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Vaknin A, Grossman A, Durham ND, Lupovitz I, Goren S, Golani G, Roichman Y, Munro JB, Sorkin R. Ebola Virus Glycoprotein Strongly Binds to Membranes in the Absence of Receptor Engagement. ACS Infect Dis 2024; 10:1590-1601. [PMID: 38684073 DOI: 10.1021/acsinfecdis.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Ebola virus (EBOV) is an enveloped virus that must fuse with the host cell membrane in order to release its genome and initiate infection. This process requires the action of the EBOV envelope glycoprotein (GP), encoded by the virus, which resides in the viral envelope and consists of a receptor binding subunit, GP1, and a membrane fusion subunit, GP2. Despite extensive research, a mechanistic understanding of the viral fusion process is incomplete. To investigate GP-membrane association, a key step in the fusion process, we used two approaches: high-throughput measurements of single-particle diffusion and single-molecule measurements with optical tweezers. Using these methods, we show that the presence of the endosomal Niemann-Pick C1 (NPC1) receptor is not required for primed GP-membrane binding. In addition, we demonstrate this binding is very strong, likely attributed to the interaction between the GP fusion loop and the membrane's hydrophobic core. Our results also align with previously reported findings, emphasizing the significance of acidic pH in the protein-membrane interaction. Beyond Ebola virus research, our approach provides a powerful toolkit for studying other protein-membrane interactions, opening new avenues for a better understanding of protein-mediated membrane fusion events.
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Affiliation(s)
- Alisa Vaknin
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Alon Grossman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Natasha D Durham
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Inbal Lupovitz
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shahar Goren
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gonen Golani
- Department of Physics and Haifa Research Center for Theoretical Physics and Astrophysics, University of Haifa, Haifa 3498838, Israel
| | - Yael Roichman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Raymond and Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Raya Sorkin
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
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Jain A, Govindan R, Berkman AR, Luban J, Díaz-Salinas MA, Durham ND, Munro JB. Regulation of Ebola GP conformation and membrane binding by the chemical environment of the late endosome. PLoS Pathog 2023; 19:e1011848. [PMID: 38055723 PMCID: PMC10727438 DOI: 10.1371/journal.ppat.1011848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
Interaction between the Ebola virus envelope glycoprotein (GP) and the endosomal membrane is an essential step during virus entry into the cell. Acidic pH and Ca2+ have been implicated in mediating the GP-membrane interaction. However, the molecular mechanism by which these environmental factors regulate the conformational changes that enable engagement of GP with the target membrane is unknown. Here, we apply fluorescence correlation spectroscopy (FCS) and single-molecule Förster resonance energy transfer (smFRET) imaging to elucidate how the acidic pH, Ca2+ and anionic phospholipids in the late endosome promote GP-membrane interaction, thereby facilitating virus entry. We find that bis(monoacylglycero)phosphate (BMP), which is specific to the late endosome, is especially critical in determining the Ca2+-dependence of the GP-membrane interaction. Molecular dynamics (MD) simulations suggested residues in GP that sense pH and induce conformational changes that make the fusion loop available for insertion into the membrane. We similarly confirm residues in the fusion loop that mediate GP's interaction with Ca2+, which likely promotes local conformational changes in the fusion loop and mediates electrostatic interactions with the anionic phospholipids. Collectively, our results provide a mechanistic understanding of how the environment of the late endosome regulates the timing and efficiency of virus entry.
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Affiliation(s)
- Aastha Jain
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ramesh Govindan
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
- Medical Scientist Training Program, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alex R. Berkman
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Jeremy Luban
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Marco A. Díaz-Salinas
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Natasha D. Durham
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - James B. Munro
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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Palmateer NC, Munro JB, Nagaraj S, Crabtree J, Pelle R, Tallon L, Nene V, Bishop R, Silva JC. The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species. J Mol Evol 2023; 91:897-911. [PMID: 38017120 PMCID: PMC10730637 DOI: 10.1007/s00239-023-10142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/07/2023] [Indexed: 11/30/2023]
Abstract
Multigene families often play an important role in host-parasite interactions. One of the largest multigene families in Theileria parva, the causative agent of East Coast fever, is the T. parva repeat (Tpr) gene family. The function of the putative Tpr proteins remains unknown. The initial publication of the T. parva reference genome identified 39 Tpr family open reading frames (ORFs) sharing a conserved C-terminal domain. Twenty-eight of these are clustered in a central region of chromosome 3, termed the "Tpr locus", while others are dispersed throughout all four nuclear chromosomes. The Tpr locus contains three of the four assembly gaps remaining in the genome, suggesting the presence of additional, as yet uncharacterized, Tpr gene copies. Here, we describe the use of long-read sequencing to attempt to close the gaps in the reference assembly of T. parva (located among multigene families clusters), characterize the full complement of Tpr family ORFs in the T. parva reference genome, and evaluate their evolutionary relationship with Tpr homologs in other Theileria species. We identify three new Tpr family genes in the T. parva reference genome and show that sequence similarity among paralogs in the Tpr locus is significantly higher than between genes outside the Tpr locus. We also identify sequences homologous to the conserved C-terminal domain in five additional Theileria species. Using these sequences, we show that the evolution of this gene family involves conservation of a few orthologs across species, combined with gene gains/losses, and species-specific expansions.
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Affiliation(s)
- Nicholas C Palmateer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sushma Nagaraj
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roger Pelle
- International Livestock Research Institute, Nairobi, Kenya
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vish Nene
- International Livestock Research Institute, Nairobi, Kenya
| | - Richard Bishop
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal.
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4
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Mbambo G, Dwivedi A, Ifeonu OO, Munro JB, Shrestha B, Bromley RE, Hodges T, Adkins RS, Kouriba B, Diarra I, Niangaly A, Kone AK, Coulibaly D, Traore K, Dolo A, Thera MA, Laurens MB, Doumbo OK, Plowe CV, Berry AA, Travassos M, Lyke KE, Silva JC. Immunogenomic profile at baseline predicts host susceptibility to clinical malaria. Front Immunol 2023; 14:1179314. [PMID: 37465667 PMCID: PMC10351378 DOI: 10.3389/fimmu.2023.1179314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction Host gene and protein expression impact susceptibility to clinical malaria, but the balance of immune cell populations, cytokines and genes that contributes to protection, remains incompletely understood. Little is known about the determinants of host susceptibility to clinical malaria at a time when acquired immunity is developing. Methods We analyzed peripheral blood mononuclear cells (PBMCs) collected from children who differed in susceptibility to clinical malaria, all from a small town in Mali. PBMCs were collected from children aged 4-6 years at the start, peak and end of the malaria season. We characterized the immune cell composition and cytokine secretion for a subset of 20 children per timepoint (10 children with no symptomatic malaria age-matched to 10 children with >2 symptomatic malarial illnesses), and gene expression patterns for six children (three per cohort) per timepoint. Results We observed differences between the two groups of children in the expression of genes related to cell death and inflammation; in particular, inflammatory genes such as CXCL10 and STAT1 and apoptotic genes such as XAF1 were upregulated in susceptible children before the transmission season began. We also noted higher frequency of HLA-DR+ CD4 T cells in protected children during the peak of the malaria season and comparable levels cytokine secretion after stimulation with malaria schizonts across all three time points. Conclusion This study highlights the importance of baseline immune signatures in determining disease outcome. Our data suggests that differences in apoptotic and inflammatory gene expression patterns can serve as predictive markers of susceptibility to clinical malaria.
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Affiliation(s)
- Gillian Mbambo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Olukemi O. Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - James B. Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Biraj Shrestha
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Robin E. Bromley
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Theresa Hodges
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ricky S. Adkins
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Bourema Kouriba
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Issa Diarra
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Amadou Niangaly
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye K. Kone
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Drissa Coulibaly
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Karim Traore
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Amagana Dolo
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Matthew B. Laurens
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, International Centers for Excellence in Research (NIH), University of Science Techniques and Technologies of Bamako, Bamako, Mali
| | - Christopher V. Plowe
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Andrea A. Berry
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mark Travassos
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kirsten E. Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Global Health and Tropical Medicine, Instituto deHigiene e Medicina Tropical, Universidade Nova de Lisboa (GHTM, IHMT, UNL), Lisboa, Portugal
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5
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Chen C, Zhu R, Hodge EA, Díaz-Salinas MA, Nguyen A, Munro JB, Lee KK. hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics. ACS Infect Dis 2023; 9:1180-1189. [PMID: 37166130 PMCID: PMC10228703 DOI: 10.1021/acsinfecdis.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Indexed: 05/12/2023]
Abstract
SARS-CoV and SARS-CoV-2 cell entry begins when spike glycoprotein (S) docks with the human ACE2 (hACE2) receptor. While the two coronaviruses share a common receptor and architecture of S, they exhibit differences in interactions with hACE2 as well as differences in proteolytic processing of S that trigger the fusion machine. Understanding how those differences impact S activation is key to understand its function and viral pathogenesis. Here, we investigate hACE2-induced activation in SARS-CoV and SARS-CoV-2 S using hydrogen/deuterium-exchange mass spectrometry (HDX-MS). HDX-MS revealed differences in dynamics in unbound S, including open/closed conformational switching and D614G-induced S stability. Upon hACE2 binding, notable differences in transduction of allosteric changes were observed extending from the receptor binding domain to regions proximal to proteolytic cleavage sites and the fusion peptide. Furthermore, we report that dimeric hACE2, the native oligomeric form of the receptor, does not lead to any more pronounced structural effect in S compared to saturated monomeric hACE2 binding. These experiments provide mechanistic insights into receptor-induced activation of Sarbecovirus spike proteins.
