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RNA Biology 2010HIV-1 nucleocapsid protein (NC) is a small basic protein generated by the cleavage of the Gag structural polyprotein precusor by the viral protease during virus assembly... (Review)
Review
HIV-1 nucleocapsid protein (NC) is a small basic protein generated by the cleavage of the Gag structural polyprotein precusor by the viral protease during virus assembly in the infected cell. HIV-1 NC possesses two copies of a highly conserved CCHC zinc finger (ZnF), flanked by basic residues. HIV-1 NC and more generally retroviral NC proteins are nucleic acid binding proteins possessing potent nucleic acid condensing and chaperoning activities. As such NC protein drives critical structural rearrangements of the genomic RNA, notably RNA dimerization in the course of virus assembly and viral nucleic acid annealing required for genomic RNA replication by the viral reverse transcriptase (RT). Here we review the relationships between the 3D structure of HIV-1 NC, notably the central globular domain encompassing the two zinc fingers and the basic linker and NC functions in the early and late phases of virus replication. One of the salient feature of the NC central globular domain is an hydrophobic plateau which appears to orchestrate the NC functions, such as chaperoning the conversion of the genomic RNA into viral DNA by RT during the early phase, and driving the selection and dimerization of the genomic RNA at the initial stage of viral particle assembly. This ensures a bona fide trafficking of early GagNC-genomic RNA complexes to the plasma membrane of the infected cell and ultimately virion formation and budding.
Topics: Animals; Gene Products, gag; Humans; Nucleocapsid Proteins; Protein Binding; Protein Structure, Tertiary; RNA, Viral; Retroviridae; Structure-Activity Relationship; Virus Assembly
PubMed: 21157181
DOI: 10.4161/rna.7.6.14065 -
Microbiology and Molecular Biology... Sep 2022Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic... (Review)
Review
Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic level, RNA virus populations consist not only of a homogeneous population of standard viral genomes but also of an extremely large number of genome variants, termed viral quasispecies, and nonstandard viral genomes, which include copy-back viral genomes, deletion viral genomes, mini viral RNAs, and hypermutated RNAs. At the particle level, RNA virus populations are composed of pleomorphic particles, particles missing or having additional genomes, and single particles or particle aggregates. As we continue discovering more about the components of negative-sense RNA virus populations and their crucial functions during virus infection, it will become more important to study RNA virus populations as a whole rather than their individual parts. In this review, we will discuss what is known about the components of negative-sense RNA virus communities, speculate how the components of the virus community interact, and summarize what vaccines and antiviral therapies are being currently developed to target or harness these components.
Topics: Antiviral Agents; Genome, Viral; Negative-Sense RNA Viruses; RNA Viruses; RNA, Viral; Virus Assembly
PubMed: 35658541
DOI: 10.1128/mmbr.00086-21 -
MBio Apr 2024A member of the Retroviridae, human immunodeficiency virus type 1 (HIV-1), uses the RNA genome packaged into nascent virions to transfer genetic information to its... (Review)
Review
A member of the Retroviridae, human immunodeficiency virus type 1 (HIV-1), uses the RNA genome packaged into nascent virions to transfer genetic information to its progeny. The genome packaging step is a highly regulated and extremely efficient process as a vast majority of virus particles contain two copies of full-length unspliced HIV-1 RNA that form a dimer. Thus, during virus assembly HIV-1 can identify and selectively encapsidate HIV-1 unspliced RNA from an abundant pool of cellular RNAs and various spliced HIV-1 RNAs. Several "" features facilitate the packaging of a dimeric RNA genome. The viral polyprotein ag orchestrates virus assembly and mediates RNA genome packaging. During this process, Gag preferentially binds unpaired uanosines within the highly structured 5' untranslated region (UTR) of HIV-1 RNA. In addition, the HIV-1 unspliced RNA provides a scaffold that promotes Gag:Gag interactions and virus assembly, thereby ensuring its packaging. Intriguingly, recent studies have shown that the use of different uanosines at the junction of U3 and R as transcription start sites results in HIV-1 unspliced RNA species with 99.9% identical sequences but dramatically distinct 5' UTR conformations. Consequently, one species of unspliced RNA is preferentially packaged over other nearly identical RNAs. These studies reveal how conformations affect the functions of HIV-1 RNA elements and the complex regulation of HIV-1 replication. In this review, we summarize - and -acting elements critical for HIV-1 RNA packaging, locations of Gag:RNA interactions that mediate genome encapsidation, and the effects of transcription start sites on the structure and packaging of HIV-1 RNA.
