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1.
PLoS Pathog ; 14(5): e1007054, 2018 05.
Article in English | MEDLINE | ID: mdl-29742155

ABSTRACT

All herpesviruses have mechanisms for passing through cell junctions, which exclude neutralizing antibodies and offer a clear path to neighboring, uninfected cells. In the case of herpes simplex virus type 1 (HSV-1), direct cell-to-cell transmission takes place between epithelial cells and sensory neurons, where latency is established. The spreading mechanism is poorly understood, but mutations in four different HSV-1 genes can dysregulate it, causing neighboring cells to fuse to produce syncytia. Because the host proteins involved are largely unknown (other than the virus entry receptor), we were intrigued by an earlier discovery that cells infected with wild-type HSV-1 will form syncytia when treated with salubrinal. A biotinylated derivative of this drug was used to pull down cellular complexes, which were analyzed by mass spectrometry. One candidate was a protein tyrosine phosphatase (PTP1B), and although it ultimately proved not to be the target of salubrinal, it was found to be critical for the mechanism of cell-to-cell spread. In particular, a highly specific inhibitor of PTP1B (CAS 765317-72-4) blocked salubrinal-induced fusion, and by itself resulted in a dramatic reduction in the ability of HSV-1 to spread in the presence of neutralizing antibodies. The importance of this phosphatase was confirmed in the absence of drugs by using PTP1B-/- cells. Importantly, replication assays showed that virus titers were unaffected when PTP1B was inhibited or absent. Only cell-to-cell spread was altered. We also examined the effects of salubrinal and the PTP1B inhibitor on the four Syn mutants of HSV-1, and strikingly different responses were found. That is, both drugs individually enhanced fusion for some mutants and reduced fusion for others. PTP1B is the first host factor identified to be specifically required for cell-to-cell spread, and it may be a therapeutic target for preventing HSV-1 reactivation disease.


Subject(s)
Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism , Protein Tyrosine Phosphatase, Non-Receptor Type 1/physiology , Animals , Cell Line , Chlorocebus aethiops , Cinnamates/metabolism , Giant Cells/metabolism , Giant Cells/virology , Herpesvirus 1, Human/physiology , Humans , Intercellular Junctions/metabolism , Mass Spectrometry/methods , Receptors, Virus/metabolism , Thiourea/analogs & derivatives , Thiourea/metabolism , Vero Cells , Viral Envelope Proteins/metabolism , Virus Internalization , Virus Replication
2.
J Am Chem Soc ; 139(5): 2006-2013, 2017 02 08.
Article in English | MEDLINE | ID: mdl-28094514

ABSTRACT

The orthoretroviral capsid protein (CA) assembles into polymorphic capsids, whose architecture, assembly, and stability are still being investigated. The N-terminal and C-terminal domains of CA (NTD and CTD, respectively) engage in both homotypic and heterotypic interactions to create the capsid. Hexameric turrets formed by the NTD decorate the majority of the capsid surface. We report nearly complete solid-state NMR (ssNMR) resonance assignments of Rous sarcoma virus (RSV) CA, assembled into hexamer tubes that mimic the authentic capsid. The ssNMR assignments show that, upon assembly, large conformational changes occur in loops connecting helices, as well as the short 310 helix initiating the CTD. The interdomain linker becomes statically disordered. Combining constraints from ssNMR and cryo-electron microscopy (cryo-EM), we establish an atomic resolution model of the RSV CA tubular assembly using molecular dynamics flexible fitting (MDFF) simulations. On the basis of comparison of this MDFF model with an earlier-derived crystallographic model for the planar assembly, the induction of curvature into the RSV CA hexamer lattice arises predominantly from reconfiguration of the NTD-CTD and CTD trimer interfaces. The CTD dimer and CTD trimer interfaces are also intrinsically variable. Hence, deformation of the CA hexamer lattice results from the variable displacement of the CTDs that surround each hexameric turret. Pervasive H-bonding is found at all interdomain interfaces, which may contribute to their malleability. Finally, we find helices at the interfaces of HIV and RSV CA assemblies have very different contact angles, which may reflect differences in the capsid assembly pathway for these viruses.


