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Viruses
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12th International Retroviral Symposium: Assembly, Maturation and Uncoating
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12th International Retroviral Symposium: Assembly, Maturation and Uncoating

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 10855

Special Issue Editors

Dr. Saveez Saffarian

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Guest Editor
University of Utah, Salt Lake City, UT, USA
Interests: RNA viruses assembly and replication; HIV; SARS-CoV-2; VSV;
Dr. Mark C. Williams

E-Mail Website
Guest Editor
Department of Physics, Northeastern University, Boston, MA, USA
Interests: nucleic acid chaperone activity; retroviral capsid uncoating; nucleic-acid protein interactions; DNA condensation; single molecule biophysics
Special Issues, Collections and Topics in MDPI journals
Dr. Eric O. Freed

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Guest Editor
National Cancer Institute, Frederick, MD, USA
Interests: HIV; retrovirus; virus assembly; virus budding; maturation; envelope glycoproteins; Gag proteins; drug resistance; maturation inhibitors
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Dr. Delphine M. Muriaux

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Guest Editor
IRIM CNRS, University of Montpellier, Montpellier, France
Interests: RNA envelopped viruses assembly; super resolution microscopy; HIV-1 assembly; CD4 T cell plasma membrane; viral proteins; host-cell lipids; sub-plasma membrane; pandemic Influenza H1N1; respiratory viruses; fluorescent replicative viruses; antiviral compounds; emerging SARS-CoV2; arboviruses
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Karin Musier-Forsyth

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Guest Editor
Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
Interests: HIV and related retroviruses; retroviral assembly, genomic RNA packaging and host cell-viral interactions; protein-RNA interactions; aminoacyl-tRNA synthetases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Between the 6th and 9th September 2023, a group of 95 scientists gathered at the Snowbird ski resort in the mountains outside Salt Lake City, Utah, for a conference focused on topics related to retroviral assembly, maturation, and early events in the virus replication cycle that are associated with maturation (e.g., nuclear import and uncoating of retroviral complexes). This conference had its genesis in what was originally named the International Retroviral Nucleocapsid Symposium (IRNCS). This meeting was launched in 1998 at the National Cancer Institute in Frederick Maryland, and was organized by Lou Henderson and Larry Arthur. The second meeting was subsequently held in Lyon, France (1999); the third in Annapolis, Maryland (2001); the fourth in Strasbourg, France (2003); the fifth in Montreal, Canada (2005); the sixth in Amsterdam, the Netherlands (2007); the seventh in Minneapolis, Minnesota (2009); and the eighth in Barcelona, Spain (2011). In 2013, its name changed slightly to reflect the broadening scope of the meeting: the ninth Retroviral Nucleocapsid Protein and Assembly Symposium was held in Montreal, Canada; the 10th in Montpelier, France (2016); and the 11th at Northeastern University in Boston, MA (2019). After a hiatus due to COVID-19, the 12th conference was held at Snowbird.This latest conference drew inspiration from the Retrovirus Assembly Meeting (RAM), which was held in Prague in the Czech Republic in 2000, 2004, and 2008, and was organized by, among others, Eric Hunter, Michaela Rumlova, and Tomas Ruml.

This 12th meeting was organized by the Guest Editors of this Special Issue: Saveez Saffarian, who served as the local and primary organizer; Delphine Muriaux, Mark Williams, Eric Freed and Karin Musier-Forsyth. The conference was arranged into a series of sessions: Envelope Incorporation, Structure, and Function; HIV-1 RNA Nuclear Trafficking, Packaging, and Translation; Virus Assembly Part I: Role of RNA and Membranes; Virus Assembly Part II; Therapeutic Strategies; Capsid Trafficking, Uncoating, and Integration; and Capsid Protein Structure and Function; Maturation; and Host Factors.

The Guest Editors of this Special Issue welcome submissions not only from conference attendees, but also from others with aligned research interests.

Dr. Saveez Saffarian
Dr. Mark C. Williams
Dr. Eric O. Freed
Dr. Delphine M. Muriaux
Prof. Dr. Karin Musier-Forsyth
Guest Editors

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Keywords

  • retrovirus
  • HIV
  • virus assembly
  • virus budding
  • virus maturation
  • uncoating
  • capsid
  • nuclear pore
  • reverse transcription
  • integration
  • envelope glycoprotein
  • matrix
  • nucleocapsid
  • retroviral RNA
  • RNA trafficking
  • RNA packaging

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Published Papers (7 papers)

