scholarly journals The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus

2021 ◽  
Vol 17 (8) ◽  
pp. e1009306
Author(s):  
Sam R. Hill ◽  
Reidun Twarock ◽  
Eric C. Dykeman
Keyword(s):  
Plant Viruses ◽  
Progeny Virus ◽  
Simple Explanation ◽  
Assembly Rules ◽  
Assembly Process ◽  
Rna Packaging ◽  
Local Assembly ◽  
Rna Genome ◽  
Protein Shell ◽  
Packaging Signals

The vast majority of viruses consist of a nucleic acid surrounded by a protective icosahedral protein shell called the capsid. During viral infection of a host cell, the timing and efficiency of the assembly process is important for ensuring the production of infectious new progeny virus particles. In the class of single-stranded RNA (ssRNA) viruses, the assembly of the capsid takes place in tandem with packaging of the ssRNA genome in a highly cooperative co-assembly process. In simple ssRNA viruses such as the bacteriophage MS2 and small RNA plant viruses such as STNV, this cooperative process results from multiple interactions between the protein shell and sites in the RNA genome which have been termed packaging signals. Using a stochastic assembly algorithm which includes cooperative interactions between the protein shell and packaging signals in the RNA genome, we demonstrate that highly efficient assembly of STNV capsids arises from a set of simple local rules. Altering the local assembly rules results in different nucleation scenarios with varying assembly efficiencies, which in some cases depend strongly on interactions with RNA packaging signals. Our results provide a potential simple explanation based on local assembly rules for the ability of some ssRNA viruses to spontaneously assemble around charged polymers and other non-viral RNAs in vitro.

scholarly journals Codon conservation in the influenza A virus genome defines RNA packaging signals

2007 ◽  
Vol 35 (6) ◽  
pp. 1897-1907 ◽  
Author(s):  
Julia R. Gog ◽  
Emmanuel Dos Santos Afonso ◽  
Rosa M. Dalton ◽  
India Leclercq ◽  
Laurence Tiley ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Virus Genome ◽  
Rna Packaging ◽  
Packaging Signals

scholarly journals RNA Structures and Their Role in Selective Genome Packaging

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1788
Author(s):  
Liqing Ye ◽  
Uddhav B. Ambi ◽  
Marco Olguin-Nava ◽  
Anne-Sophie Gribling-Burrer ◽  
Shazeb Ahmad ◽  
...  
Keyword(s):  
Viral Evolution ◽  
Complex Mixture ◽  
Rna Structures ◽  
Rna Packaging ◽  
Genome Packaging ◽  
Viral Genomes ◽  
Viral Particles ◽  
The Impact ◽  
Packaging Signals

To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.

scholarly journals Unpaired Guanosines in the 5′ Untranslated Region of HIV-1 RNA Act Synergistically To Mediate Genome Packaging

2020 ◽  
Vol 94 (21) ◽  
Author(s):  
Olga A. Nikolaitchik ◽  
Xayathed Somoulay ◽  
Jonathan M. O. Rawson ◽  
Jennifer A. Yoo ◽  
Vinay K. Pathak ◽  
...  
Keyword(s):  
Binding Sites ◽  
Untranslated Region ◽  
Virus Assembly ◽  
Viral Rna ◽  
Rna Packaging ◽  
Genome Packaging ◽  
Stem Loop ◽  
Rna Genome ◽  
Genome Encapsidation ◽  
Hiv 1

ABSTRACT The viral protein Gag selects full-length HIV-1 RNA from a large pool of mRNAs as virion genome during virus assembly. Currently, the precise mechanism that mediates the genome selection is not understood. Previous studies have identified several sites in the 5′ untranslated region (5′ UTR) of HIV-1 RNA that are bound by nucleocapsid (NC) protein, which is derived from Gag during virus maturation. However, whether these NC binding sites direct HIV-1 RNA genome packaging has not been fully investigated. In this report, we examined the roles of single-stranded exposed guanosines at NC binding sites in RNA genome packaging using stable cell lines expressing competing wild-type and mutant HIV-1 RNAs. Mutant RNA packaging efficiencies were determined by comparing their prevalences in cytoplasmic RNA and in virion RNA. We observed that multiple NC binding sites affected RNA packaging; of the sites tested, those located within stem-loop 1 of the 5′ UTR had the most significant effects. These sites were previously reported as the primary NC binding sites by using a chemical probe reverse-footprinting assay and as the major Gag binding sites by using an in vitro assay. Of the mutants tested in this report, substituting 3 to 4 guanosines resulted in <2-fold defects in packaging. However, when mutations at different NC binding sites were combined, severe defects were observed. Furthermore, combining the mutations resulted in synergistic defects in RNA packaging, suggesting redundancy in Gag-RNA interactions and a requirement for multiple Gag binding on viral RNA during HIV-1 genome encapsidation. IMPORTANCE HIV-1 must package its RNA genome during virus assembly to generate infectious viruses. To better understand how HIV-1 packages its RNA genome, we examined the roles of RNA elements identified as binding sites for NC, a Gag-derived RNA-binding protein. Our results demonstrate that binding sites within stem-loop 1 of the 5′ untranslated region play important roles in genome packaging. Although mutating one or two NC-binding sites caused only mild defects in packaging, mutating multiple sites resulted in severe defects in genome encapsidation, indicating that unpaired guanosines act synergistically to promote packaging. Our results suggest that Gag-RNA interactions occur at multiple RNA sites during genome packaging; furthermore, there are functionally redundant binding sites in viral RNA.

