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Biochemical Society Transactions Aug 2021Lipid enveloped viruses contain a lipid bilayer coat that protects their genome to help facilitate entry into the new host cell. This lipid bilayer comes from the host... (Review)
Review
Lipid enveloped viruses contain a lipid bilayer coat that protects their genome to help facilitate entry into the new host cell. This lipid bilayer comes from the host cell which they infect. After viral replication, the mature virion hijacks the host cell plasma membrane where it is then released to infect new cells. This process is facilitated by the interaction between phospholipids that make up the plasma membrane and specialized viral matrix proteins. This step in the viral lifecycle may represent a viable therapeutic strategy for small molecules that aim to block enveloped virus spread. In this review, we summarize the current knowledge on the role of plasma membrane lipid-protein interactions on viral assembly and budding.
Topics: Cell Membrane; Host-Pathogen Interactions; Lipids; Proteins; Virus Assembly
PubMed: 34431495
DOI: 10.1042/BST20200854 -
Viruses Sep 2016Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. However, in the absence of the gRNA,... (Review)
Review
Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. However, in the absence of the gRNA, cellular messenger RNAs (mRNAs) are packaged. While the gRNA is selected because of its cis-acting packaging signal, the mechanism of this selection is not understood. The affinity of Gag (the viral structural protein) for cellular RNAs at physiological ionic strength is not much higher than that for the gRNA. However, binding to the gRNA is more salt-resistant, implying that it has a higher non-electrostatic component. We have previously studied the spacer 1 (SP1) region of Gag and showed that it can undergo a concentration-dependent conformational transition. We proposed that this transition represents the first step in assembly, i.e., the conversion of Gag to an assembly-ready state. To explain selective packaging of gRNA, we suggest here that binding of Gag to gRNA, with its high non-electrostatic component, triggers this conversion more readily than binding to other RNAs; thus we predict that a Gag-gRNA complex will nucleate particle assembly more efficiently than other Gag-RNA complexes. New data shows that among cellular mRNAs, those with long 3'-untranslated regions (UTR) are selectively packaged. It seems plausible that the 3'-UTR, a stretch of RNA not occupied by ribosomes, offers a favorable binding site for Gag.
Topics: Gene Products, gag; Genome, Viral; HIV-1; Humans; RNA, Viral; Virus Assembly
PubMed: 27626441
DOI: 10.3390/v8090246 -
Proceedings of the National Academy of... Nov 2018Flaviviruses assemble initially in an immature, noninfectious state and undergo extensive conformational rearrangements to generate mature virus. Previous cryo-electron...
Flaviviruses assemble initially in an immature, noninfectious state and undergo extensive conformational rearrangements to generate mature virus. Previous cryo-electron microscopy (cryo-EM) structural studies of flaviviruses assumed icosahedral symmetry and showed the concentric organization of the external glycoprotein shell, the lipid membrane, and the internal nucleocapsid core. We show here that when icosahedral symmetry constraints were excluded in calculating the cryo-EM reconstruction of an immature flavivirus, the nucleocapsid core was positioned asymmetrically with respect to the glycoprotein shell. The core was positioned closer to the lipid membrane at the proximal pole, and at the distal pole, the outer glycoprotein spikes and inner membrane leaflet were either perturbed or missing. In contrast, in the asymmetric reconstruction of a mature flavivirus, the core was positioned concentric with the glycoprotein shell. The deviations from icosahedral symmetry demonstrated that the core and glycoproteins have varied interactions, which likely promotes viral assembly and budding.