Subject(s)
Capsid Proteins/chemistry , Rous sarcoma virus/chemistry , Crystallography, X-Ray , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Particle Size , Protein Conformation , Surface Properties
3.
J Virol ; 90(12): 5700-5714, 2016 06 15.
Article in English | MEDLINE | ID: mdl-27053549

ABSTRACT

UNLABELLED: Extensive studies of orthoretroviral capsids have shown that many regions of the CA protein play unique roles at different points in the virus life cycle. The N-terminal domain (NTD) flexible-loop (FL) region is one such example: exposed on the outer capsid surface, it has been implicated in Gag-mediated particle assembly, capsid maturation, and early replication events. We have now defined the contributions of charged residues in the FL region of the Rous sarcoma virus (RSV) CA to particle assembly. Effects of mutations on assembly were assessed in vivo and in vitro and analyzed in light of new RSV Gag lattice models. Virus replication was strongly dependent on the preservation of charge at a few critical positions in Gag-Gag interfaces. In particular, a cluster of charges at the beginning of FL contributes to an extensive electrostatic network that is important for robust Gag assembly and subsequent capsid maturation. Second-site suppressor analysis suggests that one of these charged residues, D87, has distal influence on interhexamer interactions involving helix α7. Overall, the tolerance of FL to most mutations is consistent with current models of Gag lattice structures. However, the results support the interpretation that virus evolution has achieved a charge distribution across the capsid surface that (i) permits the packing of NTD domains in the outer layer of the Gag shell, (ii) directs the maturational rearrangements of the NTDs that yield a functional core structure, and (iii) supports capsid function during the early stages of virus infection. IMPORTANCE: The production of infectious retrovirus particles is a complex process, a choreography of protein and nucleic acid that occurs in two distinct stages: formation and release from the cell of an immature particle followed by an extracellular maturation phase during which the virion proteins and nucleic acids undergo major rearrangements that activate the infectious potential of the virion. This study examines the contributions of charged amino acids on the surface of the Rous sarcoma virus capsid protein in the assembly of appropriately formed immature particles and the maturational transitions that create a functional virion. The results provide important biological evidence in support of recent structural models of the RSV immature virions and further suggest that immature particle assembly and virion maturation are controlled by an extensive network of electrostatic interactions and long-range communication across the capsid surface.


Subject(s)
Capsid Proteins/chemistry , Capsid Proteins/metabolism , Gene Products, gag/chemistry , Rous sarcoma virus/chemistry , Rous sarcoma virus/physiology , Virus Assembly , Amino Acid Sequence , Capsid/metabolism , Capsid Proteins/genetics , Cryoelectron Microscopy , Gene Products, gag/genetics , Microscopy, Electron , Models, Molecular , Mutation , Rous sarcoma virus/genetics , Rous sarcoma virus/ultrastructure , Static Electricity , Virion/metabolism , Virion/ultrastructure
4.
Structure ; 23(8): 1414-1425, 2015 Aug 04.
Article in English | MEDLINE | ID: mdl-26118533

ABSTRACT

Defining the molecular interaction between Gag proteins in an assembled hexagonal lattice of immature retrovirus particles is crucial for elucidating the mechanisms of virus assembly and maturation. Recent advances in cryo-electron microscopy have yielded subnanometer structural information on the morphology of immature Gag lattices, making computational modeling and simulations feasible for investigating the Gag-Gag interactions at the atomic level. We have examined the structure of Rous sarcoma virus (RSV) using all-atom molecular dynamics simulations and in vitro assembly, to create the first all-atom model of an immature retroviral lattice. Microseconds-long replica exchange molecular dynamics simulation of the spacer peptide (SP)-nucleocapsid (NC) subdomains results in a six-helix bundle with amphipathic properties. The resulting model of the RSV Gag lattice shows features and dynamics of the capsid protein with implications for the maturation process, and confirms the stabilizing role of the upstream and downstream regions of Gag, namely p10 and SP-NC.


Subject(s)
Gene Products, gag/chemistry , Molecular Dynamics Simulation , Nucleocapsid/chemistry , Rous sarcoma virus/chemistry , Amino Acid Sequence , Binding Sites , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Gene Products, gag/genetics , Molecular Sequence Data , Mutagenesis , Nucleocapsid/ultrastructure , Protein Binding , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Rous sarcoma virus/ultrastructure , Virus Assembly/genetics
5.
J Virol ; 88(13): 7170-7, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24719425