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Affiliation(s)
- Chengbo Chen
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
- Biological
Physics Structure and Design Program, University
of Washington, Seattle, Washington 98195, USA
| | - Richard Zhu
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Edgar A. Hodge
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Marco A. Díaz-Salinas
- Department
of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Adam Nguyen
- Biological
Physics Structure and Design Program, University
of Washington, Seattle, Washington 98195, USA
| | - James B. Munro
- Department
of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Kelly K. Lee
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
- Biological
Physics Structure and Design Program, University
of Washington, Seattle, Washington 98195, USA
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6
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Egri SB, Wang X, Díaz-Salinas MA, Luban J, Dudkina NV, Munro JB, Shen K. Detergent modulates the conformational equilibrium of SARS-CoV-2 Spike during cryo-EM structural determination. Nat Commun 2023; 14:2527. [PMID: 37137903 PMCID: PMC10154187 DOI: 10.1038/s41467-023-38251-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
The Spike glycoprotein of SARS-CoV-2 mediates viral entry into the host cell via the interaction between its receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2). Spike RBD has been reported to adopt two primary conformations, a closed conformation in which the binding site is shielded and unable to interact with ACE2, and an open conformation that is capable of binding ACE2. Many structural studies have probed the conformational space of the homotrimeric Spike from SARS-CoV-2. However, how sample buffer conditions used during structural determination influence the Spike conformation is currently unclear. Here, we systematically explored the impact of commonly used detergents on the conformational space of Spike. We show that in the presence of detergent, the Spike glycoprotein predominantly occupies a closed conformational state during cryo-EM structural determination. However, in the absence of detergent, such conformational compaction was neither observed by cryo-EM, nor by single-molecule FRET designed to visualize the movement of RBD in solution in real-time. Our results highlight the highly sensitive nature of the Spike conformational space to buffer composition during cryo-EM structural determination, and emphasize the importance of orthogonal biophysical approaches to validate the structural models obtained.
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Affiliation(s)
- Shawn B Egri
- Program in Molecular Medicine and Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 373 Plantation St, Worcester, MA, 01605, USA
| | - Xue Wang
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, The Netherlands
| | - Marco A Díaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA, 01605, USA
| | - Jeremy Luban
- Program in Molecular Medicine and Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 373 Plantation St, Worcester, MA, 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Natalya V Dudkina
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, The Netherlands.
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA, 01605, USA.
| | - Kuang Shen
- Program in Molecular Medicine and Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 373 Plantation St, Worcester, MA, 01605, USA.
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
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7
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Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. bioRxiv 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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Affiliation(s)
- Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Shawn Egri
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- These authors contributed equally
| | - Marco A. Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Javier A. Jaimes
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Manish C. Choudhary
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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8
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Kumar MS, Stallworth KM, Murthy AC, Lim SM, Li N, Jain A, Munro JB, Fawzi NL, Lagier-Tourenne C, Bosco DA. Interactions between FUS and the C-terminal Domain of Nup62 are Sufficient for their Co-phase Separation into Amorphous Assemblies. J Mol Biol 2023; 435:167972. [PMID: 36690069 PMCID: PMC10329203 DOI: 10.1016/j.jmb.2023.167972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/29/2022] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
Deficient nucleocytoplasmic transport is emerging as a pathogenic feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), including in ALS caused by mutations in Fused in Sarcoma (FUS). Recently, both wild-type and ALS-linked mutant FUS were shown to directly interact with the phenylalanine-glycine (FG)-rich nucleoporin 62 (Nup62) protein, where FUS WT/ Nup62 interactions were enriched within the nucleus but ALS-linked mutant FUS/ Nup62 interactions were enriched within the cytoplasm of cells. Nup62 is a central channel Nup that has a prominent role in forming the selectivity filter within the nuclear pore complex and in regulating effective nucleocytoplasmic transport. Under conditions where FUS phase separates into liquid droplets in vitro, the addition of Nup62 caused the synergistic formation of amorphous assemblies containing both FUS and Nup62. Here, we examined the molecular determinants of this process using recombinant FUS and Nup62 proteins and biochemical approaches. We demonstrate that the structured C-terminal domain of Nup62 containing an alpha-helical coiled-coil region plays a dominant role in binding FUS and is sufficient for inducing the formation of FUS/Nup62 amorphous assemblies. In contrast, the natively unstructured, F/G repeat-rich N-terminal domain of Nup62 modestly contributed to FUS/Nup62 phase separation behavior. Expression of individual Nup62 domain constructs in human cells confirmed that the Nup62 C-terminal domain is essential for localization of the protein to the nuclear envelope. Our results raise the possibility that interactions between FUS and the C-terminal domain of Nup62 can influence the function of Nup62 under physiological and/or pathological conditions.
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Affiliation(s)
- Meenakshi Sundaram Kumar
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA; Biochemistry and Molecular Biotechnology Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karly M Stallworth
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA
| | - Anastasia C Murthy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Su Min Lim
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nan Li
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aastha Jain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA.
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9
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Durham ND, Jain A, Munro JB. Conformational dynamics of viral fusion proteins at single-molecule resolution. Biophys J 2023; 122:305a. [PMID: 36783528 DOI: 10.1016/j.bpj.2022.11.1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Natasha D Durham
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Aastha Jain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
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10
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Charbonneau AL, Brady A, Czajkowski K, Aluvathingal J, Canchi S, Carter R, Chard K, Clarke DJB, Crabtree J, Creasy HH, D'Arcy M, Felix V, Giglio M, Gingrich A, Harris RM, Hodges TK, Ifeonu O, Jeon M, Kropiwnicki E, Lim MCW, Liming RL, Lumian J, Mahurkar AA, Mandal M, Munro JB, Nadendla S, Richter R, Romano C, Rocca-Serra P, Schor M, Schuler RE, Tangmunarunkit H, Waldrop A, Williams C, Word K, Sansone SA, Ma'ayan A, Wagner R, Foster I, Kesselman C, Brown CT, White O. Making Common Fund data more findable: catalyzing a data ecosystem. Gigascience 2022; 11:6835135. [PMID: 36409836 PMCID: PMC9677336 DOI: 10.1093/gigascience/giac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/16/2022] [Accepted: 10/10/2022] [Indexed: 11/22/2022] Open
Abstract
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. This system is centered on a catalog that integrates detailed descriptions of biomedical datasets from individual Common Fund Programs' Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by individual DCCs and can readily describe nearly all forms of biomedical research data. We detail its use to ingest and index data from 11 DCCs.
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Affiliation(s)
| | - Arthur Brady
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Karl Czajkowski
- University of Southern California Information Sciences Institute, CA 90292, USA
| | - Jain Aluvathingal
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Saranya Canchi
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Robert Carter
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Kyle Chard
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan Crabtree
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Heather H Creasy
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Mike D'Arcy
- University of Southern California Information Sciences Institute, CA 90292, USA
| | - Victor Felix
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Michelle Giglio
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | | | - Rayna M Harris
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Theresa K Hodges
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Olukemi Ifeonu
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Minji Jeon
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eryk Kropiwnicki
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marisa C W Lim
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - R Lee Liming
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Jessica Lumian
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Anup A Mahurkar
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Meisha Mandal
- RTI International, Research Triangle Park 27709-2194, USA
| | - James B Munro
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Suvarna Nadendla
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Rudyard Richter
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Cia Romano
- University of Southern California Information Sciences Institute, CA 90292, USA.,Interface Guru, Tuscon 85701, USA
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford OX1 3QG, UK
| | - Michael Schor
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Robert E Schuler
- University of Southern California Information Sciences Institute, CA 90292, USA
| | | | - Alex Waldrop
- RTI International, Research Triangle Park 27709-2194, USA
| | - Cris Williams
- University of Southern California Information Sciences Institute, CA 90292, USA
| | | | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford OX1 3QG, UK
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rick Wagner
- University of California San Diego, San Diego, CA 92093, USA
| | - Ian Foster
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Carl Kesselman
- University of Southern California Information Sciences Institute, CA 90292, USA
| | - C Titus Brown
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Owen White
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
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11
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Diaz-Salinas MA, Li Q, Ejemel M, Yurkovetskiy L, Luban J, Shen K, Wang Y, Munro JB. Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. eLife 2022; 11:75433. [PMID: 35323111 PMCID: PMC8963877 DOI: 10.7554/elife.75433] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells through binding to angiotensin-converting enzyme 2 (ACE2). This interaction is mediated by the receptor-binding domain (RBD) of the viral spike (S) glycoprotein. Structural and dynamic data have shown that S can adopt multiple conformations, which controls the exposure of the ACE2-binding site in the RBD. Here, using single-molecule Förster resonance energy transfer (smFRET) imaging, we report the effects of ACE2 and antibody binding on the conformational dynamics of S from the Wuhan-1 strain and in the presence of the D614G mutation. We find that D614G modulates the energetics of the RBD position in a manner similar to ACE2 binding. We also find that antibodies that target diverse epitopes, including those distal to the RBD, stabilize the RBD in a position competent for ACE2 binding. Parallel solution-based binding experiments using fluorescence correlation spectroscopy (FCS) indicate antibody-mediated enhancement of ACE2 binding. These findings inform on novel strategies for therapeutic antibody cocktails.