Topics: Humans; HIV-1; RNA, Viral; Virus Assembly; Genome, Viral
PubMed: 38411060
DOI: 10.1128/mbio.00861-23 -
Veterinary Immunology and... Mar 2010Infection of domestic cats with virulent strains of the feline immunodeficiency virus (FIV) leads to an acquired immunodeficiency syndrome (AIDS), similar to the... (Review)
Review
Infection of domestic cats with virulent strains of the feline immunodeficiency virus (FIV) leads to an acquired immunodeficiency syndrome (AIDS), similar to the pathogenesis induced in humans by infection with human immunodeficiency virus type 1 (HIV-1). Thus, FIV is a highly relevant model for anti-HIV therapy and vaccine development. FIV is not infectious in humans, so it is also a potentially effective non-toxic gene therapy vector. To make better use of this model, it is important to define the cellular machinery utilized by each virus to produce virus particles so that relevant similarities can be identified. It is well understood that all replication-competent retroviruses encode gag, pol, and env genes, which provide core elements for virus replication. As a result, most antiretroviral therapy targets pol-derived enzymes (protease, reverse transcriptase, and integrase) orenv-derived glycoproteins that mediate virus attachment and entry. However, resistance to drugs against these targets is a persistent problem, and novel targets must be identified to produce more effective drugs that can either substitute or be combined with current therapy. Elements of the gag gene (matrix, capsid, nucleocapsid, and "late" domains) have yet to be exploited as antiviral targets, even though the Gag precursor polyprotein is self-sufficient for the assembly and release of virus particles from cells. This process is far better understood in primate lentiviruses, especially HIV-1. However, there has been significant progress in recent years in defining how FIV Gag is targeted to the cellular plasma membrane, assembles into virions, incorporates FIV Env glycoproteins, and utilizes host cell machinery to complete virus release. Recent discoveries of intracellular restriction factors that target HIV-1 and FIV capsids after virus entry have also opened exciting new areas of research. This review summarizes currently known interactions involving HIV-1 and FIV Gag that affect virus release, infectivity, and replication.
Topics: Animals; Cats; Feline Acquired Immunodeficiency Syndrome; Gene Products, gag; Host-Pathogen Interactions; Immunodeficiency Virus, Feline; Virus Assembly; Virus Release
PubMed: 19910057
DOI: 10.1016/j.vetimm.2009.10.003 -
MBio Oct 2021In 2019, a new pandemic virus belonging to the betacoronavirus family emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This new coronavirus...
In 2019, a new pandemic virus belonging to the betacoronavirus family emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This new coronavirus appeared in Wuhan, China, and is responsible for severe respiratory pneumonia in humans, namely, coronavirus disease 2019 (COVID-19). Having infected almost 200 million people worldwide and caused more than 4.1 million deaths as of today, this new disease has raised a significant number of questions about its molecular mechanism of replication and, in particular, how infectious viral particles are produced. Although viral entry is well characterized, the full assembly steps of SARS-CoV-2 have still not been fully described. Coronaviruses, including SARS-CoV-2, have four main structural proteins, namely, the spike glycoprotein (S), the membrane glycoprotein (M), the envelope protein (E), and the nucleocapsid protein (N). All these proteins have key roles in the process of coronavirus assembly and budding. In this review, we gathered the current knowledge about betacoronavirus structural proteins involved in viral particle assembly, membrane curvature and scission, and then egress in order to suggest and question a coherent model for SARS-CoV-2 particle production and release.
Topics: Betacoronavirus; Membrane Glycoproteins; Nucleocapsid Proteins; SARS-CoV-2; Spike Glycoprotein, Coronavirus; Virus Assembly
PubMed: 34579570
DOI: 10.1128/mBio.02371-21 -
Sub-cellular Biochemistry 2013Viral particles consist essentially of a proteinaceous capsid protecting a genome and involved also in many functions during the virus life cycle. In simple viruses, the... (Review)
Review
Viral particles consist essentially of a proteinaceous capsid protecting a genome and involved also in many functions during the virus life cycle. In simple viruses, the capsid consists of a number of copies of the same, or a few different proteins organized into a symmetric oligomer. Structurally complex viruses present a larger variety of components in their capsids than simple viruses. They may contain accessory proteins with specific architectural or functional roles; or incorporate non-proteic elements such as lipids. They present a range of geometrical variability, from slight deviations from the icosahedral symmetry to complete asymmetry or even pleomorphism. Putting together the many different elements in the virion requires an extra effort to achieve correct assembly, and thus complex viruses require sophisticated mechanisms to regulate morphogenesis. This chapter provides a general view of the structure and assembly of complex viruses.
