Natl Acad Sci U S A 2019; 116:10048-10057. [PMID: 31036670 PMCID: PMC6525542 DOI: 10.1073/pnas.1900931116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR retrotransposons represent major components of animal, plant, and fungal genomes. Sequences from these elements have been exapted to perform essential host functions, including placental development, synaptic communication, and transcriptional regulation. They encode a Gag polypeptide, the capsid domains of which can oligomerize to form a virus-like particle. The structures of retroviral capsids have been extensively described. They assemble an immature viral particle through oligomerization of full-length Gag. Proteolytic cleavage of Gag results in a mature, infectious particle. In contrast, the absence of structural data on LTR retrotransposon capsids hinders our understanding of their function and evolutionary relationships. Here, we report the capsid morphology and structure of the archetypal Gypsy retrotransposon Ty3. We performed electron tomography (ET) of immature and mature Ty3 particles within cells. We found that, in contrast to retroviruses, these do not change size or shape upon maturation. Cryo-ET and cryo-electron microscopy of purified, immature Ty3 particles revealed an irregular fullerene geometry previously described for mature retrovirus core particles and a tertiary and quaternary arrangement of the capsid (CA) C-terminal domain within the assembled capsid that is conserved with mature HIV-1. These findings provide a structural basis for studying retrotransposon capsids, including those domesticated in higher organisms. They suggest that assembly via a structurally distinct immature capsid is a later retroviral adaptation, while the structure of mature assembled capsids is conserved between LTR retrotransposons and retroviruses.
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Affiliation(s)
- Svetlana O Dodonova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany
| | - Simone Prinz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Virginia Bilanchone
- Department of Biological Chemistry, University of California, Irvine, CA 92697
| | - Suzanne Sandmeyer
- Department of Biological Chemistry, University of California, Irvine, CA 92697
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, CB2 0QH Cambridge, United Kingdom
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25
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Yan R, Venkatakrishnan SV, Liu J, Bouman CA, Jiang W. MBIR: A cryo-ET 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information. J Struct Biol 2019; 206:183-192. [PMID: 30872095 PMCID: PMC6502674 DOI: 10.1016/j.jsb.2019.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022]
Abstract
Cryo-Electron Tomography (cryo-ET) has become an essential technique in revealing cellular and macromolecular assembly structures in their native states. However, due to radiation damage and the limited tilt range, cryo-ET suffers from low contrast and missing wedge artifacts, which limits the tomograms to low resolution and hinders further biological interpretation. In this study, we applied the Model-Based Iterative Reconstruction (MBIR) method to obtain tomographic 3D reconstructions of experimental cryo-ET datasets and demonstrated the advantages of MBIR in contrast improvement, missing wedge artifacts reduction, missing information restoration, and subtomogram averaging compared with other reconstruction approaches. Considering the outstanding reconstruction quality, MBIR has a great potential in the determination of high resolution biological structures with cryo-ET.
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Affiliation(s)
- Rui Yan
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, West Haven, CT 06516, USA
| | - Charles A Bouman
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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26
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Abstract
Immature retroviruses are built by the Gag polyprotein; Gag is then cut into domains, and the resulting CA capsid proteins form the mature capsid, which can mediate infection of a new cell. Murine leukemia virus (MLV) is a model retrovirus and the basis for gene-delivery vectors. We determined the capsid structures and architectures for immature and mature MLV. The mature MLV core does not enclose the genome in a closed capsid by using only part of the available proteins, as is the case for HIV-1. Instead, it wraps the genome in curved sheets incorporating most CA proteins. Retroviruses therefore have fundamentally different modes of core assembly and genome protection, which may relate to differences in their early replication. Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.
