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Viruses Sep 2020Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced... (Review)
Review
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems-a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
Topics: Base Sequence; Genome, Viral; HIV-1; Magnetic Resonance Spectroscopy; Nucleic Acid Conformation; Phylogeny; Protein Structure, Secondary; RNA, Viral; Retroviridae; Viral Genome Packaging; Virus Assembly
PubMed: 33008123
DOI: 10.3390/v12101115 -
Current Issues in Molecular Biology 2021Alphaherpesvirus tegument assembly, secondary envelopment, and exocytosis processes are understood in broad strokes, but many of the individual steps in this pathway,...
Alphaherpesvirus tegument assembly, secondary envelopment, and exocytosis processes are understood in broad strokes, but many of the individual steps in this pathway, and their molecular and cell biological details, remain unclear. Viral tegument and membrane proteins form an extensive and robust protein interaction network, such that essentially any structural protein can be deleted, yet particles are still assembled, enveloped, and released from infected cells. We conceptually divide the tegument proteins into three groups: conserved inner and outer teguments that participate in nucleocapsid and membrane contacts, respectively; and 'middle' tegument proteins, consisting of some of the most abundant tegument proteins that serve as central hubs in the protein interaction network, yet which are unique to the alphaherpesviruses. We then discuss secondary envelopment, reviewing the tegument-membrane contacts and cellular factors that drive this process. We place this viral process in the context of cell biological processes, including the endocytic pathway, ESCRT machinery, autophagy, secretory pathway, intracellular transport, and exocytosis mechanisms. Finally, we speculate about potential relationships between cellular defenses against oligomerizing or aggregating membrane proteins and the envelopment and egress of viruses.
Topics: Alphaherpesvirinae; Autophagy; Biological Transport; Endosomal Sorting Complexes Required for Transport; Exocytosis; Host-Pathogen Interactions; Humans; Virus Assembly; Virus Physiological Phenomena; Virus Release
PubMed: 33622984
DOI: 10.21775/cimb.042.551 -
Viruses Jul 2022Viral assembly and budding are the final steps and key determinants of the virus life cycle and are regulated by virus-host interaction. Several viruses are known to use...
Viral assembly and budding are the final steps and key determinants of the virus life cycle and are regulated by virus-host interaction. Several viruses are known to use their late assembly (L) domains to hijack host machinery and cellular adaptors to be used for the requirement of virus replication. The L domains are highly conserved short sequences whose mutation or deletion may lead to the accumulation of immature virions at the plasma membrane. The L domains were firstly identified within retroviral Gag polyprotein and later detected in structural proteins of many other enveloped RNA viruses. Here, we used HIV-1 as an example to describe how the HIV-1 virus hijacks ESCRT membrane fission machinery to facilitate virion assembly and release. We also introduce galectin-3, a chimera type of the galectin family that is up-regulated by HIV-1 during infection and further used to promote HIV-1 assembly and budding via the stabilization of Alix-Gag interaction. It is worth further dissecting the details and finetuning the regulatory mechanism, as well as identifying novel candidates involved in this final step of replication cycle.
Topics: Calcium-Binding Proteins; Cell Cycle Proteins; Endosomal Sorting Complexes Required for Transport; HIV-1; Virus Assembly; Virus Release; gag Gene Products, Human Immunodeficiency Virus
PubMed: 35891508
DOI: 10.3390/v14071528 -
ACS Nano Apr 2020Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various...
Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of = 12 pentamers ( = 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here "C-terminal ligands", which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the = 1 feature the ability to dynamically rearrange and are thus termed "pseudo-closed". The = 13 shell can even spontaneously "self-correct" by losing a pentamer and become a = 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing the pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.