Topics: Animals; Chlorocebus aethiops; Cryoelectron Microscopy; Glycoproteins; Lipid Bilayers; Molecular Dynamics Simulation; Nucleocapsid; Vero Cells; Viral Envelope Proteins; Virus Assembly; Virus Release; West Nile virus; Zika Virus
PubMed: 30348794
DOI: 10.1073/pnas.1809304115 -
Trends in Microbiology Jan 2024The recent revolution in imaging techniques and results from RNA footprinting in situ reveal how the bacteriophage MS2 genome regulates both particle assembly and genome... (Review)
Review
The recent revolution in imaging techniques and results from RNA footprinting in situ reveal how the bacteriophage MS2 genome regulates both particle assembly and genome release. We have proposed a model in which multiple packaging signal (PS) RNA-coat protein (CP) contacts orchestrate different stages of a viral life cycle. Programmed formation and release of specific PS contacts with CP regulates viral particle assembly and genome uncoating during cell entry. We hypothesize that molecular frustration, a concept introduced to understand protein folding, can be used to better rationalize how PSs function in both particle assembly and genome release. More broadly this concept may explain the directionality of viral life cycles, for example, the roles of host cofactors in HIV infection. We propose that this is a universal principle in virology that explains mechanisms of host-virus interaction and suggests diverse therapeutic interventions.
Topics: Humans; Capsid Proteins; RNA, Viral; HIV Infections; Genome, Viral; Virus Assembly
PubMed: 37507296
DOI: 10.1016/j.tim.2023.07.003 -
STAR Protocols Mar 2022This protocol describes the reconstitution of the filamentous Ebola virus nucleocapsid-like assembly . This is followed by solving the cryo-EM structure using helical...
This protocol describes the reconstitution of the filamentous Ebola virus nucleocapsid-like assembly . This is followed by solving the cryo-EM structure using helical reconstruction, and flexible fitting of the existing model into the 5.8 Å cryo-EM map. The protocol can be applied to other filamentous viral protein assemblies, particularly those with high flexibility and moderate resolution maps, which present technical challenges to model building. For complete details on the use and execution of this profile, please refer to Su et al. (2018).
Topics: Cryoelectron Microscopy; Ebolavirus; Hemorrhagic Fever, Ebola; Humans; Nucleocapsid; Virus Assembly
PubMed: 34977676
DOI: 10.1016/j.xpro.2021.101030 -
Journal of the American Chemical Society Jul 2022Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction...
Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction between coat proteins and that between the coat proteins and the viral RNA in assembly and disassembly processes. Here, we report on the spontaneous and reversible size conversion of the empty capsids of a CCMV capsid protein functionalized with a hydrophobic elastin-like polypeptide which occurs following a pH jump. We monitor the concentrations of = 3 and = 1 capsids as a function of time and show that the time evolution of the conversion from one number to another is not symmetric: The conversion from = 1 to = 3 is a factor of 10 slower than that of = 3 to = 1. We explain our experimental findings using a simple model based on classical nucleation theory applied to virus capsids, in which we account for the change in the free protein concentration, as the different types of shells assemble and disassemble by shedding or absorbing single protein subunits. As far as we are aware, this is the first study confirming that both the assembly and disassembly of viruslike shells can be explained through classical nucleation theory, reproducing quantitatively results from time-resolved experiments.
Topics: Bromovirus; Capsid; Capsid Proteins; RNA, Viral; Virion; Virus Assembly
PubMed: 35792573
DOI: 10.1021/jacs.2c04074 -
PloS One 2021Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12...
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12 corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of 312 genomes has been explored via computationally expensive stochastic assembly models, giving a fitness landscape in terms of the assembly efficiency. Using latest machine-learning techniques by establishing a neural network, we show that the intensive computation can be short-circuited in a matter of minutes to astounding accuracy.