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Critical Role of the Human T-Cell Leukemia Virus Type 1 Capsid N-Terminal Domain for Gag-Gag Interactions and Virus Particle Assembly. J Virol 2018; 92:JVI.00333-18. [PMID: 29695435 DOI: 10.1128/jvi.00333-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/24/2018] [Indexed: 01/28/2023] Open
Abstract
The retroviral Gag protein is the main structural protein responsible for virus particle assembly and release. Like human immunodeficiency virus type 1 (HIV-1) Gag, human T-cell leukemia virus type 1 (HTLV-1) has a structurally conserved capsid (CA) domain, including a β-hairpin turn and a centralized coiled-coil-like structure of six α helices in the CA amino-terminal domain (NTD), as well as four α-helices in the CA carboxy-terminal domain (CTD). CA drives Gag oligomerization, which is critical for both immature Gag lattice formation and particle production. The HIV-1 CA CTD has previously been shown to be a primary determinant for CA-CA interactions, and while both the HTLV-1 CA NTD and CTD have been implicated in Gag-Gag interactions, our recent observations have implicated the HTLV-1 CA NTD as encoding key determinants that dictate particle morphology. Here, we have conducted alanine-scanning mutagenesis in the HTLV-1 CA NTD nucleotide-encoding sequences spanning the loop regions and amino acids at the beginning and ends of α-helices due to their structural dissimilarity from the HIV-1 CA NTD structure. We analyzed both Gag subcellular distribution and efficiency of particle production for these mutants. We discovered several important residues (i.e., M17, Q47/F48, and Y61). Modeling implicated that these residues reside at the dimer interface (i.e., M17 and Y61) or at the trimer interface (i.e., Q47/F48). Taken together, these observations highlight the critical role of the HTLV-1 CA NTD in Gag-Gag interactions and particle assembly, which is, to the best of our knowledge, in contrast to HIV-1 and other retroviruses.IMPORTANCE Retrovirus particle assembly and release from infected cells is driven by the Gag structural protein. Gag-Gag interactions, which form an oligomeric lattice structure at a particle budding site, are essential to the biogenesis of an infectious virus particle. The CA domain of Gag is generally thought to possess the key determinants for Gag-Gag interactions, and the present study has discovered several critical amino acid residues in the CA domain of HTLV-1 Gag, an important cancer-causing human retrovirus, which are distinct from that of HIV-1 as well as other retroviruses studied to date. Altogether, our results provide important new insights into a poorly understood aspect of HTLV-1 replication that significantly enhances our understanding of the molecular nature of Gag-Gag interaction determinants crucial for virus particle assembly.
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Píchalová R, Füzik T, Vokatá B, Rumlová M, Llano M, Dostálková A, Křížová I, Ruml T, Ulbrich P. Conserved cysteines in Mason-Pfizer monkey virus capsid protein are essential for infectious mature particle formation. Virology 2018; 521:108-117. [PMID: 29906704 DOI: 10.1016/j.virol.2018.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Retrovirus assembly is driven mostly by Gag polyprotein oligomerization, which is mediated by inter and intra protein-protein interactions among its capsid (CA) domains. Mason-Pfizer monkey virus (M-PMV) CA contains three cysteines (C82, C193 and C213), where the latter two are highly conserved among most retroviruses. To determine the importance of these cysteines, we introduced mutations of these residues in both bacterial and proviral vectors and studied their impact on the M-PMV life cycle. These studies revealed that the presence of both conserved cysteines of M-PMV CA is necessary for both proper assembly and virus infectivity. Our findings suggest a crucial role of these cysteines in the formation of infectious mature particles.
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Affiliation(s)
- Růžena Píchalová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
| | - Tibor Füzik
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
| | - Barbora Vokatá
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso, 500 West University El Paso, TX 79902, USA.
| | - Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
| | - Ivana Křížová
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
| | - Pavel Ulbrich
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
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Mak J, de Marco A. Recent advances in retroviruses via cryo-electron microscopy. Retrovirology 2018; 15:23. [PMID: 29471854 PMCID: PMC5824478 DOI: 10.1186/s12977-018-0405-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/14/2018] [Indexed: 12/14/2022] Open
Abstract
Cryo-electron microscopy has undergone a revolution in recent years and it has contributed significantly to a number of different areas in biological research. In this manuscript, we will describe some of the recent advancements in cryo-electron microscopy focussing on the advantages that this technique can bring rather than on the technology. We will then conclude discussing how the field of retrovirology has benefited from cryo-electron microscopy.