ABSTRACT

UNLABELLED: During virion maturation, the Rous sarcoma virus (RSV) capsid protein is cleaved from the Gag protein as the proteolytic intermediate CA-SP. Further trimming at two C-terminal sites removes the spacer peptide (SP), producing the mature capsid proteins CA and CA-S. Abundant genetic and structural evidence shows that the SP plays a critical role in stabilizing hexameric Gag interactions that form immature particles. Freeing of CA-SP from Gag breaks immature interfaces and initiates the formation of mature capsids. The transient persistence of CA-SP in maturing virions and the identification of second-site mutations in SP that restore infectivity to maturation-defective mutant viruses led us to hypothesize that SP may play an important role in promoting the assembly of mature capsids. This study presents a biophysical and biochemical characterization of CA-SP and its assembly behavior. Our results confirm cryo-electron microscopy (cryo-EM) structures reported previously by Keller et al. (J. Virol. 87:13655-13664, 2013, doi:10.1128/JVI.01408-13) showing that monomeric CA-SP is fully capable of assembling into capsid-like structures identical to those formed by CA. Furthermore, SP confers aggressive assembly kinetics, which is suggestive of higher-affinity CA-SP interactions than observed with either of the mature capsid proteins. This aggressive assembly is largely independent of the SP amino acid sequence, but the formation of well-ordered particles is sensitive to the presence of the N-terminal ß-hairpin. Additionally, CA-SP can nucleate the assembly of CA and CA-S. These results suggest a model in which CA-SP, once separated from the Gag lattice, can actively promote the interactions that form mature capsids and provide a nucleation point for mature capsid assembly. IMPORTANCE: The spacer peptide is a documented target for antiretroviral therapy. This study examines the biochemical and biophysical properties of CA-SP, an intermediate form of the retrovirus capsid protein. The results demonstrate a previously unrecognized activity of SP in promoting capsid assembly during maturation.


Subject(s)
Capsid Proteins/chemistry , Capsid/metabolism , Peptide Fragments/chemistry , Rous sarcoma virus/physiology , Virus Assembly , Amino Acid Sequence , Capsid Proteins/genetics , Capsid Proteins/metabolism , Cryoelectron Microscopy , Humans , Models, Molecular , Molecular Sequence Data , Peptide Fragments/genetics , Peptide Fragments/metabolism , Protein Structure, Tertiary , Sequence Homology, Amino Acid
6.
J Virol ; 87(24): 13655-64, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24109217

ABSTRACT

Retrovirus maturation involves sequential cleavages of the Gag polyprotein, initially arrayed in a spherical shell, leading to formation of capsids with polyhedral or conical morphology. Evidence suggests that capsids assemble de novo inside maturing virions from dissociated capsid (CA) protein, but the possibility persists of a displacive pathway in which the CA shell remains assembled but is remodeled. Inhibition of the final cleavage between CA and spacer peptide SP1/SP blocks the production of mature capsids. We investigated whether retention of SP might render CA assembly incompetent by testing the ability of Rous sarcoma virus (RSV) CA-SP to assemble in vitro into icosahedral capsids. Capsids were indeed assembled and were indistinguishable from those formed by CA alone, indicating that SP was disordered. We also used cryo-electron tomography to characterize HIV-1 particles produced in the presence of maturation inhibitor PF-46396 or with the cleavage-blocking CA5 mutation. Inhibitor-treated virions have a shell that resembles the CA layer of the immature Gag shell but is less complete. Some CA protein is generated but usually not enough for a mature core to assemble. We propose that inhibitors like PF-46396 bind to the Gag lattice where they deny the protease access to the CA-SP1 cleavage site and prevent the release of CA. CA5 particles, which exhibit no cleavage at the CA-SP1 site, have spheroidal shells with relatively thin walls. It appears that this lattice progresses displacively toward a mature-like state but produces neither conical cores nor infectious virions. These observations support the disassembly-reassembly pathway for core formation.


Subject(s)
Capsid/chemistry , Capsid/metabolism , HIV-1/metabolism , Rous sarcoma virus/metabolism , Capsid Proteins/genetics , Capsid Proteins/metabolism , Gene Products, gag/chemistry , Gene Products, gag/genetics , Gene Products, gag/metabolism , HIV-1/chemistry , HIV-1/genetics , Humans , Models, Molecular , Mutation , Rous sarcoma virus/chemistry , Rous sarcoma virus/genetics , gag Gene Products, Human Immunodeficiency Virus/chemistry , gag Gene Products, Human Immunodeficiency Virus/genetics , gag Gene Products, Human Immunodeficiency Virus/metabolism
7.
Proteins ; 81(2): 316-25, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23011855