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Research

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17 pages, 4900 KiB  
Article
High-Yield and Quantitative Purification Method for HIV Which Minimizes Forces Applied to Virions Utilized to Investigate Maturation of HIV-1 via Cryo-Electron Tomography
by Benjamin Preece, Wiley Peppel, Rodrigo Gallegos, Gillian Ysassi, Gabriel Clinger, Nicole Bohn, Broti Adhikary, Luiza Mendonça, David Belnap, Michael Vershinin and Saveez Saffarian
Viruses 2025, 17(3), 364; https://doi.org/10.3390/v17030364 - 3 Mar 2025
Viewed by 723
Abstract
HIV is a lentivirus characterized by its cone shaped mature core. Visualization and structural examination of HIV requires the purification of virions to high concentrations. The yield and integrity of these virions are crucial for ensuring a uniform representation of all viral particles [...] Read more.
HIV is a lentivirus characterized by its cone shaped mature core. Visualization and structural examination of HIV requires the purification of virions to high concentrations. The yield and integrity of these virions are crucial for ensuring a uniform representation of all viral particles in subsequent analyses. In this study, we present a method for the purification of HIV virions which minimizes the forces applied to virions while maximizing the efficiency of collection. This method, which relies on virion sedimentation simulations, allows us to capture between 1000 and 5000 HIV virions released from individual HEK293 cells after transfection with the NL4.3 HIV backbone. We utilized this approach to investigate HIV core formation from several constructs: pNL4-3(RT:D185A&D186A) with an inactive reverse transcriptase, NL4.3(IN: V165A&R166A) with a type-II integrase mutation, and NL4.3(Ψ: Δ(105–278)&Δ(301–332)) featuring an edited Ψ packaging signal. Notably, virions from NL4.3(Ψ: Δ(105–278)&Δ(301–332)) displayed a mixed population, comprising immature virions, empty cores, and cores with detectable internal density. Conversely, virions derived from NL4.3(IN: V165A&R166A) exhibited a type II integrase mutant phenotype characterized by empty cores and RNP density localized around the cores, consistent with previous studies. In contrast, virions released from pNL4-3(RT:D185A&D186A) displayed mature cores containing detectable RNP density. We suggest that the sedimentation simulations developed in this study can facilitate the characterization of enveloped viruses. Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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39 pages, 7731 KiB  
Article
Role of the Psi Packaging Signal and Dimerization Initiation Sequence in the Organization of Rous Sarcoma Virus Gag-gRNA Co-Condensates
by Gregory S. Lambert, Rebecca J. Kaddis Maldonado and Leslie J. Parent
Viruses 2025, 17(1), 97; https://doi.org/10.3390/v17010097 - 13 Jan 2025
Viewed by 1056
Abstract
Retroviral genome selection and virion assembly remain promising targets for novel therapeutic intervention. Recent studies have demonstrated that the Gag proteins of Rous sarcoma virus (RSV) and human immunodeficiency virus type-1 (HIV-1) undergo nuclear trafficking, colocalize with nascent genomic viral RNA (gRNA) at [...] Read more.
Retroviral genome selection and virion assembly remain promising targets for novel therapeutic intervention. Recent studies have demonstrated that the Gag proteins of Rous sarcoma virus (RSV) and human immunodeficiency virus type-1 (HIV-1) undergo nuclear trafficking, colocalize with nascent genomic viral RNA (gRNA) at transcription sites, may interact with host transcription factors, and display biophysical properties characteristic of biomolecular condensates. In the present work, we utilized a controlled in vitro condensate assay and advanced imaging approaches to investigate the effects of interactions between RSV Gag condensates and viral and nonviral RNAs on condensate abundance and organization. We observed that the psi (Ψ) packaging signal and the dimerization initiation sequence (DIS) had stabilizing effects on RSV Gag condensates, while RNAs lacking these features promoted or antagonized condensation, depending on local protein concentration and condensate architecture. An RNA containing Ψ, DIS, and the dimerization linkage structure (DLS) that is capable of stable dimer formation was observed to act as a bridge between RSV Gag condensates. These observations suggest additional, condensate-related roles for Gag-Ψ binding, gRNA dimerization, and Gag dimerization/multimerization in gRNA selection and packaging, representing a significant step forward in our understanding of how these interactions collectively facilitate efficient genome packaging. Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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13 pages, 2386 KiB  
Article
Tsg101 UEV Interaction with Nedd4 HECT Relieves E3 Ligase Auto-Inhibition, Promoting HIV-1 Assembly and CA-SP1 Maturation Cleavage
by Susan M. Watanabe, David A. Nyenhuis, Mahfuz Khan, Lorna S. Ehrlich, Irene Ischenko, Michael D. Powell, Nico Tjandra and Carol A. Carter
Viruses 2024, 16(10), 1566; https://doi.org/10.3390/v16101566 - 2 Oct 2024
Cited by 3 | Viewed by 1215
Abstract
Tsg101, a component of the endosomal sorting complex required for transport (ESCRT), is responsible for recognition of events requiring the machinery, as signaled by cargo tagging with ubiquitin (Ub), and for recruitment of downstream acting subunits to the site. Although much is known [...] Read more.
Tsg101, a component of the endosomal sorting complex required for transport (ESCRT), is responsible for recognition of events requiring the machinery, as signaled by cargo tagging with ubiquitin (Ub), and for recruitment of downstream acting subunits to the site. Although much is known about the latter function, little is known about its role in the earlier event. The N-terminal domain of Tsg101 is a structural homologue of Ub conjugases (E2 enzymes) and the protein associates with Ub ligases (E3 enzymes) that regulate several cellular processes including virus budding. A pocket in the domain recognizes a motif, PT/SAP, that permits its recruitment. PT/SAP disruption makes budding dependent on Nedd4L E3 ligases. Using HIV-1 encoding a PT/SAP mutation that makes budding Nedd4L-dependent, we identified as critical for rescue the residues in the catalytic (HECT) domain of the E3 enzyme that lie in proximity to sites in Tsg101 that bind Ub non-covalently. Mutation of these residues impaired rescue by Nedd4L but the same mutations had no apparent effect in the context of a Nedd4 isomer, Nedd4-2s, whose N-terminal (C2) domain is naturally truncated, precluding C2-HECT auto-inhibition. Surprisingly, like small molecules that disrupt Tsg101 Ub-binding, small molecules that interfered with Nedd4 substrate recognition arrested budding at an early stage, supporting the conclusion that Tsg101–Ub–Nedd4 interaction promotes enzyme activation and regulates Nedd4 signaling for viral egress. Tsg101 regulation of E3 ligases may underlie its broad ability to function as an effector in various cellular activities, including viral particle assembly and budding. Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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10 pages, 4023 KiB  