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Affiliation(s)
- Johnson Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport, QLD, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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Structural Biology in Situ Using Cryo-Electron Subtomogram Analysis. BIOLOGICAL AND MEDICAL PHYSICS, BIOMEDICAL ENGINEERING 2018. [DOI: 10.1007/978-3-319-68997-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Polymorphic Nature of Human T-Cell Leukemia Virus Type 1 Particle Cores as Revealed through Characterization of a Chronically Infected Cell Line. J Virol 2017; 91:JVI.00369-17. [PMID: 28615198 DOI: 10.1128/jvi.00369-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/05/2017] [Indexed: 12/18/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 cell-to-cell transmission is dependent on the release of infectious virus particles into the virological synapse. The HTLV-1 particle structure is still poorly understood, and previous studies analyzed viruses produced by transformed lymphocytic cell lines chronically infected with HTLV-1, particularly the MT-2 cell line, which harbors truncated proviruses and expresses aberrant forms of the Gag protein. In this study, we demonstrate that the chronically infected SP cell line harbors a relatively low number of proviruses, making it a more promising experimental system for the study of the HTLV-1 particle structure. We first identified the genomic sites of integration and characterized the genetic structure of the gag region in each provirus. We also determined that despite encoding a truncated Gag protein, only the full-length Gag protein was incorporated into virus particles. Cryo-transmission electron microscopy analyses of the purified virus particles revealed three classes of particles based upon capsid core morphology: complete cores, incomplete cores, and particles without distinct electron densities that would correlate with the capsid region of a core structure. Observed cores were generally polygonal, and virus particles were on average 115 nm in diameter. These data corroborate particle morphologies previously observed for MT-2 cells and provide evidence that the known poor infectivity of HTLV-1 particles may correlate with HTLV-1 particle populations containing few virus particles possessing a complete capsid core structure.IMPORTANCE Studies of retroviral particle core morphology have demonstrated a correlation between capsid core stability and the relative infectivity of the virus. In this study, we used cryo-transmission electron microscopy to demonstrate that HTLV-1 particles produced from a distinct chronically infected cell line are polymorphic in nature, with many particles lacking organized electron densities that would correlate with a complete core structure. These findings have important implications for infectious HTLV-1 spread, particularly in the context of cell-to-cell transmission, a critical step in HTLV-1 transmission and pathogenesis.
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In vitro assembly of the Rous Sarcoma Virus capsid protein into hexamer tubes at physiological temperature. Sci Rep 2017; 7:2913. [PMID: 28588198 PMCID: PMC5460288 DOI: 10.1038/s41598-017-02060-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
During a proteolytically-driven maturation process, the orthoretroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assembles in vitro at near-physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface. Tube assembly is strongly influenced by electrostatic effects, and is a nucleated process that remains thermodynamically favored at lower temperatures, but is effectively arrested by the large Gibbs energy barrier associated with nucleation. RSV CA tubes are multi-layered, being formed by nested and concentric tubes of capsid hexamers. However the spacer peptide acts as a layering determinant during tube assembly. If only a minor fraction of CA-SP is present, multi-layered tube formation is blocked, and single-layered tubes predominate. This likely prevents formation of biologically aberrant multi-layered capsids in the virion. The generation of single-layered hexamer tubes facilitated 3D helical image reconstruction from cryo-electron microscopy data, revealing the basic tube architecture.
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Castaño-Díez D. The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services. Acta Crystallogr D Struct Biol 2017; 73:478-487. [PMID: 28580909 PMCID: PMC5458489 DOI: 10.1107/s2059798317003369] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/28/2017] [Indexed: 11/10/2022] Open
Abstract
Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance.