ABSTRACT

An infective retrovirus requires a mature capsid shell around the viral replication complex. This shell is formed by about 1500 capsid protein monomers, organized into hexamer and pentamer rings that are linked to each other by the dimerization of the C-terminal domain (CTD). The major homology region (MHR), the most highly conserved protein sequence across retroviral genomes, is part of the CTD. Several mutations in the MHR appear to block infectivity by preventing capsid formation. Suppressor mutations have been identified that are distant in sequence and structure from the MHR and restore capsid formation. The effects of two lethal and two suppressor mutations on the stability and function of the CTD were examined. No correlation with infectivity was found for the stability of the lethal mutations (D155Y-CTD, F167Y-CTD) and suppressor mutations (R185W-CTD, I190V-CTD). The stabilities of three double mutant proteins (D155Y/R185W-CTD, F167Y/R185W-CTD, and F167Y/I190V-CTD) were additive. However, the dimerization affinity of the mutant proteins correlated strongly with biological function. The CTD proteins with lethal mutations did not dimerize, while those with suppressor mutations had greater dimerization affinity than WT-CTD. The suppressor mutations were able to partially correct the dimerization defect caused by the lethal MHR mutations in double mutant proteins. Despite their dramatic effects on dimerization, none of these residues participate directly in the proposed dimerization interface in a mature capsid. These findings suggest that the conserved sequence of the MHR has critical roles in the conformation(s) of the CTD that are required for dimerization and correct capsid maturation.


Subject(s)
Capsid Proteins/genetics , Mutant Proteins/genetics , Mutation , Rous sarcoma virus/genetics , Capsid/metabolism , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Protein Multimerization , Protein Structure, Tertiary , Rous sarcoma virus/metabolism , Sequence Homology, Amino Acid
8.
J Virol ; 84(13): 6377-86, 2010 Jul.
Article in English | MEDLINE | ID: mdl-20427531

ABSTRACT

Retrovirus assembly is driven by polymerization of the Gag polyprotein as nascent virions bud from host cells. Gag is then processed proteolytically, releasing the capsid protein (CA) to assemble de novo inside maturing virions. CA has N-terminal and C-terminal domains (NTDs and CTDs, respectively) whose folds are conserved, although their sequences are divergent except in the 20-residue major homology region (MHR) in the CTD. The MHR is thought to play an important role in assembly, and some mutations affecting it, including the F167Y substitution, are lethal. A temperature-sensitive second-site suppressor mutation in the NTD, A38V, restores infectivity. We have used cryoelectron tomography to investigate the morphotypes of this double mutant. Virions produced at the nonpermissive temperature do not assemble capsids, although Gag is processed normally; moreover, they are more variable in size than the wild type and have fewer glycoprotein spikes. At the permissive temperature, virions are similar in size and spike content as in the wild type and capsid assembly is restored, albeit with altered polymorphisms. The mutation F167Y-A38V (referred to as FY/AV in this paper) produces fewer tubular capsids than wild type and more irregular polyhedra, which tend to be larger than in the wild type, containing approximately 30% more CA subunits. It follows that FY/AV CA assembles more efficiently in situ than in the wild type and has a lower critical concentration, reflecting altered nucleation properties. However, its infectivity is lower than that of the wild type, due to a 4-fold-lower budding efficiency. We conclude that the wild-type CA protein sequence represents an evolutionary compromise between competing requirements for optimization of Gag assembly (of the immature virion) and CA assembly (in the maturing virion).


Subject(s)
Capsid Proteins/genetics , Mutation, Missense , Rous sarcoma virus/physiology , Rous sarcoma virus/ultrastructure , Suppression, Genetic , Virion/ultrastructure , Virus Assembly , Animals , Cryoelectron Microscopy , Electron Microscope Tomography , Microbial Viability , Models, Molecular , Protein Structure, Quaternary , Protein Structure, Tertiary , Rous sarcoma virus/genetics
9.
J Mol Biol ; 389(2): 438-51, 2009 Jun 05.
Article in English | MEDLINE | ID: mdl-19361521

ABSTRACT

In maturing retroviral virions, CA protein assembles to form a capsid shell that is essential for infectivity. The structure of the two folded domains [N-terminal domain (NTD) and C-terminal domain (CTD)] of CA is highly conserved among various retroviruses, and the capsid assembly pathway, although poorly understood, is thought to be conserved as well. In vitro assembly reactions with purified CA proteins of the Rous sarcoma virus (RSV) were used to define factors that influence the kinetics of capsid assembly and provide insights into underlying mechanisms. CA multimerization was triggered by multivalent anions providing evidence that in vitro assembly is an electrostatically controlled process. In the case of RSV, in vitro assembly was a well-behaved nucleation-driven process that led to the formation of structures with morphologies similar to those found in virions. Isolated RSV dimers, when mixed with monomeric protein, acted as efficient seeds for assembly, eliminating the lag phase characteristic of a monomer-only reaction. This demonstrates for the first time the purification of an intermediate on the assembly pathway. Differences in the intrinsic tryptophan fluorescence of monomeric protein and the assembly-competent dimer fraction suggest the involvement of the NTD in the formation of the functional dimer. Furthermore, in vitro analysis of well-characterized CTD mutants provides evidence for assembly dependence on the second domain and suggests that the establishment of an NTD-CTD interface is a critical step in capsid assembly initiation. Overall, the data provide clear support for a model whereby capsid assembly within the maturing virion is dependent on the formation of a specific nucleating complex that involves a CA dimer and is directed by additional virion constituents.