Article
Kinetic Studies on the Interaction of HIV-1 Gag Protein with the HIV-1 RNA Packaging Signal
by Constance Rink, Tomas Kroupa, Siddhartha A. K. Datta and Alan Rein
Viruses 2024, 16(10), 1517; https://doi.org/10.3390/v16101517 - 25 Sep 2024
Viewed by 1013
Abstract
During HIV-1 virus assembly, the genomic RNA (vRNA) is selected for packaging by the viral protein Gag because it contains a specific packaging signal, Psi. While there have been numerous studies of Gag–Psi interactions, there is almost no information on the kinetic aspects [...] Read more.
During HIV-1 virus assembly, the genomic RNA (vRNA) is selected for packaging by the viral protein Gag because it contains a specific packaging signal, Psi. While there have been numerous studies of Gag–Psi interactions, there is almost no information on the kinetic aspects of this interaction. We investigated the kinetics of Gag binding to different RNAs using switchSENSE DRX2 technology. We measured the association rate of Gag binding to monomeric Psi, to a “Multiple Binding Site Mutant” Psi that is inactive for genome packaging in vivo, and to a scrambled Psi. We discovered that Gag binds more rapidly to Psi RNA than to the mutant or scrambled RNAs. Furthermore, rapid Gag association kinetics are retained within sub-regions of Psi: Gag associates more rapidly with RNA containing only the 3′ two of the three Psi stem-loops than with monomeric RNA containing the 5′ two stem-loops or a scrambled RNA. No differences were detectable with individual Psi stem-loops. Interestingly, the rate of binding of Gag molecules to Psi increases with increasing Gag concentration, suggesting cooperativity in binding. The results are consistent with the hypothesis that selectivity in packaging derives from kinetic differences in initiation of particle assembly. Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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15 pages, 7138 KiB  
Article
Arg18 Substitutions Reveal the Capacity of the HIV-1 Capsid Protein for Non-Fullerene Assembly
by Randall T. Schirra, Nayara F. B. dos Santos, Barbie K. Ganser-Pornillos and Owen Pornillos
Viruses 2024, 16(7), 1038; https://doi.org/10.3390/v16071038 - 27 Jun 2024
Cited by 3 | Viewed by 1675
Abstract
In the fullerene cone HIV-1 capsid, the central channels of the hexameric and pentameric capsomers each contain a ring of arginine (Arg18) residues that perform essential roles in capsid assembly and function. In both the hexamer and pentamer, the Arg18 rings coordinate inositol [...] Read more.
In the fullerene cone HIV-1 capsid, the central channels of the hexameric and pentameric capsomers each contain a ring of arginine (Arg18) residues that perform essential roles in capsid assembly and function. In both the hexamer and pentamer, the Arg18 rings coordinate inositol hexakisphosphate, an assembly and stability factor for the capsid. Previously, it was shown that amino-acid substitutions of Arg18 can promote pentamer incorporation into capsid-like particles (CLPs) that spontaneously assemble in vitro under high-salt conditions. Here, we show that these Arg18 mutant CLPs contain a non-canonical pentamer conformation and distinct lattice characteristics that do not follow the fullerene geometry of retroviral capsids. The Arg18 mutant pentamers resemble the hexamer in intra-oligomeric contacts and form a unique tetramer-of-pentamers that allows for incorporation of an octahedral vertex with a cross-shaped opening in the hexagonal capsid lattice. Our findings highlight an unexpected degree of structural plasticity in HIV-1 capsid assembly. Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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19 pages, 3834 KiB  
Article
Cationic Residues of the HIV-1 Nucleocapsid Protein Enable DNA Condensation to Maintain Viral Core Particle Stability during Reverse Transcription
by Helena Gien, Michael Morse, Micah J. McCauley, Ioulia Rouzina, Robert J. Gorelick and Mark C. Williams
Viruses 2024, 16(6), 872; https://doi.org/10.3390/v16060872 - 29 May 2024
Cited by 1 | Viewed by 1395
Abstract
The HIV-1 nucleocapsid protein (NC) is a multifunctional viral protein necessary for HIV-1 replication. Recent studies have demonstrated that reverse transcription (RT) completes in the intact viral capsid, and the timing of RT and uncoating are correlated. How the small viral core stably [...] Read more.
The HIV-1 nucleocapsid protein (NC) is a multifunctional viral protein necessary for HIV-1 replication. Recent studies have demonstrated that reverse transcription (RT) completes in the intact viral capsid, and the timing of RT and uncoating are correlated. How the small viral core stably contains the ~10 kbp double stranded (ds) DNA product of RT, and the role of NC in this process, are not well understood. We showed previously that NC binds and saturates dsDNA in a non-specific electrostatic binding mode that triggers uniform DNA self-attraction, condensing dsDNA into a tight globule against extending forces up to 10 pN. In this study, we use optical tweezers and atomic force microscopy to characterize the role of NC’s basic residues in dsDNA condensation. Basic residue mutations of NC lead to defective interaction with the dsDNA substrate, with the constant force plateau condensation observed with wild-type (WT) NC missing or diminished. These results suggest that NC’s high positive charge is essential to its dsDNA condensing activity, and electrostatic interactions involving NC’s basic residues are responsible in large part for the conformation, size, and stability of the dsDNA-protein complex inside the viral core. We observe DNA re-solubilization and charge reversal in the presence of excess NC, consistent with the electrostatic nature of NC-induced DNA condensation. Previous studies of HIV-1 replication in the presence of the same cationic residue mutations in NC showed significant defects in both single- and multiple-round viral infectivity. Although NC participates in many stages of viral replication, our results are consistent with the hypothesis that cationic residue mutations inhibit genomic DNA condensation, resulting in increased premature capsid uncoating and contributing to viral replication defects. Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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Review