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Affiliation(s)
- Daniel Castaño-Díez
- BioEM Lab at C-CINA, Biozentrum, University of Basel, Matenstrasse 26, CH-4058 Basel, Switzerland
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36
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Galaz-Montoya JG, Ludtke SJ. The advent of structural biology in situ by single particle cryo-electron tomography. BIOPHYSICS REPORTS 2017; 3:17-35. [PMID: 28781998 PMCID: PMC5516000 DOI: 10.1007/s41048-017-0040-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/30/2017] [Indexed: 01/06/2023] Open
Abstract
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
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Hagen WJH, Wan W, Briggs JAG. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J Struct Biol 2017; 197:191-198. [PMID: 27313000 PMCID: PMC5287356 DOI: 10.1016/j.jsb.2016.06.007] [Citation(s) in RCA: 405] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/09/2016] [Accepted: 06/11/2016] [Indexed: 12/31/2022]
Abstract
Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In combination with subtomogram averaging, detailed structures of repeating features can be resolved. CryoET data is collected as a series of images of the sample from different tilt angles; this is performed by physically rotating the sample in the microscope between each image. The angles at which the images are collected, and the order in which they are collected, together are called the tilt-scheme. Here we describe a "dose-symmetric tilt-scheme" that begins at low tilt and then alternates between increasingly positive and negative tilts. This tilt-scheme maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications. We describe implementation of the tilt-scheme in combination with further data-collection refinements including setting thresholds on acceptable drift and improving focus accuracy. Requirements for microscope set-up are introduced, and a macro is provided which automates the application of the tilt-scheme within SerialEM.
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Affiliation(s)
- Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
| | - William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany.
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Repression of the Chromatin-Tethering Domain of Murine Leukemia Virus p12. J Virol 2016; 90:11197-11207. [PMID: 27707926 DOI: 10.1128/jvi.01084-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/28/2016] [Indexed: 12/28/2022] Open
Abstract
Murine leukemia virus (MLV) p12, encoded within Gag, binds the viral preintegration complex (PIC) to the mitotic chromatin. This acts to anchor the viral PIC in the nucleus as the nuclear envelope re-forms postmitosis. Mutations within the p12 C terminus (p12 PM13 to PM15) block early stages in viral replication. Within the p12 PM13 region (p12 60PSPMA65), our studies indicated that chromatin tethering was not detected when the wild-type (WT) p12 protein (M63) was expressed as a green fluorescent protein (GFP) fusion; however, constructs bearing p12-I63 were tethered. N-terminal truncations of the activated p12-I63-GFP indicated that tethering increased further upon deletion of p12 25DLLTEDPPPY34, which includes the late domain required for viral assembly. The p12 PM15 sequence (p12 70RREPP74) is critical for wild-type viral viability; however, virions bearing the PM15 mutation (p12 70AAAAA74) with a second M63I mutant were viable, with a titer 18-fold lower than that of the WT. The p12 M63I mutation amplified chromatin tethering and compensated for the loss of chromatin binding of p12 PM15. Rescue of the p12-M63-PM15 nonviable mutant with prototype foamy virus (PFV) and Kaposi's sarcoma herpesvirus (KSHV) tethering sequences confirmed the function of p1270-74 in chromatin binding. Minimally, full-strength tethering was seen with only p12 61SPIASRLRGRR71 fused to GFP. These results indicate that the p12 C terminus alone is sufficient for chromatin binding and that the presence of the p12 25DLLTEDPPPY34 motif in the N terminus suppresses the ability to tether. IMPORTANCE This study defines a regulatory mechanism controlling the differential roles of the MLV p12 protein in early and late replication. During viral assembly and egress, the late domain within the p12 N terminus functions to bind host vesicle release factors. During viral entry, the C terminus of p12 is required for tethering to host mitotic chromosomes. Our studies indicate that the p12 domain including the PPPY late sequence temporally represses the p12 chromatin tethering motif. Maximal p12 tethering was identified with only an 11-amino-acid minimal chromatin tethering motif encoded at p1261-71 Within this region, the p12-M63I substitution switches p12 into a tethering-competent state, partially rescuing the p12-PM15 tethering mutant. A model for how this conformational change regulates early versus late functions is presented.
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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] [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.