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Affiliation(s)
- Marco A Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Qi Li
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Monir Ejemel
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Yang Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
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12
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Durham ND, Munro JB. Conformational dynamics of the Ebola virus glycoprotein (GP) under conditions relevant for membrane fusion. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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13
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Chen C, Munro JB, Lee KK. Structural dynamic changes in the SARS-CoV and SARS-CoV-2 S spike assemblies upon ACE2 activation. Biophys J 2022. [PMCID: PMC8833021 DOI: 10.1016/j.bpj.2021.11.497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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14
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Zhou AE, Shah ZV, Bradwell KR, Munro JB, Berry AA, Serre D, Takala-Harrison S, O'Connor TD, Silva JC, Travassos MA. STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. BMC Bioinformatics 2022; 23:15. [PMID: 34991452 PMCID: PMC8733436 DOI: 10.1186/s12859-021-04515-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023] Open
Abstract
Background RIFINs and STEVORs are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion. These two highly diverse multigene families feature multiple paralogs, making their classification challenging using traditional bioinformatic methods. Results STRIDE (STevor and RIfin iDEntifier) is an HMM-based, command-line program that automates the identification and classification of RIFIN and STEVOR protein sequences in the malaria parasite Plasmodium falciparum. STRIDE is more sensitive in detecting RIFINs and STEVORs than available PFAM and TIGRFAM tools and reports RIFIN subtypes and the number of sequences with a FHEYDER amino acid motif, which has been associated with severe malaria pathogenesis. Conclusions STRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04515-8.
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Affiliation(s)
- Albert E Zhou
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zalak V Shah
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Katie R Bradwell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrea A Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark A Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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15
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Schriml LM, Munro JB, Schor M, Olley D, McCracken C, Felix V, Baron JA, Jackson R, Bello SM, Bearer C, Lichenstein R, Bisordi K, Dialo NC, Giglio M, Greene C. The Human Disease Ontology 2022 update. Nucleic Acids Res 2021; 50:D1255-D1261. [PMID: 34755882 PMCID: PMC8728220 DOI: 10.1093/nar/gkab1063] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 01/31/2023] Open
Abstract
The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO’s 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years. The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational research projects and genomic resources around the world. This update reports on the addition of 1,793 new disease terms, a 14% increase of textual definitions and the integration of 22 137 new SubClassOf axioms defining disease to disease connections representing the DO’s complex disease classification. The DO’s updated website provides multifaceted etiology searching, enhanced documentation and educational resources.
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Affiliation(s)
- Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - James B Munro
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Mike Schor
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Dustin Olley
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Carrie McCracken
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Victor Felix
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - J Allen Baron
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | - Susan M Bello
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA
| | | | | | | | | | - Michelle Giglio
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Carol Greene
- University of Maryland School of Medicine, Baltimore, MD, USA
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16
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Díaz-Salinas MA, Li Q, Ejemel M, Yurkovetskiy L, Luban J, Shen K, Wang Y, Munro JB. Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. bioRxiv 2021. [PMID: 34790979 DOI: 10.1101/2021.10.29.466470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells through binding to angiotensin-converting enzyme 2 (ACE2). This interaction is mediated by the receptor-binding domain (RBD) of the viral spike (S) glycoprotein. Structural and dynamic data have shown that S can adopt multiple conformations, which controls the exposure of the ACE2-binding site in the RBD. Here, using single-molecule Förster resonance energy transfer (smFRET) imaging we report the effects of ACE2 and antibody binding on the conformational dynamics of S from the Wuhan-1 strain and the B.1 variant (D614G). We find that D614G modulates the energetics of the RBD position in a manner similar to ACE2 binding. We also find that antibodies that target diverse epitopes, including those distal to the RBD, stabilize the RBD in a position competent for ACE2 binding. Parallel solution-based binding experiments using fluorescence correlation spectroscopy (FCS) indicate antibody-mediated enhancement of ACE2 binding. These findings inform on novel strategies for therapeutic antibody cocktails.
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17
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Blakemore RJ, Burnett C, Swanson C, Kharytonchyk S, Telesnitsky A, Munro JB. Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR. Biophys J 2021; 120:4874-4890. [PMID: 34529947 PMCID: PMC8595565 DOI: 10.1016/j.bpj.2021.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
During HIV-1 assembly, the viral Gag polyprotein specifically selects the dimeric RNA genome for packaging into new virions. The 5′ untranslated region (5′UTR) of the dimeric genome may adopt a conformation that is optimal for recognition by Gag. Further conformational rearrangement of the 5′UTR, promoted by the nucleocapsid (NC) domain of Gag, is predicted during virus maturation. Two 5′UTR dimer conformations, the kissing dimer (KD) and the extended dimer (ED), have been identified in vitro, which differ in the extent of intermolecular basepairing. Whether 5′UTRs from different HIV-1 strains with distinct sequences have access to the same dimer conformations has not been determined. Here, we applied fluorescence cross-correlation spectroscopy and single-molecule Förster resonance energy transfer imaging to demonstrate that 5′UTRs from two different HIV-1 subtypes form (KDs) with divergent stabilities. We further show that both 5′UTRs convert to a stable dimer in the presence of the viral NC protein, adopting a conformation consistent with extensive intermolecular contacts. These results support a unified model in which the genomes of diverse HIV-1 strains adopt an ED conformation.
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Affiliation(s)
- Robert J Blakemore
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Graduate Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Canessa Swanson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore Country, Baltimore, Maryland
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.
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18
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Hobbs ET, Goralski SM, Mitchell A, Simpson A, Leka D, Kotey E, Sekira M, Munro JB, Nadendla S, Jackson R, Gonzalez-Aguirre A, Krallinger M, Giglio M, Erill I. ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. Front Res Metr Anal 2021; 6:674205. [PMID: 34327299 PMCID: PMC8313968 DOI: 10.3389/frma.2021.674205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/28/2021] [Indexed: 11/20/2022] Open
Abstract
Analysis of high-throughput experiments in the life sciences frequently relies upon standardized information about genes, gene products, and other biological entities. To provide this information, expert curators are increasingly relying on text mining tools to identify, extract and harmonize statements from biomedical journal articles that discuss findings of interest. For determining reliability of the statements, curators need the evidence used by the authors to support their assertions. It is important to annotate the evidence directly used by authors to qualify their findings rather than simply annotating mentions of experimental methods without the context of what findings they support. Text mining tools require tuning and adaptation to achieve accurate performance. Many annotated corpora exist to enable developing and tuning text mining tools; however, none currently provides annotations of evidence based on the extensive and widely used Evidence and Conclusion Ontology. We present the ECO-CollecTF corpus, a novel, freely available, biomedical corpus of 84 documents that captures high-quality, evidence-based statements annotated with the Evidence and Conclusion Ontology.
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Affiliation(s)
- Elizabeth T Hobbs
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Stephen M Goralski
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Ashley Mitchell
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Andrew Simpson
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Dorjan Leka
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Emmanuel Kotey
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Matt Sekira
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Suvarna Nadendla
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Rebecca Jackson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Martin Krallinger
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Michelle Giglio
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
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19
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Gao R, Yu CCJ, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES. A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy. Nat Nanotechnol 2021; 16:698-707. [PMID: 33782587 PMCID: PMC8197733 DOI: 10.1038/s41565-021-00875-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/11/2021] [Indexed: 05/08/2023]
Abstract
Expansion microscopy (ExM) physically magnifies biological specimens to enable nanoscale-resolution imaging using conventional microscopes. Current ExM methods permeate specimens with free-radical-chain-growth-polymerized polyacrylate hydrogels, whose network structure limits the local isotropy of expansion as well as the preservation of morphology and shape at the nanoscale. Here we report that ExM is possible using hydrogels that have a more homogeneous network structure, assembled via non-radical terminal linking of tetrahedral monomers. As with earlier forms of ExM, such 'tetra-gel'-embedded specimens can be iteratively expanded for greater physical magnification. Iterative tetra-gel expansion of herpes simplex virus type 1 (HSV-1) virions by ~10× in linear dimension results in a median spatial error of 9.2 nm for localizing the viral envelope layer, rather than 14.3 nm from earlier versions of ExM. Moreover, tetra-gel-based expansion better preserves the virion spherical shape. Thus, tetra-gels may support ExM with reduced spatial errors and improved local isotropy, pointing the way towards single-biomolecule accuracy ExM.
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Affiliation(s)
- Ruixuan Gao
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Chih-Chieh Jay Yu
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Linyi Gao
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Broad Institute, MIT, Cambridge, MA, USA
| | - Kiryl D Piatkevich
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
| | - Rachael L Neve
- Department of Neurology, Massachusetts General Hospital, Cambridge, MA, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Srigokul Upadhyayula
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Advanced Bioimaging Center, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Edward S Boyden
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.