Subject(s)
Capsid Proteins/physiology , Capsid/chemistry , Rous sarcoma virus/physiology , Virus Assembly , Kinetics , Protein Multimerization , Retroviridae , Static Electricity
10.
Nature ; 457(7230): 694-8, 2009 Feb 05.
Article in English | MEDLINE | ID: mdl-19194444

ABSTRACT

For a retrovirus such as HIV to be infectious, a properly formed capsid is needed; however, unusually among viruses, retrovirus capsids are highly variable in structure. According to the fullerene conjecture, they are composed of hexamers and pentamers of capsid protein (CA), with the shape of a capsid varying according to how the twelve pentamers are distributed and its size depending on the number of hexamers. Hexamers have been studied in planar and tubular arrays, but the predicted pentamers have not been observed. Here we report cryo-electron microscopic analyses of two in-vitro-assembled capsids of Rous sarcoma virus. Both are icosahedrally symmetric: one is composed of 12 pentamers, and the other of 12 pentamers and 20 hexamers. Fitting of atomic models of the two CA domains into the reconstructions shows three distinct inter-subunit interactions. These observations substantiate the fullerene conjecture, show how pentamers are accommodated at vertices, support the inference that nucleation is a crucial morphologic determinant, and imply that electrostatic interactions govern the differential assembly of pentamers and hexamers.


Subject(s)
Capsid/metabolism , Capsid/ultrastructure , Rous sarcoma virus/chemistry , Rous sarcoma virus/ultrastructure , Virus Assembly , Capsid/chemistry , Capsid Proteins/chemistry , Capsid Proteins/genetics , Capsid Proteins/metabolism , Capsid Proteins/ultrastructure , Cryoelectron Microscopy , HIV/chemistry , HIV/genetics , HIV/ultrastructure , Models, Molecular , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Mutant Proteins/ultrastructure , Mutation , Polymorphism, Genetic , Protein Multimerization , Protein Structure, Quaternary , Protein Subunits/chemistry , Protein Subunits/metabolism , Rous sarcoma virus/genetics , Static Electricity
11.
J Virol ; 82(12): 5951-61, 2008 Jun.
Article in English | MEDLINE | ID: mdl-18400856

ABSTRACT

During retroviral maturation, the CA protein undergoes dramatic structural changes and establishes unique intermolecular interfaces in the mature capsid shell that are different from those that existed in the immature precursor. The most conserved region of CA, the major homology region (MHR), has been implicated in both immature and mature assembly, although the precise contribution of the MHR residues to each event has been largely undefined. To test the roles of specific MHR residues in mature capsid assembly, an in vitro system was developed that allowed for the first-time formation of Rous sarcoma virus CA into structures resembling authentic capsids. The ability of CA to assemble organized structures was destroyed by substitutions of two conserved hydrophobic MHR residues and restored by second-site suppressors, demonstrating that these MHR residues are required for the proper assembly of mature capsids in addition to any role that these amino acids may play in immature particle assembly. The defect caused by the MHR mutations was identified as an early step in the capsid assembly process. The results provide strong evidence for a model in which the hydrophobic residues of the MHR control a conformational reorganization of CA that is needed to initiate capsid assembly and suggest that the formation of an interdomain interaction occurs early during maturation.


Subject(s)
Capsid Proteins/chemistry , Capsid/physiology , Retroviridae/chemistry , Virus Assembly , Amino Acid Sequence , Amino Acid Substitution , Capsid/ultrastructure , Capsid Proteins/genetics , Capsid Proteins/isolation & purification , Capsid Proteins/ultrastructure , Circular Dichroism , Hydrophobic and Hydrophilic Interactions , Models, Chemical , Molecular Sequence Data , Protein Denaturation , Protein Structure, Secondary , Protein Structure, Tertiary , Retroviridae/genetics , Rous sarcoma virus/chemistry , Rous sarcoma virus/genetics , Sequence Homology, Amino Acid , Spectrophotometry, Ultraviolet , Thermodynamics , Tryptophan/metabolism
12.
Virology ; 376(1): 191-8, 2008 Jun 20.
Article in English | MEDLINE | ID: mdl-18433823