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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
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Distinct Particle Morphologies Revealed through Comparative Parallel Analyses of Retrovirus-Like Particles. J Virol 2016; 90:8074-84. [PMID: 27356903 DOI: 10.1128/jvi.00666-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/21/2016] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED The Gag protein is the main retroviral structural protein, and its expression alone is usually sufficient for production of virus-like particles (VLPs). In this study, we sought to investigate-in parallel comparative analyses-Gag cellular distribution, VLP size, and basic morphological features using Gag expression constructs (Gag or Gag-YFP, where YFP is yellow fluorescent protein) created from all representative retroviral genera: Alpharetrovirus, Betaretrovirus, Deltaretrovirus, Epsilonretrovirus, Gammaretrovirus, Lentivirus, and Spumavirus. We analyzed Gag cellular distribution by confocal microscopy, VLP budding by thin-section transmission electron microscopy (TEM), and general morphological features of the VLPs by cryogenic transmission electron microscopy (cryo-TEM). Punctate Gag was observed near the plasma membrane for all Gag constructs tested except for the representative Beta- and Epsilonretrovirus Gag proteins. This is the first report of Epsilonretrovirus Gag localizing to the nucleus of HeLa cells. While VLPs were not produced by the representative Beta- and Epsilonretrovirus Gag proteins, the other Gag proteins produced VLPs as confirmed by TEM, and morphological differences were observed by cryo-TEM. In particular, we observed Deltaretrovirus-like particles with flat regions of electron density that did not follow viral membrane curvature, Lentivirus-like particles with a narrow range and consistent electron density, suggesting a tightly packed Gag lattice, and Spumavirus-like particles with large envelope protein spikes and no visible electron density associated with a Gag lattice. Taken together, these parallel comparative analyses demonstrate for the first time the distinct morphological features that exist among retrovirus-like particles. Investigation of these differences will provide greater insights into the retroviral assembly pathway. IMPORTANCE Comparative analysis among retroviruses has been critically important in enhancing our understanding of retroviral replication and pathogenesis, including that of important human pathogens such as human T-cell leukemia virus type 1 (HTLV-1) and HIV-1. In this study, parallel comparative analyses have been used to study Gag expression and virus-like particle morphology among representative retroviruses in the known retroviral genera. Distinct differences were observed, which enhances current knowledge of the retroviral assembly pathway.
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Wagner JM, Zadrozny KK, Chrustowicz J, Purdy MD, Yeager M, Ganser-Pornillos BK, Pornillos O. Crystal structure of an HIV assembly and maturation switch. eLife 2016; 5. [PMID: 27416583 PMCID: PMC4946879 DOI: 10.7554/elife.17063] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/13/2016] [Indexed: 12/25/2022] Open
Abstract
Virus assembly and maturation proceed through the programmed operation of molecular switches, which trigger both local and global structural rearrangements to produce infectious particles. HIV-1 contains an assembly and maturation switch that spans the C-terminal domain (CTD) of the capsid (CA) region and the first spacer peptide (SP1) of the precursor structural protein, Gag. The crystal structure of the CTD-SP1 Gag fragment is a goblet-shaped hexamer in which the cup comprises the CTD and an ensuing type II β-turn, and the stem comprises a 6-helix bundle. The β-turn is critical for immature virus assembly and the 6-helix bundle regulates proteolysis during maturation. This bipartite character explains why the SP1 spacer is a critical element of HIV-1 Gag but is not a universal property of retroviruses. Our results also indicate that HIV-1 maturation inhibitors suppress unfolding of the CA-SP1 junction and thereby delay access of the viral protease to its substrate. DOI:http://dx.doi.org/10.7554/eLife.17063.001 Viruses like HIV must undergo a process called maturation in order to successfully infect cells. Maturation involves a dramatic rearrangement in the architecture of the virus. That is to say, the virus’s internal protein coat – called the capsid – must change from an immature sphere into a mature cone-shaped coat. Notably, this maturation process is what is disrupted by the protease inhibitors that are a major component of anti-HIV drug cocktails. Structural changes in small portions of the capsid protein, termed molecular switches, commonly trigger the viral capsids to reorganize. The HIV capsid has two of these switches, and Wagner, Zadrozny et al. set out to understand how one of them – called the CA-SP1 switch – works. Solving the three-dimensional structure of the immature form of the CA-SP1 switch