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Bera S, Shi K, Aihara H, Grandgenett DP, Pandey KK. Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration. J Biol Chem 2023; 299:104730. [PMID: 37084813 PMCID: PMC10209032 DOI: 10.1016/j.jbc.2023.104730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023] Open
Abstract
Integration of retroviral DNA into the host genome involves the formation of integrase (IN)-DNA complexes termed intasomes. Further characterization of these complexes is needed to understand their assembly process. Here, we report the single-particle cryo-EM structure of the Rous sarcoma virus (RSV) strand transfer complex (STC) intasome produced with IN and a preassembled viral/target DNA substrate at 3.36 Å resolution. The conserved intasome core region consisting of IN subunits contributing active sites interacting with viral/target DNA has a resolution of 3 Å. Our structure demonstrated the flexibility of the distal IN subunits relative to the IN subunits in the conserved intasome core, similar to results previously shown with the RSV octameric cleaved synaptic complex intasome produced with IN and viral DNA only. An extensive analysis of higher resolution STC structure helped in the identification of nucleoprotein interactions important for intasome assembly. Using structure-function studies, we determined the mechanisms of several IN-DNA interactions critical for assembly of both RSV intasomes. We determined the role of IN residues R244, Y246, and S124 in cleaved synaptic complex and STC intasome assemblies and their catalytic activities, demonstrating differential effects. Taken together, these studies advance our understanding of different RSV intasome structures and molecular determinants involved in their assembly.
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Affiliation(s)
- Sibes Bera
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Duane P Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA
| | - Krishan K Pandey
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA.
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Pandey KK, Bera S, Shi K, Rau MJ, Oleru AV, Fitzpatrick JAJ, Engelman AN, Aihara H, Grandgenett DP. Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome. Commun Biol 2021; 4:330. [PMID: 33712691 PMCID: PMC7955051 DOI: 10.1038/s42003-021-01855-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
Despite conserved catalytic integration mechanisms, retroviral intasomes composed of integrase (IN) and viral DNA possess diverse structures with variable numbers of IN subunits. To investigate intasome assembly mechanisms, we employed the Rous sarcoma virus (RSV) IN dimer that assembles a precursor tetrameric structure in transit to the mature octameric intasome. We determined the structure of RSV octameric intasome stabilized by a HIV-1 IN strand transfer inhibitor using single particle cryo-electron microscopy. The structure revealed significant flexibility of the two non-catalytic distal IN dimers along with previously unrecognized movement of the conserved intasome core, suggesting ordered conformational transitions between intermediates that may be important to capture the target DNA. Single amino acid substitutions within the IN C-terminal domain affected intasome assembly and function in vitro and infectivity of pseudotyped RSV virions. Unexpectedly, 17 C-terminal amino acids of IN were dispensable for virus infection despite regulating the transition of the tetrameric intasome to the octameric form in vitro. We speculate that this region may regulate the binding of highly flexible distal IN dimers to the intasome core to form the octameric complex. Our studies reveal key steps in the assembly of RSV intasomes. Pandey, Bera, Shi et al. report the cryo-electron microscopy structure of the Rous sarcoma virus octameric intasome complex stabilized by a HIV-1 integrase strand transfer inhibitor. This new structure highlights the intrinsic flexibility of the distal integrase subunits and suggests that ordered conformational transitions occur within the conserved intasome core during the assembly process.
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Affiliation(s)
- Krishan K Pandey
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA.
| | - Sibes Bera
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA
| | - Amarachi V Oleru
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA.,Departments of Cell Biology & Physiology and Neuroscience, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Duane P Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA.
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Bhatt V, Shi K, Salamango DJ, Moeller NH, Pandey KK, Bera S, Bohl HO, Kurniawan F, Orellana K, Zhang W, Grandgenett DP, Harris RS, Sundborger-Lunna AC, Aihara H. Structural basis of host protein hijacking in human T-cell leukemia virus integration. Nat Commun 2020; 11:3121. [PMID: 32561747 PMCID: PMC7305164 DOI: 10.1038/s41467-020-16963-6] [Citation(s) in RCA: 22] [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: 03/03/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Integration of the reverse-transcribed viral DNA into host chromosomes is a critical step in the life-cycle of retroviruses, including an oncogenic delta(δ)-retrovirus human T-cell leukemia virus type-1 (HTLV-1). Retroviral integrase forms a higher order nucleoprotein assembly (intasome) to catalyze the integration reaction, in which the roles of host factors remain poorly understood. Here, we use cryo-electron microscopy to visualize the HTLV-1 intasome at 3.7-Å resolution. The structure together with functional analyses reveal that the B56γ (B'γ) subunit of an essential host enzyme, protein phosphatase 2 A (PP2A), is repurposed as an integral component of the intasome to mediate HTLV-1 integration. Our studies reveal a key host-virus interaction underlying the replication of an important human pathogen and highlight divergent integration strategies of retroviruses.
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Affiliation(s)
- Veer Bhatt
- The Hormel Institute, University of Minnesota, 801 16th Avenue N.E., Austin, MN, 55912, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
| | - Ke Shi
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Daniel J Salamango
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Nicholas H Moeller
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Krishan K Pandey
- Department of Molecular Microbiology and Immunology, Saint Louis University, 1100 S. Grand Boulevard, St. Louis, MO, 63104, USA
| | - Sibes Bera
- Department of Molecular Microbiology and Immunology, Saint Louis University, 1100 S. Grand Boulevard, St. Louis, MO, 63104, USA
| | - Heather O Bohl
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Fredy Kurniawan
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Kayo Orellana
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Wei Zhang
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
- Characterization Facility, College of Science and Engineering, University of Minnesota, 100 Union Street S.E., Minneapolis, MN, 55455, USA
| | - Duane P Grandgenett
- Department of Molecular Microbiology and Immunology, Saint Louis University, 1100 S. Grand Boulevard, St. Louis, MO, 63104, USA
| | - Reuben S Harris
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
| | - Anna C Sundborger-Lunna
- The Hormel Institute, University of Minnesota, 801 16th Avenue N.E., Austin, MN, 55912, USA.
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA.
| | - Hideki Aihara
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA.
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA.
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