- Media Arts and Sciences, MIT, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Koch Institute, MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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20
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Murray LP, Govindan R, Mora AC, Munro JB, Mace CR. Antibody affinity as a driver of signal generation in a paper-based immunoassay for Ebola virus surveillance. Anal Bioanal Chem 2021; 413:3695-3706. [PMID: 33852053 PMCID: PMC8044655 DOI: 10.1007/s00216-021-03317-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/09/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
During epidemics, such as the frequent and devastating Ebola virus outbreaks that have historically plagued regions of Africa, serological surveillance efforts are critical for viral containment and the development of effective antiviral therapeutics. Antibody serology can also be used retrospectively for population-level surveillance to provide a more complete estimate of total infections. Ebola surveillance efforts rely on enzyme-linked immunosorbent assays (ELISAs), which restrict testing to laboratories and are not adaptable for use in resource-limited settings. In this manuscript, we describe a paper-based immunoassay capable of detecting anti-Ebola IgG using Ebola virus envelope glycoprotein ectodomain (GP) as the affinity reagent. We evaluated seven monoclonal antibodies (mAbs) against GP—KZ52, 13C6, 4G7, 2G4, c6D8, 13F6, and 4F3—to elucidate the impact of binding affinity and binding epitope on assay performance and, ultimately, result interpretation. We used biolayer interferometry to characterize the binding of each antibody to GP before assessing their performance in our paper-based device. Binding affinity (KD) and on rate (kon) were major factors influencing the sensitivity of the paper-based immunoassay. mAbs with the best KD (3–25 nM) exhibited the lowest limits of detection (ca. μg mL−1), while mAbs with KD > 25 nM were undetectable in our device. Additionally, and most surprisingly, we determined that observed signals in paper devices were directly proportional to kon. These results highlight the importance of ensuring that the quality of recognition reagents is sufficient to support desired assay performance and suggest that the strength of an individual’s immune response can impact the interpretation of assay results.
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Affiliation(s)
- Lara P Murray
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Ramesh Govindan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Graduate School of Biomedical Sciences, Boston, MA, 02111, USA
| | - Andrea C Mora
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Graduate School of Biomedical Sciences, Boston, MA, 02111, USA
| | - Charles R Mace
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA.
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21
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Posavi M, Gulisija D, Munro JB, Silva JC, Lee CE. Rapid evolution of genome-wide gene expression and plasticity during saline to freshwater invasions by the copepod Eurytemora affinis species complex. Mol Ecol 2020; 29:4835-4856. [PMID: 33047351 DOI: 10.1111/mec.15681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
Saline migrants into freshwater habitats constitute among the most destructive invaders in aquatic ecosystems throughout the globe. However, the evolutionary and physiological mechanisms underlying such habitat transitions remain poorly understood. To explore the mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome-wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common-garden conditions (0 versus 15 PSU). We found that evolutionary shifts in gene expression (between saline and freshwater inbred lines) showed far greater changes and were more widespread than acclimatory responses to salinity (0 versus 15 PSU). Most notably, 30-40 genes showing evolutionary shifts in gene expression across the salinity boundary were associated with ion transport function, with inorganic cation transmembrane transport forming the largest Gene Ontology category. Of particular interest was the sodium transporter, the Na+ /H+ antiporter (NHA) gene family, which was discovered in animals relatively recently. Thirty key ion regulatory genes, such as NHA paralogue #7, demonstrated concordant evolutionary and plastic shifts in gene expression, suggesting the evolution of ion transporter function and plasticity during rapid invasions into novel salinities. Moreover, freshwater invasions were associated with the evolution of reduced plasticity in the freshwater population, again for the same key ion transporters, consistent with the predicted evolution of canalization following adaptation to stressful conditions. Our results have important implications for understanding evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.
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Affiliation(s)
- Marijan Posavi
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
| | - Davorka Gulisija
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
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22
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Abstract
Lassa virus (LASV) is the causative agent of Lassa hemorrhagic fever, a lethal disease endemic to Western Africa. LASV entry is mediated by the viral envelope glycoprotein (GP), a class I membrane fusogen and the sole viral surface antigen. Previous studies have identified components of the LASV entry pathway, including several cellular receptors and the requirement of endosomal acidification for infection. Here, we first demonstrate that incubation at a physiological temperature and pH consistent with the late endosome is sufficient to render pseudovirions, bearing LASV GP, non-infectious. Antibody binding indicates that this loss of infectivity is due to a conformational change in GP. Finally, we developed a single-particle fluorescence assay to directly visualize individual pseudovirions undergoing LASV GP-mediated lipid mixing with a supported planar bilayer. We report that exposure to endosomal pH at a physiologic temperature is sufficient to trigger GP-mediated lipid mixing. Furthermore, while a cellular receptor is not necessary to trigger lipid mixing, the presence of lysosomal-associated membrane protein 1 (LAMP1) increases the kinetics of lipid mixing at an endosomal pH. Furthermore, we find that LAMP1 permits robust lipid mixing under less acidic conditions than in its absence. These findings clarify our understanding of LASV GP-mediated fusion and the role of LAMP1 binding.
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Affiliation(s)
- Uriel Bulow
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA; (U.B.); (R.G.)
| | - Ramesh Govindan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA; (U.B.); (R.G.)
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - James B. Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA; (U.B.); (R.G.)
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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23
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Joshi VR, Newman RM, Pack ML, Power KA, Munro JB, Okawa K, Madani N, Sodroski JG, Schmidt AG, Allen TM. Gp41-targeted antibodies restore infectivity of a fusion-deficient HIV-1 envelope glycoprotein. PLoS Pathog 2020; 16:e1008577. [PMID: 32392227 PMCID: PMC7241850 DOI: 10.1371/journal.ppat.1008577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
The HIV-1 envelope glycoprotein (Env) mediates viral entry via conformational changes associated with binding the cell surface receptor (CD4) and coreceptor (CCR5/CXCR4), resulting in subsequent fusion of the viral and cellular membranes. While the gp120 Env surface subunit has been extensively studied for its role in viral entry and evasion of the host immune response, the gp41 transmembrane glycoprotein and its role in natural infection are less well characterized. Here, we identified a primary HIV-1 Env variant that consistently supports >300% increased viral infectivity in the presence of autologous or heterologous HIV-positive plasma. However, in the absence of HIV-positive plasma, viruses with this Env exhibited reduced infectivity that was not due to decreased CD4 binding. Using Env chimeras and sequence analysis, we mapped this phenotype to a change Q563R, in the gp41 heptad repeat 1 (HR1) region. We demonstrate that Q563R reduces viral infection by disrupting formation of the gp41 six-helix bundle required for virus-cell membrane fusion. Intriguingly, antibodies that bind cluster I epitopes on gp41 overcome this inhibitory effect, restoring infectivity to wild-type levels. We further demonstrate that the Q563R change increases HIV-1 sensitivity to broadly neutralizing antibodies (bNAbs) targeting the gp41 membrane-proximal external region (MPER). In summary, we identify an HIV-1 Env variant with impaired infectivity whose Env functionality is restored through the binding of host antibodies. These data contribute to our understanding of gp41 residues involved in membrane fusion and identify a mechanism by which host factors can alleviate a viral defect.
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Affiliation(s)
- Vinita R. Joshi
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruchi M. Newman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Melissa L. Pack
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Karen A. Power
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ken Okawa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Joseph G. Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Todd M. Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
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Das DK, Bulow U, Diehl WE, Durham ND, Senjobe F, Chandran K, Luban J, Munro JB. Conformational changes in the Ebola virus membrane fusion machine induced by pH, Ca2+, and receptor binding. PLoS Biol 2020; 18:e3000626. [PMID: 32040508 PMCID: PMC7034923 DOI: 10.1371/journal.pbio.3000626] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/21/2020] [Accepted: 01/23/2020] [Indexed: 12/22/2022] Open
Abstract
The Ebola virus (EBOV) envelope glycoprotein (GP) is a membrane fusion machine required for virus entry into cells. Following endocytosis of EBOV, the GP1 domain is cleaved by cellular cathepsins in acidic endosomes, removing the glycan cap and exposing a binding site for the Niemann-Pick C1 (NPC1) receptor. NPC1 binding to cleaved GP1 is required for entry. How this interaction translates to GP2 domain-mediated fusion of viral and endosomal membranes is not known. Here, using a bulk fluorescence dequenching assay and single-molecule Förster resonance energy transfer (smFRET)-imaging, we found that acidic pH, Ca2+, and NPC1 binding synergistically induce conformational changes in GP2 and permit virus-liposome lipid mixing. Acidic pH and Ca2+ shifted the GP2 conformational equilibrium in favor of an intermediate state primed for NPC1 binding. Glycan cap cleavage on GP1 enabled GP2 to transition from a reversible intermediate to an irreversible conformation, suggestive of the postfusion 6-helix bundle; NPC1 binding further promoted transition to the irreversible conformation. Thus, the glycan cap of GP1 may allosterically protect against inactivation of EBOV by premature triggering of GP2. The Ebola virus envelope glycoprotein is a membrane fusion machine required for the virus to enter into host cells. This study presents direct observation of the conformational changes that the envelope glycoprotein undergoes during the membrane fusion process.
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Affiliation(s)
- Dibyendu Kumar Das
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
- * E-mail: (JBM); (DKD)
| | - Uriel Bulow
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Natasha D. Durham
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Fernando Senjobe
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - James B. Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (JBM); (DKD)
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C Silva M, Chibucos M, Munro JB, Daugherty S, Coelho MM, C Silva J. Signature of adaptive evolution in olfactory receptor genes in Cory's Shearwater supports molecular basis for smell in procellariiform seabirds. Sci Rep 2020; 10:543. [PMID: 31953474 PMCID: PMC6969042 DOI: 10.1038/s41598-019-56950-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
Olfactory receptors (ORs), encoded by the largest vertebrate multigene family, enable the detection of thousands of unique odorants in the environment and consequently play a critical role in species survival. Here, we advance our knowledge of OR gene evolution in procellariiform seabirds, an avian group which relies on the sense of olfaction for critical ecological functions. We built a cosmid library of Cory's Shearwater (Calonectris borealis) genomic DNA, a model species for the study of olfaction-based navigation, and sequence OR gene-positive cosmid clones with a combination of sequencing technologies. We identified 220 OR open reading frames, 20 of which are full length, intact OR genes, and found a large ratio of partial and pseudogenes to intact OR genes (2:1), suggestive of a dynamic mode of evolution. Phylogenetic analyses revealed that while a few genes cluster with those of other sauropsid species in a γ (gamma) clade that predates the divergence of different avian lineages, most genes belong to an avian-specific γ-c clade, within which sequences cluster by species, suggesting frequent duplication and/or gene conversion events. We identified evidence of positive selection on full length γ-c clade genes. These patterns are consistent with a key role of adaptation in the functional diversification of olfactory receptor genes in a bird lineage that relies extensively on olfaction.