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25 pages, 5680 KiB  
Review
The Assembly of HTLV-1—How Does It Differ from HIV-1?
by Dominik Herrmann, Shuyu Meng, Huixin Yang, Louis M. Mansky and Jamil S. Saad
Viruses 2024, 16(10), 1528; https://doi.org/10.3390/v16101528 - 27 Sep 2024
Viewed by 3005
Abstract
Retroviral assembly is a highly coordinated step in the replication cycle. The process is initiated when the newly synthesized Gag and Gag-Pol polyproteins are directed to the inner leaflet of the plasma membrane (PM), where they facilitate the budding and release of immature [...] Read more.
Retroviral assembly is a highly coordinated step in the replication cycle. The process is initiated when the newly synthesized Gag and Gag-Pol polyproteins are directed to the inner leaflet of the plasma membrane (PM), where they facilitate the budding and release of immature viral particles. Extensive research over the years has provided crucial insights into the molecular determinants of this assembly step. It is established that Gag targeting and binding to the PM is mediated by interactions of the matrix (MA) domain and acidic phospholipids such as phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This binding event, along with binding to viral RNA, initiates oligomerization of Gag on the PM, a process mediated by the capsid (CA) domain. Much of the previous studies have focused on human immunodeficiency virus type 1 (HIV-1). Although the general steps of retroviral replication are consistent across different retroviruses, comparative studies revealed notable differences in the structure and function of viral components. In this review, we present recent findings on the assembly mechanisms of Human T-cell leukemia virus type 1 and highlight key differences from HIV-1, focusing particularly on the molecular determinants of Gag–PM interactions and CA assembly. Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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