Topics: Computational Biology; Machine Learning; Mutation; Phenotype; Virus Assembly
PubMed: 33951035
DOI: 10.1371/journal.pone.0250227 -
Trends in Biochemical Sciences Dec 2023Giant viruses (Nucleocytoviricota) have a largely conserved lifecycle, yet how they cram their large genomes into viral capsids is mostly unknown. The major capsid... (Review)
Review
Giant viruses (Nucleocytoviricota) have a largely conserved lifecycle, yet how they cram their large genomes into viral capsids is mostly unknown. The major capsid protein and the packaging ATPase (pATPase) comprise a highly conserved morphogenesis module in giant viruses, yet some giant viruses dispense with an icosahedral capsid, and others encode multiple versions of pATPases, including conjoined ATPase doublets, or encode none. Some giant viruses have acquired DNA-condensing proteins to compact their genomes, including sheath-like structures encasing folded DNA or densely packed viral nucleosomes that show a resemblance to eukaryotic nucleosomes at the telomeres. Here, we review what is known and unknown about these ATPases and condensing proteins, and place these variations in the context of viral lifecycles.
Topics: Viral Genome Packaging; Nucleosomes; Capsid Proteins; DNA; Adenosine Triphosphatases; Genome, Viral; Virus Assembly
PubMed: 37777391
DOI: 10.1016/j.tibs.2023.09.003 -
Journal of Virology Feb 2020The assembly of an orthoretrovirus such as HIV-1 requires the coordinated functioning of multiple biochemical activities of the viral Gag protein. These activities...
The assembly of an orthoretrovirus such as HIV-1 requires the coordinated functioning of multiple biochemical activities of the viral Gag protein. These activities include membrane targeting, lattice formation, packaging of the RNA genome, and recruitment of cellular cofactors that modulate assembly. In most previous studies, these Gag activities have been investigated individually, which provided somewhat limited insight into how they functionally integrate during the assembly process. Here, we report the development of a biochemical reconstitution system that allowed us to investigate how Gag lattice formation, RNA binding, and the assembly cofactor inositol hexakisphosphate (IP6) synergize to generate immature virus particles The results identify an important rate-limiting step in assembly and reveal new insights into how RNA and IP6 promote immature Gag lattice formation. The immature virus-like particles can be converted into mature capsid-like particles by the simple addition of viral protease, suggesting that it is possible in principle to fully biochemically reconstitute the sequential processes of HIV-1 assembly and maturation from purified components. Assembly and maturation are essential steps in the replication of orthoretroviruses such as HIV-1 and are proven therapeutic targets. These processes require the coordinated functioning of the viral Gag protein's multiple biochemical activities. We describe here the development of an experimental system that allows an integrative analysis of how Gag's multiple functionalities cooperate to generate a retrovirus particle. Our current studies help to illuminate how Gag synergizes the formation of the virus compartment with RNA binding and how these activities are modulated by the small molecule IP6. Further development and use of this system should lead to a more comprehensive understanding of the molecular mechanisms of HIV-1 assembly and maturation and may provide new insights for the development of antiretroviral drugs.
Topics: Capsid; HIV-1; Humans; Microscopy, Electron; Models, Molecular; Phytic Acid; Virion; Virus Assembly; gag Gene Products, Human Immunodeficiency Virus
PubMed: 31801870
DOI: 10.1128/JVI.01844-19 -
Viruses Oct 2014Vaccinia virus (VACV) has achieved unprecedented success as a live viral vaccine for smallpox which mitigated eradication of the disease. Vaccinia virus has a complex... (Review)
Review
Vaccinia virus (VACV) has achieved unprecedented success as a live viral vaccine for smallpox which mitigated eradication of the disease. Vaccinia virus has a complex virion morphology and recent advances have been made to answer some of the key outstanding questions, in particular, the origin and biogenesis of the virion membrane, the transformation from immature virion (IV) to mature virus (MV), and the role of several novel genes, which were previously uncharacterized, but have now been shown to be essential for VACV virion formation. This new knowledge will undoubtedly contribute to the rational design of safe, immunogenic vaccine candidates, or effective antivirals in the future. This review endeavors to provide an update on our current knowledge of the VACV maturation processes with a specific focus on the initiation of VACV replication through to the formation of mature virions.
Topics: Humans; Smallpox; Vaccinia; Vaccinia virus; Viral Vaccines; Virion; Virus Assembly; Virus Replication
PubMed: 25296112
DOI: 10.3390/v6103787