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Affiliation(s)
- Mónica C Silva
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
| | - Marcus Chibucos
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Sean Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - M Manuela Coelho
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
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26
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Durham ND, Howard AR, Govindan R, Senjobe F, Fels JM, Diehl WE, Luban J, Chandran K, Munro JB. Real-Time Analysis of Individual Ebola Virus Glycoproteins Reveals Pre-Fusion, Entry-Relevant Conformational Dynamics. Viruses 2020; 12:v12010103. [PMID: 31952255 PMCID: PMC7019799 DOI: 10.3390/v12010103] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/21/2022] Open
Abstract
The Ebola virus (EBOV) envelope glycoprotein (GP) mediates the fusion of the virion membrane with the membrane of susceptible target cells during infection. While proteolytic cleavage of GP by endosomal cathepsins and binding of the cellular receptor Niemann-Pick C1 protein (NPC1) are essential steps for virus entry, the detailed mechanisms by which these events promote membrane fusion remain unknown. Here, we applied single-molecule Förster resonance energy transfer (smFRET) imaging to investigate the structural dynamics of the EBOV GP trimeric ectodomain, and the functional transmembrane protein on the surface of pseudovirions. We show that in both contexts, pre-fusion GP is dynamic and samples multiple conformations. Removal of the glycan cap and NPC1 binding shift the conformational equilibrium, suggesting stabilization of conformations relevant to viral fusion. Furthermore, several neutralizing antibodies enrich alternative conformational states. This suggests that these antibodies neutralize EBOV by restricting access to GP conformations relevant to fusion. This work demonstrates previously unobserved dynamics of pre-fusion EBOV GP and presents a platform with heightened sensitivity to conformational changes for the study of GP function and antibody-mediated neutralization.
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Affiliation(s)
- Natasha D. Durham
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA;
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
- Correspondence: (N.D.D.); (J.B.M.)
| | - Angela R. Howard
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
| | - Ramesh Govindan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA;
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
| | - Fernando Senjobe
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
| | - J. Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (J.M.F.); (K.C.)
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (J.M.F.); (K.C.)
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA;
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
- Correspondence: (N.D.D.); (J.B.M.)
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27
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Moser KA, Drábek EF, Dwivedi A, Stucke EM, Crabtree J, Dara A, Shah Z, Adams M, Li T, Rodrigues PT, Koren S, Phillippy AM, Munro JB, Ouattara A, Sparklin BC, Dunning Hotopp JC, Lyke KE, Sadzewicz L, Tallon LJ, Spring MD, Jongsakul K, Lon C, Saunders DL, Ferreira MU, Nyunt MM, Laufer MK, Travassos MA, Sauerwein RW, Takala-Harrison S, Fraser CM, Sim BKL, Hoffman SL, Plowe CV, Silva JC. Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential. Genome Med 2020; 12:6. [PMID: 31915075 PMCID: PMC6950926 DOI: 10.1186/s13073-019-0708-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation of these results and understanding of their relevance to vaccine efficacy have been hampered by the lack of knowledge on genetic differences between vaccine and CHMI strains, and how these strains are related to parasites in malaria endemic regions. METHODS Whole genome sequencing using long-read (Pacific Biosciences) and short-read (Illumina) sequencing platforms was conducted to generate de novo genome assemblies for the vaccine strain, NF54, and for strains used in heterologous CHMI (7G8 from Brazil, NF166.C8 from Guinea, and NF135.C10 from Cambodia). The assemblies were used to characterize sequences in each strain relative to the reference 3D7 (a clone of NF54) genome. Strains were compared to each other and to a collection of clinical isolates (sequenced as part of this study or from public repositories) from South America, sub-Saharan Africa, and Southeast Asia. RESULTS While few variants were detected between 3D7 and NF54, we identified tens of thousands of variants between NF54 and the three heterologous strains. These variants include SNPs, indels, and small structural variants that fall in regulatory and immunologically important regions, including transcription factors (such as PfAP2-L and PfAP2-G) and pre-erythrocytic antigens that may be key for sporozoite vaccine-induced protection. Additionally, these variants directly contributed to diversity in immunologically important regions of the genomes as detected through in silico CD8+ T cell epitope predictions. Of all heterologous strains, NF135.C10 had the highest number of unique predicted epitope sequences when compared to NF54. Comparison to global clinical isolates revealed that these four strains are representative of their geographic origin despite long-term culture adaptation; of note, NF135.C10 is from an admixed population, and not part of recently formed subpopulations resistant to artemisinin-based therapies present in the Greater Mekong Sub-region. CONCLUSIONS These results will assist in the interpretation of vaccine efficacy of whole-organism vaccines against homologous and heterologous CHMI.
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Affiliation(s)
- Kara A. Moser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Present address: Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, USA
| | - Elliott F. Drábek
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Emily M. Stucke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Antoine Dara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Zalak Shah
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Tao Li
- Sanaria, Inc., Rockville, MD 20850 USA
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - James B. Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Benjamin C. Sparklin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Kirsten E. Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Luke J. Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Michele D. Spring
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Krisada Jongsakul
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chanthap Lon
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - David L. Saunders
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Present address: Warfighter Expeditionary Medicine and Treatment, US Army Medical Material Development Activity, Frederick, USA
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Myaing M. Nyunt
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Present address: Duke Global Health Institute, Duke University, Durham, NC 27708 USA
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Mark A. Travassos
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Robert W. Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | | | | | - Christopher V. Plowe
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Present address: Duke Global Health Institute, Duke University, Durham, NC 27708 USA
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
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Alsahafi N, Bakouche N, Kazemi M, Richard J, Ding S, Bhattacharyya S, Das D, Anand SP, Prévost J, Tolbert WD, Lu H, Medjahed H, Gendron-Lepage G, Ortega Delgado GG, Kirk S, Melillo B, Mothes W, Sodroski J, Smith AB, Kaufmann DE, Wu X, Pazgier M, Rouiller I, Finzi A, Munro JB. An Asymmetric Opening of HIV-1 Envelope Mediates Antibody-Dependent Cellular Cytotoxicity. Cell Host Microbe 2019; 25:578-587.e5. [PMID: 30974085 DOI: 10.1016/j.chom.2019.03.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/03/2018] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
The HIV-1 envelope glycoprotein (Env) (gp120-gp41)3 is the target for neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC). HIV-1 Env is flexible, sampling different conformational states. Before engaging CD4, Env adopts a closed conformation (State 1) that is largely antibody resistant. CD4 binding induces an intermediate state (State 2), followed by an open conformation (State 3) that is susceptible to engagement by antibodies that recognize otherwise occluded epitopes. We investigate conformational changes in Env that induce ADCC in the presence of a small-molecule CD4-mimetic compound (CD4mc). We uncover an asymmetric Env conformation (State 2A) recognized by antibodies targeting the conserved gp120 inner domain and mediating ADCC. Sera from HIV+ individuals contain these antibodies, which can stabilize Env State 2A in combination with CD4mc. Additionally, triggering State 2A on HIV-infected primary CD4+ T cells exposes epitopes that induce ADCC. Strategies that induce this Env conformation may represent approaches to fight HIV-1 infection.
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Affiliation(s)
- Nirmin Alsahafi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Nordine Bakouche
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Mohsen Kazemi
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Durba Das
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - William D Tolbert
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, USA
| | | | | | | | - Sharon Kirk
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Bruno Melillo
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montreal, QC, Canada; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Isabelle Rouiller
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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Munro JB, Lee KK. Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein. Curr HIV Res 2019; 16:5-12. [PMID: 29268688 DOI: 10.2174/1570162x16666171222110025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in structural characterization of the HIV envelope glycoprotein (Env) have provided a high-resolution glimpse of the architecture of this target for neutralizing antibodies and the machinery responsible for mediating receptor binding and membrane fusion. These structures primarily capture the detailed organization of the receptor-naive, prefusion conformation of Env, but under native solution conditions Env is highly dynamic, sampling multiple conformational states as well as exhibiting local protein flexibility. METHODS Special emphasis is placed on the use of biophysical methods, including single-molecule fluorescence microscopy and hydrogen/deuterium-exchange mass spectrometry. RESULTS Using novel biophysical approaches, striking isolate-specific differences in Env's dynamic profile have been revealed that appear to underlie phenotypic differences of the viral isolates such as neutralization sensitivity and CD4 receptor reactivity. CONCLUSION Structural studies are complemented by novel biophysical investigations that enable visualization of the dynamics of HIV-1 Env under native conditions. These approaches will also enable us to gain new insights into the mechanisms of action of antibodies and drugs.