Topics: Animals; Humans; Virus Assembly; Viruses
PubMed: 23737057
DOI: 10.1007/978-94-007-6552-8_11 -
Cell Host & Microbe Nov 2019Dengue virus assembly requires cleavage of viral C-prM-E polyprotein into three structural proteins (capsid, premembrane, and envelope), packaging of viral RNA with C...
Dengue virus assembly requires cleavage of viral C-prM-E polyprotein into three structural proteins (capsid, premembrane, and envelope), packaging of viral RNA with C protein into nucleocapsid, and budding of prM and E proteins into virions. The molecular mechanisms underlying these assembly events are unclear. Here, we show that dengue nonstructural protein 2A (NS2A protein) recruits viral RNA, structural proteins, and protease to the site of virion assembly and coordinates nucleocapsid and virus formation. The last 285 nucleotides of viral 3' UTR serve as a "recruiting signal for packaging" that binds to a cytosolic loop of NS2A. This interaction allows NS2A to recruit nascent RNA from the replication complex to the virion assembly site. NS2A also recruits the C-prM-E polyprotein and NS2B-NS3 protease to the virion assembly site by interacting with prM, E, and NS3, leading to coordinated C-prM-E cleavage. Mature C protein assembles onto genomic RNA to form nucleocapsid, followed by prM and E envelopment and virion formation.
Topics: Aedes; Animals; Cell Line; Chlorocebus aethiops; Cricetinae; Dengue Virus; HEK293 Cells; Humans; Nucleocapsid; RNA Helicases; RNA, Viral; Serine Endopeptidases; Vero Cells; Viral Envelope Proteins; Viral Nonstructural Proteins; Viral Proteins; Virus Assembly
PubMed: 31631053
DOI: 10.1016/j.chom.2019.09.015 -
Nano Letters Apr 2021Designer virus-inspired proteins drive the manufacturing of more effective, safer gene-delivery systems and simpler models to study viral assembly. However,...
Designer virus-inspired proteins drive the manufacturing of more effective, safer gene-delivery systems and simpler models to study viral assembly. However, self-assembly of engineered viromimetic proteins on specific nucleic acid templates, a distinctive viral property, has proved difficult. Inspired by viral packaging signals, we harness the programmability of CRISPR-Cas12a to direct the nucleation and growth of a self-assembling synthetic polypeptide into virus-like particles (VLP) on specific DNA molecules. Positioning up to ten nuclease-dead Cas12a (dCas12a) proteins along a 48.5 kbp DNA template triggers particle growth and full DNA encapsidation at limiting polypeptide concentrations. Particle growth rate is further increased when dCas12a is dimerized with a polymerization silk-like domain. Such improved self-assembly efficiency allows for discrimination between cognate versus noncognate DNA templates by the synthetic polypeptide. CRISPR-guided VLPs will help to develop programmable bioinspired nanomaterials with applications in biotechnology as well as viromimetic scaffolds to improve our understanding of viral self-assembly.