revealed that it forms a well-structured bundle of six helices. This helical bundle captures another section of the capsid protein that would otherwise be cut by a viral protease. The CA-SP1 switch therefore controls how quickly the protein is cut and the start of the maturation process. Wagner, Zadrozny et al. then discovered that other small molecule inhibitors of HIV, called maturation inhibitors, work by binding to and disrupting the transformation of the CA-SP1 switch. Finally, further experiments showed that the formation of the CA-SP1 helical bundle controls when the immature capsid shell forms and coordinates the process with the capsid gaining the genetic material of the virus. The new structure means that researchers now know what the HIV capsid looks like at the start and end of maturation. The next challenge will be to figure out exactly how the capsid changes from one form to the next as HIV matures. DOI:http://dx.doi.org/10.7554/eLife.17063.002
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Affiliation(s)
- Jonathan M Wagner
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Kaneil K Zadrozny
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Jakub Chrustowicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Michael D Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Mark Yeager
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States.,Department of Medicine, Division of Cardiovascular Medicine, University of Virginia Health System, Charlottesville, United States
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
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42
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Cryo-electron Microscopy Structure of the Native Prototype Foamy Virus Glycoprotein and Virus Architecture. PLoS Pathog 2016; 12:e1005721. [PMID: 27399201 PMCID: PMC4939959 DOI: 10.1371/journal.ppat.1005721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022] Open
Abstract
Foamy viruses (FV) belong to the genus Spumavirus, which forms a distinct lineage in the Retroviridae family. Although the infection in natural hosts and zoonotic transmission to humans is asymptomatic, FVs can replicate well in human cells making it an attractive gene therapy vector candidate. Here we present cryo-electron microscopy and (cryo-)electron tomography ultrastructural data on purified prototype FV (PFV) and PFV infected cells. Mature PFV particles have a distinct morphology with a capsid of constant dimension as well as a less ordered shell of density between the capsid and the membrane likely formed by the Gag N-terminal domain and the cytoplasmic part of the Env leader peptide gp18LP. The viral membrane contains trimeric Env glycoproteins partly arranged in interlocked hexagonal assemblies. In situ 3D reconstruction by subtomogram averaging of wild type Env and of a Env gp48TM- gp80SU cleavage site mutant showed a similar spike architecture as well as stabilization of the hexagonal lattice by clear connections between lower densities of neighboring trimers. Cryo-EM was employed to obtain a 9 Å resolution map of the glycoprotein in its pre-fusion state, which revealed extensive trimer interactions by the receptor binding subunit gp80SU at the top of the spike and three central helices derived from the fusion protein subunit gp48TM. The lower part of Env, presumably composed of interlaced parts of gp48TM, gp80SU and gp18LP anchors the spike at the membrane. We propose that the gp48TM density continues into three central transmembrane helices, which interact with three outer transmembrane helices derived from gp18LP. Our ultrastructural data and 9 Å resolution glycoprotein structure provide important new insights into the molecular architecture of PFV and its distinct evolutionary relationship with other members of the Retroviridae. Foamy viruses (FVs), which belong to the retroviral genus Spumavirus, are endemic to non-human primates and can be transmitted to humans. They are considered as potential vectors for gene therapy due to their broad cell tropism and their apparent apathogenicity in natural hosts and humans. In order to gain more insight into the ultrastructure of the prototype FV (PFV) we performed (cryo-)electron tomography and microscopy of infected cells and of isolated virions. We find that PFV contains a nucleocapsid of constant dimensions at its center, an intermediate shell of protein positioned between the core capsid and the viral membrane and glycoprotein that arranges into regular hexagonal lattices on the virus membrane. Structural analysis of the glycoprotein was performed in situ to a resolution of 9Å, which shows regular helical features such as a trimeric coiled coil of the fusion protein subunit, a hallmark of class I fusion proteins, spacer arms between the glycoprotein trimers and the arrangement of six transmembrane helices, a characteristic feature of the PFV Env glycoprotein. We discuss our results in light of the evolutionary relationship of PFV with other retroviruses as well as the role of the unique glycoprotein architecture on the virus life cycle.