ABSTRACT

The second helix in the C-terminal domain of retroviral capsid (CA) protein functions as the site of dimerization between subunits in capsid assembly and is believed to participate in a unique interface between Gag molecules in immature particles. This study reports isolation of two substitutions in the dimerization helix of Rous sarcoma virus CA protein that have the ability to suppress lethal defects in core maturation imposed by alterations to the major homology region (MHR) motif just upstream. Together with two previously published suppressors, these define an extended region of the dimerization helix that is unlikely to contribute directly to CA-CA contacts but whose assembly-competence may be strongly affected by conformation. The broad-spectrum suppression and temperature-sensitivity exhibited by some mutants argues that they act through modulation of protein conformation. These findings provide important biological evidence in support of a significant conformational change involving the dimerization helix and the MHR during maturation.


Subject(s)
Capsid Proteins/metabolism , Rous sarcoma virus/physiology , Virus Assembly , Amino Acid Motifs , Amino Acid Sequence , Amino Acid Substitution/genetics , Animals , Capsid Proteins/chemistry , Capsid Proteins/genetics , Cell Line , Chickens , Dimerization , Hot Temperature , Models, Molecular , Molecular Sequence Data , Protein Structure, Secondary , Quail , Rous sarcoma virus/genetics , Suppression, Genetic , Turkey
13.
J Mol Biol ; 376(4): 1168-81, 2008 Feb 29.
Article in English | MEDLINE | ID: mdl-18206161

ABSTRACT

We used cryo-electron tomography to visualize Rous sarcoma virus, the prototypic alpharetrovirus. Its polyprotein Gag assembles into spherical procapsids, concomitant with budding. In maturation, Gag is dissected into its matrix, capsid protein (CA), and nucleocapsid moieties. CA reassembles into cores housing the viral RNA and replication enzymes. Evidence suggests that a correctly formed core is essential for infectivity. The virions in our data set range from approximately 105 to approximately 175 nm in diameter. Their cores are highly polymorphic. We observe angular cores, including some that are distinctively "coffin-shaped" for which we propose a novel fullerene geometry; cores with continuous curvature including, rarely, fullerene cones; and tubular cores. Angular cores are the most voluminous and densely packed; tubes and some curved cores contain less material, suggesting incomplete packaging. From the tomograms, we measured the surface areas of cores and, hence, their contents of CA subunits. From the virion diameters, we estimated their original complements of Gag. We find that Rous sarcoma virus virions, like the human immunodeficiency virus, contain unassembled CA subunits and that the fraction of CA that is assembled correlates with core type; angular cores incorporate approximately 80% of the available subunits, and open-ended tubes, approximately 30%. The number of glycoprotein spikes is variable (approximately 0 to 118) and also correlates with core type; virions with angular cores average 82 spikes, whereas those with tubular cores average 14 spikes. These observations imply that initiation of CA assembly, in which interactions of spike endodomains with the Gag layer play a role, is a critical determinant of core morphology.


Subject(s)
Capsid/chemistry , Polymers/chemistry , Rous sarcoma virus/chemistry , Viral Envelope Proteins/chemistry , Capsid/ultrastructure , Capsid Proteins/chemistry , Cryoelectron Microscopy , Gene Products, gag/chemistry , Models, Biological , Protein Subunits/chemistry , Rous sarcoma virus/ultrastructure , Tomography , Virion/chemistry , Virion/ultrastructure
14.
Comput Math Methods Med ; 9(3-4): 197-210, 2008.
Article in English | MEDLINE | ID: mdl-19122884

ABSTRACT

Whereas many viruses have capsids of uniquely defined sizes that observe icosahedral symmetry, retrovirus capsids are highly polymorphic. Nevertheless, they may also be described as polyhedral foldings of a fullerene lattice on which the capsid protein (CA) is arrayed. Lacking the high order of symmetry that facilitates the reconstruction of icosahedral capsids from cryo-electron micrographs, the three-dimensional structures of individual retrovirus capsids may be determined by cryo-electron tomography, albeit at lower resolution. Here we describe computational and graphical methods to construct polyhedral models that match in size and shape, capsids of Rous sarcoma virus (RSV) observed within intact virions [8]. The capsids fall into several shape classes, including tubes, "lozenges", and "coffins". The extent to which a capsid departs from icosahedral symmetry reflects the irregularity of the distribution of pentamers, which are always 12 in number for a closed polyhedral capsid. The number of geometrically distinct polyhedra grows rapidly with increasing quotas of hexamers, and ranks in the millions for RSV capsids, which typically have 150 - 300 hexamers. Unlike the capsid proteins of icosahedral viruses that assume a minimal number of quasi-equivalent conformations equal to the triangulation number (T), retroviral CAs exhibit a near-continuum of quasi-equivalent conformations - a property that may be attributed to the flexible hinge linking the N- and C-terminal domains.