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Affiliation(s)
- James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States
| | - Kelly K Lee
- Department of Medicinal Chemistry and Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
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30
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Lu M, Ma X, Castillo-Menendez LR, Gorman J, Alsahafi N, Ermel U, Terry DS, Chambers M, Peng D, Zhang B, Zhou T, Reichard N, Wang K, Grover JR, Carman BP, Gardner MR, Nikić-Spiegel I, Sugawara A, Arthos J, Lemke EA, Smith AB, Farzan M, Abrams C, Munro JB, McDermott AB, Finzi A, Kwong PD, Blanchard SC, Sodroski JG, Mothes W. Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET. Nature 2019; 568:415-419. [PMID: 30971821 PMCID: PMC6655592 DOI: 10.1038/s41586-019-1101-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/08/2019] [Indexed: 11/09/2022]
Abstract
The HIV-1 envelope glycoprotein (Env) trimer mediates cell entry and is
conformationally dynamic1–8. Imaging
by single-molecule fluorescence resonance energy transfer (smFRET) has revealed
that, on the surface of intact virions, mature pre-fusion Env transitions from a
pre-triggered conformation (state 1) through a default intermediate conformation
(state 2) to a conformation in which it is bound to three CD4 receptor molecules
(state 3)8–10. It is currently unclear how these
states relate to known structures. Breakthroughs in the structural
characterization of the HIV-1 Env trimer have previously been achieved by
generating soluble and proteolytically cleaved trimers of gp140 Env that are
stabilized by a disulfide bond, an isoleucine-to-proline substitution at residue
559 and a truncation at residue 664 (SOSIP.664 trimers)5,11–18.
Cryo-electron microscopy studies have been performed with C-terminally truncated
Env of the HIV-1JR-FL strain in complex with the antibody PGT15119. Both approaches have revealed similar
structures for Env. Although these structures have been presumed to represent
the pre-triggered state 1 of HIV-1 Env, this hypothesis has never directly been
tested. Here we use smFRET to compare the conformational states of Env trimers
used for structural studies with native Env on intact virus. We find that the
constructs upon which extant high-resolution structures are based predominantly
occupy downstream conformations that represent states 2 and 3. Therefore, the
structure of the pretriggered state-1 conformation of viral Env that has been
identified by smFRET and that is preferentially stabilized by many broadly
neutralizing antibodies—and thus of interest for the design of
immunogens—remains unknown.
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Affiliation(s)
- Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Xiaochu Ma
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Luis R Castillo-Menendez
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nirmin Alsahafi
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Utz Ermel
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Michael Chambers
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dongjun Peng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nick Reichard
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Kevin Wang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Brennan P Carman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew R Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, University of Tuebingen, Tuebingen, Germany
| | - Akihiro Sugawara
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg University Mainz, Mainz, Germany.,Institute of Molecular Biology (IMB), Johannes Gutenberg University Mainz, Mainz, Germany.,Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Cameron Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, USA
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrés Finzi
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
| | - Joseph G Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
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31
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Kumar Das D, Durham N, Howard A, Munro JB. Conformational Dynamics Related to Membrane Fusion Observed in Single Viral Envelope Glycoproteins. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. Both Anaplasma and Neorickettsia fail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria, Wolbachia organisms are delineated into species different from the currently used supergroup designations, while Rickettsia organisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results. IMPORTANCE With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the order Rickettsiales, where species designations have been applied inconsistently. Our results indicate that the Rickettsia genus has an overabundance of species designations, that the current Anaplasma and Neorickettsia genus designations are both too broad and need to be divided, and that there are clear demarcations of Wolbachia species that do not align precisely with the existing supergroup designations.
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Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA
| | - James B. Munro
- Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, Maryland, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA
- Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore, Baltimore, Maryland, USA
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Abstract
No immunogen has been found that elicits a broadly neutralizing antibody (bNAb) response sufficient for development into an HIV vaccine. In this issue of Cell Host and Microbe, Zhang et al. (2018) rationally design an HIV envelope glycoprotein variant that provides new hope that such an immunogen may be attainable.
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Affiliation(s)
- James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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34
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Das DK, Govindan R, Nikić-Spiegel I, Krammer F, Lemke EA, Munro JB. Direct Visualization of the Conformational Dynamics of Single Influenza Hemagglutinin Trimers. Cell 2018; 174:926-937.e12. [PMID: 29961575 DOI: 10.1016/j.cell.2018.05.050] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/17/2018] [Accepted: 05/24/2018] [Indexed: 01/02/2023]
Abstract
Influenza hemagglutinin (HA) is the canonical type I viral envelope glycoprotein and provides a template for the membrane-fusion mechanisms of numerous viruses. The current model of HA-mediated membrane fusion describes a static "spring-loaded" fusion domain (HA2) at neutral pH. Acidic pH triggers a singular irreversible conformational rearrangement in HA2 that fuses viral and cellular membranes. Here, using single-molecule Förster resonance energy transfer (smFRET)-imaging, we directly visualized pH-triggered conformational changes of HA trimers on the viral surface. Our analyses reveal reversible exchange between the pre-fusion and two intermediate conformations of HA2. Acidification of pH and receptor binding shifts the dynamic equilibrium of HA2 in favor of forward progression along the membrane-fusion reaction coordinate. Interaction with the target membrane promotes irreversible transition of HA2 to the post-fusion state. The reversibility of HA2 conformation may protect against transition to the post-fusion state prior to arrival at the target membrane.
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Affiliation(s)
- Dibyendu Kumar Das
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA.
| | - Ramesh Govindan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, University of Tuebingen, 72076 Tuebingen, Germany
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy, and Geosciences, Johannes Gutenberg-University Mainz, Johannes-von-Mullerweg 6, 55128 Mainz, Germany; Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA.
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35
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Pettigrew MM, Ahearn CP, Gent JF, Kong Y, Gallo MC, Munro JB, D'Mello A, Sethi S, Tettelin H, Murphy TF. Haemophilus influenzae genome evolution during persistence in the human airways in chronic obstructive pulmonary disease. Proc Natl Acad Sci U S A 2018; 115:E3256-E3265. [PMID: 29555745 PMCID: PMC5889651 DOI: 10.1073/pnas.1719654115] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) exclusively colonize and infect humans and are critical to the pathogenesis of chronic obstructive pulmonary disease (COPD). In vitro and animal models do not accurately capture the complex environments encountered by NTHi during human infection. We conducted whole-genome sequencing of 269 longitudinally collected cleared and persistent NTHi from a 15-y prospective study of adults with COPD. Genome sequences were used to elucidate the phylogeny of NTHi isolates, identify genomic changes that occur with persistence in the human airways, and evaluate the effect of selective pressure on 12 candidate vaccine antigens. Strains persisted in individuals with COPD for as long as 1,422 d. Slipped-strand mispairing, mediated by changes in simple sequence repeats in multiple genes during persistence, regulates expression of critical virulence functions, including adherence, nutrient uptake, and modification of surface molecules, and is a major mechanism for survival in the hostile environment of the human airways. A subset of strains underwent a large 400-kb inversion during persistence. NTHi does not undergo significant gene gain or loss during persistence, in contrast to other persistent respiratory tract pathogens. Amino acid sequence changes occurred in 8 of 12 candidate vaccine antigens during persistence, an observation with important implications for vaccine development. These results indicate that NTHi alters its genome during persistence by regulation of critical virulence functions primarily by slipped-strand mispairing, advancing our understanding of how a bacterial pathogen that plays a critical role in COPD adapts to survival in the human respiratory tract.
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Affiliation(s)
- Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510
| | - Christian P Ahearn
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
| | - Janneane F Gent
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06510
| | - Yong Kong
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06510
- W.M. Keck Foundation Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT 06510
| | - Mary C Gallo
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Adonis D'Mello
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Sanjay Sethi
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Department of Medicine, Veterans Affairs Western New York Healthcare System, Buffalo, NY 14215
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Timothy F Murphy
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14203;
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Division of Infectious Diseases, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14203
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36
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Ma X, Lu M, Gorman J, Terry DS, Hong X, Zhou Z, Zhao H, Altman RB, Arthos J, Blanchard SC, Kwong PD, Munro JB, Mothes W. HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations. eLife 2018; 7:e34271. [PMID: 29561264 PMCID: PMC5896952 DOI: 10.7554/elife.34271] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/20/2018] [Indexed: 01/02/2023] Open
Abstract
HIV-1 entry into cells requires binding of the viral envelope glycoprotein (Env) to receptor CD4 and coreceptor. Imaging of individual Env molecules on native virions shows Env trimers to be dynamic, spontaneously transitioning between three distinct well-populated conformational states: a pre-triggered Env (State 1), a default intermediate (State 2) and a three-CD4-bound conformation (State 3), which can be stabilized by binding of CD4 and coreceptor-surrogate antibody 17b. Here, using single-molecule Fluorescence Resonance Energy Transfer (smFRET), we show the default intermediate configuration to be asymmetric, with individual protomers adopting distinct conformations. During entry, this asymmetric intermediate forms when a single CD4 molecule engages the trimer. The trimer can then transition to State 3 by binding additional CD4 molecules and coreceptor.