Topics: Clustered Regularly Interspaced Short Palindromic Repeats; DNA; Nucleocapsid; Virion; Virus Assembly
PubMed: 33729813
DOI: 10.1021/acs.nanolett.0c04640 -
Virus Research Dec 2004Influenza viruses are causative agents of an acute febrile respiratory disease called influenza (commonly known as "flu") and belong to the Orthomyxoviridae family.... (Review)
Review
Influenza viruses are causative agents of an acute febrile respiratory disease called influenza (commonly known as "flu") and belong to the Orthomyxoviridae family. These viruses possess segmented, negative stranded RNA genomes (vRNA) and are enveloped, usually spherical and bud from the plasma membrane (more specifically, the apical plasma membrane of polarized epithelial cells). Complete virus particles, therefore, are not found inside infected cells. Virus particles consist of three major subviral components, namely the viral envelope, matrix protein (M1), and core (viral ribonucleocapsid [vRNP]). The viral envelope surrounding the vRNP consists of a lipid bilayer containing spikes composed of viral glycoproteins (HA, NA, and M2) on the outer side and M1 on the inner side. Viral lipids, derived from the host plasma membrane, are selectively enriched in cholesterol and glycosphingolipids. M1 forms the bridge between the viral envelope and the core. The viral core consists of helical vRNP containing vRNA (minus strand) and NP along with minor amounts of NEP and polymerase complex (PA, PB1, and PB2). For viral morphogenesis to occur, all three viral components, namely the viral envelope (containing lipids and transmembrane proteins), M1, and the vRNP must be brought to the assembly site, i.e. the apical plasma membrane in polarized epithelial cells. Finally, buds must be formed at the assembly site and virus particles released with the closure of buds. Transmembrane viral proteins are transported to the assembly site on the plasma membrane via the exocytic pathway. Both HA and NA possess apical sorting signals and use lipid rafts for cell surface transport and apical sorting. These lipid rafts are enriched in cholesterol, glycosphingolipids and are relatively resistant to neutral detergent extraction at low temperature. M1 is synthesized on free cytosolic polyribosomes. vRNPs are made inside the host nucleus and are exported into the cytoplasm through the nuclear pore with the help of M1 and NEP. How M1 and vRNPs are directed to the assembly site on the plasma membrane remains unclear. The likely possibilities are that they use a piggy-back mechanism on viral glycoproteins or cytoskeletal elements. Alternatively, they may possess apical determinants or diffuse to the assembly site, or a combination of these pathways. Interactions of M1 with M1, M1 with vRNP, and M1 with HA and NA facilitate concentration of viral components and exclusion of host proteins from the budding site. M1 interacts with the cytoplasmic tail (CT) and transmembrane domain (TMD) of glycoproteins, and thereby functions as a bridge between the viral envelope and vRNP. Lipid rafts function as microdomains for concentrating viral glycoproteins and may serve as a platform for virus budding. Virus bud formation requires membrane bending at the budding site. A combination of factors including concentration of and interaction among viral components, increased viscosity and asymmetry of the lipid bilayer of the lipid raft as well as pulling and pushing forces of viral and host components are likely to cause outward curvature of the plasma membrane at the assembly site leading to bud formation. Eventually, virus release requires completion of the bud due to fusion of the apposing membranes, leading to the closure of the bud, separation of the virus particle from the host plasma membrane and release of the virus particle into the extracellular environment. Among the viral components, M1 contains an L domain motif and plays a critical role in budding. Bud completion requires not only viral components but also host components. However, how host components facilitate bud completion remains unclear. In addition to bud completion, influenza virus requires NA to release virus particles from sialic acid residues on the cell surface and spread from cell to cell. Elucidation of both viral and host factors involved in viral morphogenesis and budding may lead to the development of drugs interfering with the steps of viral morphogenesis and in disease progression.
Topics: Animals; Humans; Nucleocapsid; Orthomyxoviridae; Protein Transport; Viral Matrix Proteins; Viral Proteins; Virus Assembly
PubMed: 15567494
DOI: 10.1016/j.virusres.2004.08.012 -
Current Opinion in Virology Dec 2020Viral structural proteins are emerging as effective targets for new antivirals. In a viral lifecycle, the capsid must assemble, disassemble, and respond to host... (Review)
Review
Viral structural proteins are emerging as effective targets for new antivirals. In a viral lifecycle, the capsid must assemble, disassemble, and respond to host proteins, all at the right time and place. These reactions work within a narrow range of conditions, making them susceptible to small molecule interference. In at least three specific viruses, this approach has had met with preliminary success. In rhinovirus and poliovirus, compounds like pleconaril bind capsid and block RNA release. Bevirimat binds to Gag protein in HIV, inhibiting maturation. In Hepatitis B virus, core protein allosteric modulators (CpAMs) promote spontaneous assembly of capsid protein leading to empty and aberrant particles. Despite the biological diversity between viruses and the chemical diversity between antiviral molecules, we observe common features in these antivirals' mechanisms of action. These approaches work by stabilizing protein-protein interactions.
Topics: Antiviral Agents; Capsid; Drug Discovery; Hepatitis B virus; Viral Structural Proteins; Virus Assembly; Virus Replication; Viruses
PubMed: 32777753
DOI: 10.1016/j.coviro.2020.07.001