15.
J Virol ; 81(19): 10718-28, 2007 Oct.
Article in English | MEDLINE | ID: mdl-17634229

ABSTRACT

Nucleocytoplasmic shuttling of the Rous sarcoma virus (RSV) Gag polyprotein is an integral step in virus particle assembly. A nuclear export signal (NES) was previously identified within the p10 domain of RSV Gag. Gag mutants containing deletions of the p10 NES or mutations of critical hydrophobic residues at positions 219, 222, 225, or 229 become trapped within the nucleus and exhibit defects in the efficiency of virus particle release. To investigate other potential roles for Gag nuclear trafficking in RSV replication, we created viruses bearing NES mutant Gag proteins. Viruses carrying p10 mutations produced low levels of particles, as anticipated, and those particles that were released were noninfectious. The p10 mutant viruses contained approximately normal amounts of Gag, Gag-Pol, and Env proteins and genomic viral RNA (vRNA), but several major structural defects were found. Thin-section transmission electron microscopy revealed that the mature particles appeared misshapen, while the viral cores were cylindrical, horseshoe-shaped, or fragmented, with some particles containing multiple small, electron-dense aggregates. Immature virus-like particles produced by the expression of Gag proteins bearing p10 mutations were also aberrant, with both spherical and tubular filamentous particles produced. Interestingly, the secondary structure of the encapsidated vRNA was altered; although dimeric vRNA was predominant, there was an additional high-molecular-weight fraction. Together, these results indicate that the p10 NES domain of Gag is critical for virus replication and that it plays overlapping roles required for the nuclear shuttling of Gag and for the maintenance of proper virion core morphology.


Subject(s)
Gene Products, gag/metabolism , Nuclear Export Signals , Rous sarcoma virus/ultrastructure , Virion/ultrastructure , Virus Assembly/genetics , Active Transport, Cell Nucleus , Amino Acid Sequence , Animals , Cell Nucleus/chemistry , Cell Nucleus/metabolism , Cells, Cultured , Gene Products, gag/genetics , Green Fluorescent Proteins/analysis , Green Fluorescent Proteins/genetics , Microscopy, Electron, Transmission , Molecular Sequence Data , Mutation , Nuclear Export Signals/genetics , Protein Structure, Tertiary , RNA, Viral/metabolism , Recombinant Fusion Proteins/analysis , Recombinant Fusion Proteins/genetics , Rous sarcoma virus/genetics , Rous sarcoma virus/physiology , Virion/genetics , Virion/physiology , Virus Replication/genetics
16.
J Virol ; 81(3): 1288-96, 2007 Feb.
Article in English | MEDLINE | ID: mdl-17093186

ABSTRACT

The first few residues of the Rous sarcoma virus (RSV) CA protein comprise a structurally dynamic region that forms part of a Gag-Gag interface in immature virus particles. Dissociation of this interaction during maturation allows refolding and formation of a beta-hairpin structure important for assembly of CA monomers into the mature capsid shell. A consensus binding site for the cellular Ubc9 protein was previously identified within this region, suggesting that binding of Ubc9 and subsequent small ubiquitin-like modifier protein 1 (SUMO-1) modification of CA may play a role either in regulating the assembly activity of CA in immature particles or mature cores or in controlling postentry function(s) during the establishment of infection. In the present study, mutations designed to eliminate the consensus binding site were used to dissect the potentially overlapping functions of these residues. The resulting replication defects could not be traced to a failure to form particles of normal composition but, rather, to a deficit in genome replication. Genetic suppressors of two detrimental beta-hairpin mutations improved infectivity without restoring the consensus site or creating a novel one elsewhere. Optimal restoration of infectivity to a Lys-to-Arg mutant required a combination of secondary changes, one on the surface of each domain of CA. Rather than arguing for a critical role of Ubc9 and SUMO in RSV replication, these findings provide strong support for a structural role of the N-terminal residues and a particularly striking example of long-range interactions between regions of CA in achieving a functional core competent for genome replication.