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Affiliation(s)
- Xiaochu Ma
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Maolin Lu
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaUnited States
| | - Daniel S Terry
- Department of Physiology and BiophysicsWeill Cornell Medical College of Cornell UniversityNew YorkUnited States
| | - Xinyu Hong
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Zhou Zhou
- Department of Physiology and BiophysicsWeill Cornell Medical College of Cornell UniversityNew YorkUnited States
| | - Hong Zhao
- Department of Physiology and BiophysicsWeill Cornell Medical College of Cornell UniversityNew YorkUnited States
| | - Roger B Altman
- Department of Physiology and BiophysicsWeill Cornell Medical College of Cornell UniversityNew YorkUnited States
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaUnited States
| | - Scott C Blanchard
- Department of Physiology and BiophysicsWeill Cornell Medical College of Cornell UniversityNew YorkUnited States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaUnited States
| | - James B Munro
- Department of Molecular Biology and MicrobiologyTufts University School of MedicineBostonUnited States
| | - Walther Mothes
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
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37
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Lu M, Ma X, Luis R. CM, Ermel U, Daniel S. T, Gorman J, Reichard N, Wang K, Grover J, Finzi A, Munro JB, Kwong PD, Blanchard SC, Sodroski J, Mothes W. Single-Molecule FRET Reveals an Additional Conformational State of HIV-1 Envelope Glycoprotein Critical for Vaccine Design. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Eyun SI, Soh HY, Posavi M, Munro JB, Hughes DS, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Park EO, Silva JC, Gibbs RA, Richards S, Lee CE. Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda. Mol Biol Evol 2017; 34:1838-1862. [PMID: 28460028 PMCID: PMC5850775 DOI: 10.1093/molbev/msx147] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to have proliferated during terrestrial colonization by insects (hexapods), but their association with other pancrustacean clades and with independent terrestrial colonizations in other arthropod subphyla have been unclear. We also examine hypotheses on which arthropod CRG family is most ancient. Thus, we reconstructed phylogenies of CRGs, including those from new arthropod genomes and transcriptomes, and mapped CRG gains and losses across arthropod lineages. Our analysis was strengthened by including crustaceans, especially copepods, which reside outside the hexapod/branchiopod clade within the subphylum Pancrustacea. We generated the first high-resolution genome sequence of the copepod Eurytemora affinis and annotated its CRGs. We found odorant receptors and odorant binding proteins present only in hexapods (insects) and absent from all other arthropod lineages, indicating that they are not universal adaptations to land. Gustatory receptors likely represent the oldest chemosensory receptors among CRGs, dating back to the Placozoa. We also clarified and confirmed the evolutionary history of antennal ionotropic receptors across the Arthropoda. All antennal ionotropic receptors in E. affinis were expressed more highly in males than in females, suggestive of an association with male mate-recognition behavior. This study is the most comprehensive comparative analysis to date of CRG family evolution across the largest and most speciose metazoan phylum Arthropoda.
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Affiliation(s)
- Seong-il Eyun
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE
| | - Ho Young Soh
- Faculty of Marine Technology, Chonnam National University, Yeosu, Korea
| | - Marijan Posavi
- Center of Rapid Evolution (CORE) and Department of Integrative Biology, University of Wisconsin, Madison, WI
| | - James B. Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | | | - Shwetha C. Murali
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jiaxin Qu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Sandra L. Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Huyen Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | - Kim C. Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Eun-Ok Park
- Fisheries Science Institute, Chonnam National University, Yeosu, Korea
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Carol Eunmi Lee
- Center of Rapid Evolution (CORE) and Department of Integrative Biology, University of Wisconsin, Madison, WI
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Ma X, Lu M, Terry DS, Gorman J, Kwong PD, Blanchard SC, Munro JB, Mothes W. Single-Molecule FRET Delineates Asymmetric Trimer Conformations during HIV-1 Entry. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Gotia HT, Munro JB, Knowles DP, Daubenberger CA, Bishop RP, Silva JC. Absolute Quantification of the Host-To-Parasite DNA Ratio in Theileria parva-Infected Lymphocyte Cell Lines. PLoS One 2016; 11:e0150401. [PMID: 26930209 PMCID: PMC4773007 DOI: 10.1371/journal.pone.0150401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Theileria parva is a tick-transmitted intracellular apicomplexan pathogen of cattle in sub-Saharan Africa that causes East Coast fever (ECF). ECF is an acute fatal disease that kills over one million cattle annually, imposing a tremendous burden on African small-holder cattle farmers. The pathology and level of T. parva infections in its wildlife host, African buffalo (Syncerus caffer), and in cattle are distinct. We have developed an absolute quantification method based on quantitative PCR (qPCR) in which recombinant plasmids containing single copy genes specific to the parasite (apical membrane antigen 1 gene, ama1) or the host (hypoxanthine phosphoribosyltransferase 1, hprt1) are used as the quantification reference standards. Our study shows that T. parva and bovine cells are present in similar numbers in T. parva-infected lymphocyte cell lines and that consequently, due to its much smaller genome size, T. parva DNA comprises between 0.9% and 3% of the total DNA samples extracted from these lines. This absolute quantification assay of parasite and host genome copy number in a sample provides a simple and reliable method of assessing T. parva load in infected bovine lymphocytes, and is accurate over a wide range of host-to-parasite DNA ratios. Knowledge of the proportion of target DNA in a sample, as enabled by this method, is essential for efficient high-throughput genome sequencing applications for a variety of intracellular pathogens. This assay will also be very useful in future studies of interactions of distinct host-T. parva stocks and to fully characterize the dynamics of ECF infection in the field.
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Affiliation(s)
- Hanzel T. Gotia
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore Maryland, United States of America
| | - James B. Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore Maryland, United States of America
| | - Donald P. Knowles
- Animal Disease Research Unit, Agricultural Research Service, US Department of Agriculture, Pullman, Washington, United States of America
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, Maryland, United States of America
| | - Claudia A. Daubenberger
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Richard P. Bishop
- International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore Maryland, United States of America
- * E-mail:
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Abstract
Understanding the structure of the native HIV-1 envelope spike protein is critical for the development of vaccines and antiviral therapies. In this issue of Structure, Guttman and colleagues use hydrogen-deuterium exchange (HDX) to provide new insights into the structure of the HIV-1 Env trimer and enhance our understanding of how HIV-1 Env is activated for virus fusion.
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Affiliation(s)
- James B Munro
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
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Pancera M, Zhou T, Druz A, Georgiev IS, Soto C, Gorman J, Huang J, Acharya P, Chuang GY, Ofek G, Stewart-Jones GBE, Stuckey J, Bailer RT, Joyce MG, Louder MK, Tumba N, Yang Y, Zhang B, Cohen MS, Haynes BF, Mascola JR, Morris L, Munro JB, Blanchard SC, Mothes W, Connors M, Kwong PD. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 2014; 514:455-61. [PMID: 25296255 PMCID: PMC4348022 DOI: 10.1038/nature13808] [Citation(s) in RCA: 592] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.
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Affiliation(s)
- Marie Pancera
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Aliaksandr Druz
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ivelin S. Georgiev
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Cinque Soto
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jason Gorman
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jinghe Huang
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Priyamvada Acharya
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gilad Ofek
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Guillaume B. E. Stewart-Jones
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jonathan Stuckey
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Robert T. Bailer
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - M. Gordon Joyce
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mark K. Louder
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nancy Tumba
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and University of the Witwatersrand, Johannesburg, South Africa, and Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Yongping Yang
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Myron S. Cohen
- Departments of Medicine, Epidemiology, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Barton F. Haynes
- Duke University Human Vaccine Institute, Departments of Medicine, Surgery, Pediatrics and Immunology, Duke University School of Medicine, and the Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, North Carolina 27710, USA
| | - John R. Mascola
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and University of the Witwatersrand, Johannesburg, South Africa, and Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - James B. Munro
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10021, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Mark Connors
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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43
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Munro JB, Gorman J, Ma X, Zhou Z, Arthos J, Burton DR, Koff WC, Courter JR, Smith AB, Kwong PD, Blanchard SC, Mothes W. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science 2014; 346:759-63. [PMID: 25298114 DOI: 10.1126/science.1254426] [Citation(s) in RCA: 377] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The HIV-1 envelope (Env) mediates viral entry into host cells. To enable the direct imaging of conformational dynamics within Env, we introduced fluorophores into variable regions of the glycoprotein gp120 subunit and measured single-molecule fluorescence resonance energy transfer within the context of native trimers on the surface of HIV-1 virions. Our observations revealed unliganded HIV-1 Env to be intrinsically dynamic, transitioning between three distinct prefusion conformations, whose relative occupancies were remodeled by receptor CD4 and antibody binding. The distinct properties of neutralization-sensitive and neutralization-resistant HIV-1 isolates support a dynamics-based mechanism of immune evasion and ligand recognition.
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Affiliation(s)
- James B Munro
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaochu Ma
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10021, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Wayne C Koff
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Joel R Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10021, USA.
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
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44
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Uchil PD, Pawliczek T, Reynolds TD, Ding S, Hinz A, Munro JB, Huang F, Floyd RW, Yang H, Hamilton WL, Bewersdorf J, Xiong Y, Calderwood DA, Mothes W. TRIM15 is a focal adhesion protein that regulates focal adhesion disassembly. J Cell Sci 2014; 127:3928-42. [PMID: 25015296 DOI: 10.1242/jcs.143537] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Focal adhesions are macromolecular complexes that connect the actin cytoskeleton to the extracellular matrix. Dynamic turnover of focal adhesions is crucial for cell migration. Paxillin is a multi-adaptor protein that plays an important role in regulating focal adhesion dynamics. Here, we identify TRIM15, a member of the tripartite motif protein family, as a paxillin-interacting factor and a component of focal adhesions. TRIM15 localizes to focal contacts in a myosin-II-independent manner by an interaction between its coiled-coil domain and the LD2 motif of paxillin. Unlike other focal adhesion proteins, TRIM15 is a stable focal adhesion component with restricted mobility due to its ability to form oligomers. TRIM15-depleted cells display impaired cell migration and reduced focal adhesion disassembly rates, in addition to enlarged focal adhesions. Thus, our studies demonstrate a cellular function for TRIM15 as a regulatory component of focal adhesion turnover and cell migration.