Topics: Capsid; Capsid Proteins; Simian virus 40; Virus Assembly
PubMed: 32208635
DOI: 10.1021/acsnano.9b10004 -
Advances in Virus Research 2020The human betaherpesviruses, human cytomegalovirus (HCMV; species Human betaherpesvirus 5) and human herpesviruses 6A, 6B, and 7 (HHV-6A, -6B, and -7; species Human... (Review)
Review
The human betaherpesviruses, human cytomegalovirus (HCMV; species Human betaherpesvirus 5) and human herpesviruses 6A, 6B, and 7 (HHV-6A, -6B, and -7; species Human betaherpesviruses 6A, 6B, and 7) are highly prevalent and can cause severe disease in immune-compromised and immune-naive populations in well- and under-developed communities. Herpesvirus virion assembly is an intricate process that requires viral orchestration of host systems. In this review, we describe recent advances in some of the many cellular events relevant to assembly and egress of betaherpesvirus virions. These include modifications of host metabolic, immune, and autophagic/recycling systems. In addition, we discuss unique aspects of betaherpesvirus virion structure, virion assembly, and the cellular pathways employed during virion egress.
Topics: Animals; Books; DNA, Viral; Genome, Viral; Herpesvirus 6, Human; Humans; Virion; Virus Assembly; Virus Release
PubMed: 33837722
DOI: 10.1016/bs.aivir.2020.09.003 -
Current Opinion in Virology Jun 2021A central quest in gene therapy and vaccination is to achieve effective and long-lasting gene expression at minimal dosage. Adenovirus vectors are widely used... (Review)
Review
A central quest in gene therapy and vaccination is to achieve effective and long-lasting gene expression at minimal dosage. Adenovirus vectors are widely used therapeutics and safely deliver genes into many cell types. Adenoviruses evolved to use elaborate trafficking and particle deconstruction processes, and efficient gene expression and progeny formation. Here, we discuss recent insights into how human adenoviruses deliver their double-stranded DNA genome into cell nuclei, and effect lytic cell killing, non-lytic persistent infection or vector gene expression. The mechanisms underlying adenovirus entry, uncoating, nuclear transport and gene expression provide a blueprint for the emerging field of synthetic virology, where artificial virus-like particles are evolved to deliver therapeutic payload into human cells without viral proteins and genomes.
Topics: Adenoviridae; Adenoviruses, Human; Animals; Cell Nucleus; DNA; DNA, Viral; Endocytosis; Gene Expression; Gene Transfer Techniques; Genetic Therapy; Genetic Vectors; Genome, Viral; Genomic Instability; Humans; Virion; Virus Assembly; Virus Attachment; Virus Replication
PubMed: 33892224
DOI: 10.1016/j.coviro.2021.03.006 -
MBio Oct 2019The flavivirus virion consists of an envelope outer layer, formed by envelope (E) and membrane (M) proteins on a lipid bilayer, and an internal core, formed by capsid...
The flavivirus virion consists of an envelope outer layer, formed by envelope (E) and membrane (M) proteins on a lipid bilayer, and an internal core, formed by capsid (C) protein and genomic RNA. The molecular mechanism of flavivirus assembly is not well understood. Here, we show that Zika virus (ZIKV) NS2A protein recruits genomic RNA, the structural protein prM/E complex, and the NS2B/NS3 protease complex to the virion assembly site and orchestrates virus morphogenesis. Coimmunoprecipitation analysis showed that ZIKV NS2A binds to prM, E, NS2B, and NS3 (but not C, NS4B, or NS5) in a viral RNA-independent manner, whereas prM/E complex does not interact with NS2B/NS3 complex. Remarkably, a single-amino-acid mutation (E103A) of NS2A impairs its binding to prM/E and NS2B/NS3 and abolishes virus production, demonstrating the indispensable role of NS2A/prM/E and NS2A/NS2B/NS3 interactions in virion assembly. In addition, RNA-protein pulldown analysis identified a stem-loop RNA from the 3' untranslated region (UTR) of the viral genome as an "RNA recruitment signal" for ZIKV assembly. The 3' UTR RNA binds to a cytoplasmic loop of NS2A protein. Mutations of two positively charged residues (R96A and R102A) from the cytoplasmic loop reduce NS2A binding to viral RNA, leading to a complete loss of virion assembly. Collectively, our results support a virion assembly model in which NS2A recruits viral NS2B/NS3 protease and structural C-prM-E polyprotein to the virion assembly site; once the C-prM-E polyprotein has been processed, NS2A presents viral RNA to the structural proteins for virion assembly. ZIKV is a recently emerged mosquito-borne flavivirus that can cause devastating congenital Zika syndrome in pregnant women and Guillain-Barré syndrome in adults. The molecular mechanism of ZIKV virion assembly is largely unknown. Here, we report that ZIKV NS2A plays a central role in recruiting viral RNA, structural protein prM/E, and viral NS2B/NS3 protease to the virion assembly site and orchestrating virion morphogenesis. One mutation that impairs these interactions does not significantly affect viral RNA replication but selectively abolishes virion assembly, demonstrating the specific role of these interactions in virus morphogenesis. We also show that the 3' UTR of ZIKV RNA may serve as a "recruitment signal" through binding to NS2A to enter the virion assembly site. Following a coordinated cleavage of C-prM-E at the virion assembly site, NS2A may present the viral RNA to C protein for nucleocapsid formation followed by envelopment with prM/E proteins. The results have provided new insights into flavivirus virion assembly.