Subject(s)
Capsid/chemistry , Protein Structure, Secondary/genetics , Rous sarcoma virus/chemistry , Amino Acid Motifs/genetics , Capsid/metabolism , Rous sarcoma virus/genetics , Virion/chemistry
17.
J Virol ; 78(19): 10606-16, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15367628

ABSTRACT

The release of retroviruses from the plasma membrane requires host factors that are believed to be recruited to the site of budding by the late (L) domain of the virus-encoded Gag protein. The L domain of Rous sarcoma virus (RSV) has been shown to interact with a ubiquitin (Ub) ligase, and budding of this virus is dependent on Ub. RSV is similar to other retroviruses in that it contains approximately 100 molecules of Ub, but it is unique in that none of these molecules has been found to be conjugated to Gag. If transient ubiquitination of RSV Gag is required for budding, then replacement of the target lysine(s) with arginine should prevent the addition of Ub and reduce budding. Based on known sites of ubiquitination in other viruses, the important lysines would likely reside near the L domain. In RSV, there are five lysines located just upstream of the L domain in a region of the matrix (MA) protein that is dispensable for membrane binding, and replacement of these with arginine (mutant 1-5KR) reduced budding 80 to 90%. The block to budding was found to be on the plasma membrane; however, the few virions that were released had normal size, morphology, and infectivity. Budding was restored when any one of the residues was changed back to lysine or when lysines were inserted in novel positions, either within this region of MA or within the downstream p10 sequence. Moreover, the 1-5KR mutant could be rescued into particles by coexpression of budding-competent Gag molecules. These data argue that the phenotype of mutant 1-5KR is not due to a conformational defect. Consistent with the idea that efficient budding requires a specific role for lysines, human T-cell leukemia virus type 1, which does not bud well compared to RSV and lacks lysines close to its L domain, was found to be released at a higher level upon introduction of lysines near its L domain. This report strongly supports the hypothesis that ubiquitination of the RSV Gag protein (and perhaps those of other retroviruses) is needed for efficient budding.


Subject(s)
Avian Sarcoma Viruses/growth & development , Avian Sarcoma Viruses/genetics , Gene Products, gag/chemistry , Lysine/physiology , Amino Acid Substitution , Animals , Biological Transport , Cell Line , Gene Products, gag/genetics , Gene Products, gag/physiology , Genetic Complementation Test , Humans , Lysine/genetics , Mutagenesis, Site-Directed , Mutation, Missense , Protein Structure, Tertiary , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/metabolism , Viral Matrix Proteins/chemistry , Viral Matrix Proteins/genetics , Virion/metabolism , Virion/ultrastructure , Virus Replication
18.
Proc Natl Acad Sci U S A ; 100(22): 12978-83, 2003 Oct 28.
Article in English | MEDLINE | ID: mdl-14563923

ABSTRACT

By using a reverse genetics system that is based on the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV), we have identified the arenavirus small RING finger Z protein as the main driving force of virus budding. Both LCMV and Lassa fever virus (LFV) Z proteins exhibited self-budding activity, and both substituted efficiently for the late domain that is present in the Gag protein of Rous sarcoma virus. LCMV and LFV Z proteins contain proline-rich motifs that are characteristic of late domains. Mutations in the PPPY motif of LCMV Z severely impaired the formation of virus-like particles. LFV Z contains two different proline-rich motifs, PPPY and PTAP, which are separated by eight amino acids. Mutational analysis revealed that both motifs are required for efficient LFV Z-mediated budding. Both LCMV and LFV Z proteins recruited to the plasma membrane Tsg101, which is a component of the class E vacuolar protein sorting machinery that has been implicated in budding of HIV and Ebola virus. Targeting of Tsg101 by RNA interference caused a strong reduction in Z-mediated budding. These results indicate that Z is the arenavirus functional counterpart of the matrix proteins found in other negative strand enveloped RNA viruses. Moreover, members of the vacuolar protein sorting pathway appear to play an important role in arena-virus budding. These findings open possibilities for antiviral strategies to combat LFV and other hemorrhagic fever arenaviruses.


Subject(s)
Arenavirus/growth & development , Blood Proteins/physiology , Carrier Proteins/physiology , Lymphocytic choriomeningitis virus/growth & development , Viral Proteins/physiology , Amino Acid Sequence , Animals , Arenavirus/genetics , Blood Proteins/genetics , COS Cells , Carrier Proteins/genetics , Cell Line , Chlorocebus aethiops , Conserved Sequence , Cricetinae , Kidney , Lymphocytic choriomeningitis virus/genetics , Molecular Sequence Data , Plasmids , RNA, Viral/genetics , RNA, Viral/isolation & purification , Sequence Alignment , Sequence Homology, Amino Acid , Transfection , Viral Proteins/genetics , Zinc Fingers
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