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Affiliation(s)
- Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Tobias Pawliczek
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Tracy D Reynolds
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Siyuan Ding
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Angelika Hinz
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - James B Munro
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Fang Huang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Robert W Floyd
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Haitao Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - William L Hamilton
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - David A Calderwood
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA Departments of Pharmacology and Yale Cancer Center, Yale University, New Haven, CT 06520, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
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Munro JB, Jacob CG, Silva JC. A novel clade of unique eukaryotic ribonucleotide reductase R2 subunits is exclusive to apicomplexan parasites. J Mol Evol 2013; 77:92-106. [PMID: 24046025 PMCID: PMC3824934 DOI: 10.1007/s00239-013-9583-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/05/2013] [Indexed: 11/30/2022]
Abstract
Apicomplexa are protist parasites of tremendous medical and economic importance, causing millions of deaths and billions of dollars in losses each year. Apicomplexan-related diseases may be controlled via inhibition of essential enzymes. Ribonucleotide reductase (RNR) provides the only de novo means of synthesizing deoxyribonucleotides, essential precursors for DNA replication and repair. RNR has long been the target of antibacterial and antiviral therapeutics. However, targeting this ubiquitous protein in eukaryotic pathogens may be problematic unless these proteins differ significantly from that of their respective host. The typical eukaryotic RNR enzymes belong to class Ia, and the holoenzyme consists minimally of two R1 and two R2 subunits (α2β2). We generated a comparative, annotated, structure-based, multiple-sequence alignment of R2 subunits, identified a clade of R2 subunits unique to Apicomplexa, and determined its phylogenetic position. Our analyses revealed that the apicomplexan-specific sequences share characteristics with both class I R2 and R2lox proteins. The putative radical-harboring residue, essential for the reduction reaction by class Ia R2-containing holoenzymes, was not conserved within this group. Phylogenetic analyses suggest that class Ia subunits are not monophyletic and consistently placed the apicomplexan-specific clade sister to the remaining class Ia eukaryote R2 subunits. Our research suggests that the novel apicomplexan R2 subunit may be a promising candidate for chemotherapeutic-induced inhibition as it differs greatly from known eukaryotic host RNRs and may be specifically targeted.
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Affiliation(s)
- James B Munro
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
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46
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Abstract
The life cycle of most viruses involves the release of particles into the extracellular space. Consequently, the study of virus egress as well as virus entry has focused almost exclusively on the biology of cell-free virus. However, cell-free virus spread is often very inefficient. Specific barriers, either located in the donor cell or in the target cell, prevent efficient spread by the cell-free mode. In contrast, viral spread by direct cell-cell contact is largely unaffected by most of these barriers resulting in preferential spread by cell-to-cell transmission. Virus cell-to-cell transmission allows an efficient coordination of several steps of the viral life cycle. It often involves complex inter-cellular adhesion, cellular polarity and intra-cellular trafficking. Because virus cell-to-cell transmission can involve transmission through zones of tight cell-cell contact that are resistant to neutralizing antibodies and reach a high local particle concentration, cell-to-cell transmission can contribute to the pathogenesis of viral infections.
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Affiliation(s)
- Peng Zhong
- Department of Microbial Pathogenesis, Yale University School of Medicine, 295 Congress Ave., New Haven, CT 06536, USA
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47
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Munro JB, Heraty JM, Burks RA, Hawks D, Mottern J, Cruaud A, Rasplus JY, Jansta P. A molecular phylogeny of the Chalcidoidea (Hymenoptera). PLoS One 2011; 6:e27023. [PMID: 22087244 PMCID: PMC3207832 DOI: 10.1371/journal.pone.0027023] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 10/07/2011] [Indexed: 11/19/2022] Open
Abstract
Chalcidoidea (Hymenoptera) are extremely diverse with more than 23,000 species described and over 500,000 species estimated to exist. This is the first comprehensive phylogenetic analysis of the superfamily based on a molecular analysis of 18S and 28S ribosomal gene regions for 19 families, 72 subfamilies, 343 genera and 649 species. The 56 outgroups are comprised of Ceraphronoidea and most proctotrupomorph families, including Mymarommatidae. Data alignment and the impact of ambiguous regions are explored using a secondary structure analysis and automated (MAFFT) alignments of the core and pairing regions and regions of ambiguous alignment. Both likelihood and parsimony approaches are used to analyze the data. Overall there is no impact of alignment method, and few but substantial differences between likelihood and parsimony approaches. Monophyly of Chalcidoidea and a sister group relationship between Mymaridae and the remaining Chalcidoidea is strongly supported in all analyses. Either Mymarommatoidea or Diaprioidea are the sister group of Chalcidoidea depending on the analysis. Likelihood analyses place Rotoitidae as the sister group of the remaining Chalcidoidea after Mymaridae, whereas parsimony nests them within Chalcidoidea. Some traditional family groups are supported as monophyletic (Agaonidae, Eucharitidae, Encyrtidae, Eulophidae, Leucospidae, Mymaridae, Ormyridae, Signiphoridae, Tanaostigmatidae and Trichogrammatidae). Several other families are paraphyletic (Perilampidae) or polyphyletic (Aphelinidae, Chalcididae, Eupelmidae, Eurytomidae, Pteromalidae, Tetracampidae and Torymidae). Evolutionary scenarios discussed for Chalcidoidea include the evolution of phytophagy, egg parasitism, sternorrhynchan parasitism, hypermetamorphic development and heteronomy.
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Affiliation(s)
- James B. Munro
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - John M. Heraty
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Roger A. Burks
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - David Hawks
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Jason Mottern
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Astrid Cruaud
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Jean-Yves Rasplus
- INRA, Centre de Biologie et de Gestion des Populations, Montferrier-sur-Lez, France
| | - Petr Jansta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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48
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Munro JB, Silva JC. Ribonucleotide reductase as a target to control apicomplexan diseases. Curr Issues Mol Biol 2011; 14:9-26. [PMID: 21791713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
Malaria is caused by species in the apicomplexan genus Plasmodium, which infect hundreds of millions of people each year and kill close to one million. While malaria is the most notorious of the apicomplexan-caused diseases, other members of eukaryotic phylum Apicomplexa are responsible for additional, albeit less well-known, diseases in humans, economically important livestock, and a variety of other vertebrates. Diseases such as babesiosis (hemolytic anemia), theileriosis and East Coast Fever, cryptosporidiosis, and toxoplasmosis are caused by the apicomplexans Babesia, Theileria, Cryptosporidium and Toxoplasma, respectively. In addition to the loss of human life, these diseases are responsible for losses of billions of dollars annually. Hence, the research into new drug targets remains a high priority. Ribonucleotide reductase (RNR) is an essential enzyme found in all domains of life. It is the only means by which de novo synthesis of deoxyribonucleotides occurs, without which DNA replication and repair cannot proceed. RNR has long been the target of antiviral, antibacterial and anti-cancer therapeutics. Herein, we review the chemotherapeutic methods used to inhibit RNR, with particular emphasis on the role of RNR inhibition in Apicomplexa, and in light of the novel RNR R2_e2 subunit recently identified in apicomplexan parasites.
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Affiliation(s)
- James B Munro
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, 21201, USA
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Munro JB, Wasserman MR, Altman RB, Wang L, Blanchard SC. Correlated conformational events in EF-G and the ribosome regulate translocation. Nat Struct Mol Biol 2010; 17:1470-7. [PMID: 21057527 PMCID: PMC2997181 DOI: 10.1038/nsmb.1925] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 09/09/2010] [Indexed: 11/09/2022]
Abstract
In bacteria, the translocation of tRNA and mRNA with respect to the ribosome is catalyzed by the conserved GTPase elongation factor-G (EF-G). To probe the rate-determining features in this process, we imaged EF-G-catalyzed translocation from two unique structural perspectives using single-molecule fluorescence resonance energy transfer. The data reveal that the rate at which the ribosome spontaneously achieves a transient, 'unlocked' state is closely correlated with the rate at which the tRNA-like domain IV-V element of EF-G engages the A site. After these structural transitions, translocation occurs comparatively fast, suggesting that conformational processes intrinsic to the ribosome determine the rate of translocation. Experiments conducted in the presence of non-hydrolyzable GTP analogs and specific antibiotics further reveal that allosterically linked conformational events in EF-G and the ribosome mediate rapid, directional substrate movement and EF-G release.
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Affiliation(s)
- James B Munro
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, USA
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Abstract
A key intermediate in translocation is an 'unlocked state' of the pre-translocation ribosome in which the P-site tRNA adopts the P/E hybrid state, the L1 stalk domain closes and ribosomal subunits adopt a ratcheted configuration. Here, through two- and three-colour smFRET imaging from multiple structural perspectives, EF-G is shown to accelerate structural and kinetic pathways in the ribosome, leading to this transition. The EF-G-bound ribosome remains highly dynamic in nature, wherein, the unlocked state is transiently and reversibly formed. The P/E hybrid state is energetically favoured, but exchange with the classical P/P configuration persists; the L1 stalk adopts a fast dynamic mode characterized by rapid cycles of closure and opening. These data support a model in which P/E hybrid state formation, L1 stalk closure and subunit ratcheting are loosely coupled, independent processes that must converge to achieve the unlocked state. The highly dynamic nature of these motions, and their sensitivity to conformational and compositional changes in the ribosome, suggests that regulating the formation of this intermediate may present an effective avenue for translational control.
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Affiliation(s)
- James B Munro
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Chang-Shung Tung
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kevin Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
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