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Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly. J Virol 2016; 90:5700-5714. [PMID: 27053549 DOI: 10.1128/jvi.00378-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED Extensive studies of orthoretroviral capsids have shown that many regions of the CA protein play unique roles at different points in the virus life cycle. The N-terminal domain (NTD) flexible-loop (FL) region is one such example: exposed on the outer capsid surface, it has been implicated in Gag-mediated particle assembly, capsid maturation, and early replication events. We have now defined the contributions of charged residues in the FL region of the Rous sarcoma virus (RSV) CA to particle assembly. Effects of mutations on assembly were assessed in vivo and in vitro and analyzed in light of new RSV Gag lattice models. Virus replication was strongly dependent on the preservation of charge at a few critical positions in Gag-Gag interfaces. In particular, a cluster of charges at the beginning of FL contributes to an extensive electrostatic network that is important for robust Gag assembly and subsequent capsid maturation. Second-site suppressor analysis suggests that one of these charged residues, D87, has distal influence on interhexamer interactions involving helix α7. Overall, the tolerance of FL to most mutations is consistent with current models of Gag lattice structures. However, the results support the interpretation that virus evolution has achieved a charge distribution across the capsid surface that (i) permits the packing of NTD domains in the outer layer of the Gag shell, (ii) directs the maturational rearrangements of the NTDs that yield a functional core structure, and (iii) supports capsid function during the early stages of virus infection. IMPORTANCE The production of infectious retrovirus particles is a complex process, a choreography of protein and nucleic acid that occurs in two distinct stages: formation and release from the cell of an immature particle followed by an extracellular maturation phase during which the virion proteins and nucleic acids undergo major rearrangements that activate the infectious potential of the virion. This study examines the contributions of charged amino acids on the surface of the Rous sarcoma virus capsid protein in the assembly of appropriately formed immature particles and the maturational transitions that create a functional virion. The results provide important biological evidence in support of recent structural models of the RSV immature virions and further suggest that immature particle assembly and virion maturation are controlled by an extensive network of electrostatic interactions and long-range communication across the capsid surface.
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Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annu Rev Biophys 2016; 45:253-78. [PMID: 27145875 DOI: 10.1146/annurev-biophys-062215-011113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed.
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Affiliation(s)
- Boon Chong Goh
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Jodi A Hadden
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rafael C Bernardi
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Abhishek Singharoy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Ryan McGreevy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Till Rudack
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - C Keith Cassidy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801;
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45
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Abstract
The HIV genome materials are encaged by a proteinaceous shell called the capsid, constructed from ∼1000-1500 copies of the capsid proteins. Because its stability and integrity are critical to the normal life cycle and infectivity of the virus, the HIV capsid is a promising antiviral drug target. In this paper, we review the studies shaping our understanding of the structure and dynamics of the capsid proteins and various forms of their assemblies, as well as the assembly mechanism.
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Affiliation(s)
- Bo Chen
- Department of Physics, University of Central Florida , Orlando, Florida 32816, United States
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46
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Perilla JR, Gronenborn AM. Molecular Architecture of the Retroviral Capsid. Trends Biochem Sci 2016; 41:410-420. [PMID: 27039020 DOI: 10.1016/j.tibs.2016.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/21/2016] [Accepted: 02/26/2016] [Indexed: 12/13/2022]
Abstract
Retroviral capsid cores are proteinaceous containers that self-assemble to encase the viral genome and a handful of proteins that promote infection. Their function is to protect and aid in the delivery of viral genes to the nucleus of the host, and, in many cases, infection pathways are influenced by capsid-cellular interactions. From a mathematical perspective, capsid cores are polyhedral cages and, as such, follow well-defined geometric rules. However, marked morphological differences in shapes exist, depending on virus type. Given the specific roles of capsid in the viral life cycle, the availability of detailed molecular structures, particularly at assembly interfaces, opens novel avenues for targeted drug development against these pathogens. Here, we summarize recent advances in the structure and understanding of retroviral capsid, with particular emphasis on assemblies and the capsid cores.
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Affiliation(s)
- Juan R Perilla
- Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, and Pittsburgh Center for HIV Protein Interactions, Pittsburgh, PA 15260, USA.