Topics: Female; Flavivirus; Genome, Viral; Humans; Mutation; Nucleocapsid; Peptide Hydrolases; Pregnancy; RNA, Viral; Serine Endopeptidases; Viral Envelope Proteins; Viral Nonstructural Proteins; Viral Proteins; Virus Assembly; Virus Replication; Zika Virus; Zika Virus Infection
PubMed: 31662457
DOI: 10.1128/mBio.02375-19 -
Viruses Dec 2021Understanding the molecular mechanisms of retroviral assembly has been a decades-long endeavor. With the recent discovery of inositol hexakisphosphate (IP6) acting as an... (Review)
Review
Understanding the molecular mechanisms of retroviral assembly has been a decades-long endeavor. With the recent discovery of inositol hexakisphosphate (IP6) acting as an assembly co-factor for human immunodeficiency virus (HIV), great strides have been made in retroviral research. In this review, the enzymatic pathways to synthesize and metabolize inositol phosphates (IPs) relevant to retroviral assembly are discussed. The functions of these enzymes and IPs are outlined in the context of the cellular biology important for retroviruses. Lastly, the recent advances in understanding the role of IPs in retroviral biology are surveyed.
Topics: Biosynthetic Pathways; HIV Infections; Humans; Inositol Phosphates; Phytic Acid; Retroviridae; Virion; Virus Assembly; gag Gene Products, Human Immunodeficiency Virus
PubMed: 34960784
DOI: 10.3390/v13122516 -
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 -
Viruses May 2023Gumboro illness is caused by the highly contagious immunosuppressive infectious bursal disease virus (IBDV), which affects the poultry industry globally. We have...
Gumboro illness is caused by the highly contagious immunosuppressive infectious bursal disease virus (IBDV), which affects the poultry industry globally. We have previously shown that IBDV hijacks the endocytic pathway to construct viral replication complexes on endosomes linked to the Golgi complex (GC). Then, analyzing crucial proteins involved in the secretory pathway, we showed the essential requirement of Rab1b, the Rab1b downstream effector Golgi-specific BFA resistance factor 1 (GBF1), and its substrate, the small GTPase ADP-ribosylation factor 1 (ARF1), for IBDV replication. In the current work, we focused on elucidating the IBDV assembly sites. We show that viral assembly occurs within single-membrane compartments closely associated with endoplasmic reticulum (ER) membranes, though we failed to elucidate the exact nature of the virus-wrapping membranes. Additionally, we show that IBDV infection promotes the stress of the ER, characterized by an accumulation of the chaperone binding protein (BiP) and lipid droplets (LDs) in the host cells. Overall, our results represent further original data showing the interplay between IBDV and the secretory pathway, making a substantial contribution to the field of birnaviruses-host cell interactions.
Topics: Animals; Infectious bursal disease virus; Lipid Droplets; Virus Assembly; Endosomes; Endoplasmic Reticulum Stress; Chickens; Poultry Diseases; Birnaviridae Infections
PubMed: 37376595
DOI: 10.3390/v15061295