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47
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Mattei S, Schur FK, Briggs JA. Retrovirus maturation-an extraordinary structural transformation. Curr Opin Virol 2016; 18:27-35. [PMID: 27010119 DOI: 10.1016/j.coviro.2016.02.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/13/2016] [Indexed: 10/22/2022]
Abstract
Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered.
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Affiliation(s)
- Simone Mattei
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Florian Km Schur
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - John Ag Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany.
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48
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Thompson RF, Walker M, Siebert CA, Muench SP, Ranson NA. An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology. Methods 2016; 100:3-15. [PMID: 26931652 PMCID: PMC4854231 DOI: 10.1016/j.ymeth.2016.02.017] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/11/2016] [Accepted: 02/25/2016] [Indexed: 11/22/2022] Open
Abstract
Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150 kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a ‘resolution revolution’, owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM.
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Affiliation(s)
- Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Matt Walker
- MLW Consulting, 11 Race Hill, Launceston, Cornwall PL15 9BB, United Kingdom
| | - C Alistair Siebert
- Electron Bio-Imaging Centre, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Stephen P Muench
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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49
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Membrane Binding of the Rous Sarcoma Virus Gag Protein Is Cooperative and Dependent on the Spacer Peptide Assembly Domain. J Virol 2015; 90:2473-85. [PMID: 26676779 DOI: 10.1128/jvi.02733-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/09/2015] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED The principles underlying membrane binding and assembly of retroviral Gag proteins into a lattice are understood. However, little is known about how these processes are related. Using purified Rous sarcoma virus Gag and Gag truncations, we studied the interrelation of Gag-Gag interaction and Gag-membrane interaction. Both by liposome binding and by surface plasmon resonance on a supported bilayer, Gag bound to membranes much more tightly than did matrix (MA), the isolated membrane binding domain. In principle, this difference could be explained either by protein-protein interactions leading to cooperativity in membrane binding or by the simultaneous interaction of the N-terminal MA and the C-terminal nucleocapsid (NC) of Gag with the bilayer, since both are highly basic. However, we found that NC was not required for strong membrane binding. Instead, the spacer peptide assembly domain (SPA), a putative 24-residue helical sequence comprising the 12-residue SP segment of Gag and overlapping the capsid (CA) C terminus and the NC N terminus, was required. SPA is known to be critical for proper assembly of the immature Gag lattice. A single amino acid mutation in SPA that abrogates assembly in vitro dramatically reduced binding of Gag to liposomes. In vivo, plasma membrane localization was dependent on SPA. Disulfide cross-linking based on ectopic Cys residues showed that the contacts between Gag proteins on the membrane are similar to the known contacts in virus-like particles. Taken together, we interpret these results to mean that Gag membrane interaction is cooperative in that it depends on the ability of Gag to multimerize. IMPORTANCE The retroviral structural protein Gag has three major domains. The N-terminal MA domain interacts directly with the plasma membrane (PM) of cells. The central CA domain, together with immediately adjoining sequences, facilitates the assembly of thousands of Gag molecules into a lattice. The C-terminal NC domain interacts with the genome, resulting in packaging of viral RNA. For assembly in vitro with purified Gag, in the absence of membranes, binding of NC to nucleic acid somehow facilitates further Gag-Gag interactions that lead to formation of the Gag lattice. The contributions of MA-mediated membrane binding to virus particle assembly are not well understood. Here, we report that in the absence of nucleic acid, membranes provide a platform that facilitates Gag-Gag interactions. This study demonstrates that the binding of Gag, but not of MA, to membranes is cooperative and identifies SPA as a major factor that controls this cooperativity.
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50
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Carroni M, Saibil HR. Cryo electron microscopy to determine the structure of macromolecular complexes. Methods 2015; 95:78-85. [PMID: 26638773 PMCID: PMC5405050 DOI: 10.1016/j.ymeth.2015.11.023] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/14/2015] [Accepted: 11/26/2015] [Indexed: 01/28/2023] Open
Abstract
Structural biology. Cryo electron microscopy. Macromolecular complexes. Single particle analysis.
Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field.
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Affiliation(s)
- Marta Carroni
- ISMB, Birkbeck College, Malet St, London WC1E 7HX, UK
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