RNA Repubilcation of Plant Viruses Containing an RNA Genome

1992 ◽  
pp. 157-227 ◽  
Author(s):  
Chantald David ◽  
Radhia Gargouri-Bouzid ◽  
Anne-Lise Haenni
Keyword(s):  
Plant Viruses ◽  
Rna Genome

scholarly journals Mutational Analyses of Packaging Signals in Influenza Virus PA, PB1, and PB2 Genomic RNA Segments

2007 ◽  
Vol 82 (1) ◽  
pp. 229-236 ◽  
Author(s):  
Yuhong Liang ◽  
Taoying Huang ◽  
Hinh Ly ◽  
Tristram G. Parslow ◽  
Yuying Liang
Keyword(s):  
Protein Function ◽  
Influenza A ◽  
Virus Genome ◽  
Coding Region ◽  
Rna Packaging ◽  
Sequence Comparisons ◽  
Protein Subunits ◽  
Coding Regions ◽  
Negative Sense ◽  
Packaging Signals

ABSTRACT The influenza A virus genome consists of eight negative-sense RNA segments that must each be packaged to produce an infectious virion. We have previously mapped the minimal cis-acting regions necessary for efficient packaging of the PA, PB1, and PB2 segments, which encode the three protein subunits of the viral RNA polymerase. The packaging signals in each of these RNAs lie within two separate regions at the 3′ and 5′ termini, each encompassing the untranslated region and extending up to 80 bases into the adjacent coding sequence. In this study, we introduced scanning mutations across the coding regions in each of these RNA segments in order to finely define the packaging signals. We found that mutations producing the most severe defects were confined to a few discrete 5′ sites in the PA or PB1 coding regions but extended across the entire (80-base) 5′ coding region of PB2. In sequence comparisons among more than 580 influenza A strains from diverse hosts, these highly deleterious mutations were each found to affect one or more conserved bases, though they did not all lie within the most broadly conserved portions of the regions that we interrogated. We have introduced silent and conserved mutations to the critical packaging sites, which did not affect protein function but impaired viral replication at levels roughly similar to those of their defects in RNA packaging. Interestingly, certain mutations showed strong tendencies to revert to wild-type sequences, which implies that these putative packaging signals are critical for the influenza life cycle.

scholarly journals HIV-1 Gag co-opts a cellular complex containing DDX6, a helicase that facilitates capsid assembly

2012 ◽  
Vol 198 (3) ◽  
pp. 439-456 ◽  
Author(s):  
Jonathan C. Reed ◽  
Britta Molter ◽  
Clair D. Geary ◽  
John McNevin ◽  
Julie McElrath ◽  
...  
Keyword(s):  
Rna Helicase ◽  
Progeny Virus ◽  
Type I ◽  
Capsid Assembly ◽  
Rna Packaging ◽  
Human T Cells ◽  
Immunodeficiency Virus ◽  
Processing Body ◽  
Related Proteins ◽  
Hiv 1

To produce progeny virus, human immunodeficiency virus type I (HIV-1) Gag assembles into capsids that package the viral genome and bud from the infected cell. During assembly of immature capsids, Gag traffics through a pathway of assembly intermediates (AIs) that contain the cellular adenosine triphosphatase ABCE1 (ATP-binding cassette protein E1). In this paper, we showed by coimmunoprecipitation and immunoelectron microscopy (IEM) that these Gag-containing AIs also contain endogenous processing body (PB)–related proteins, including AGO2 and the ribonucleic acid (RNA) helicase DDX6. Moreover, we found a similar complex containing ABCE1 and PB proteins in uninfected cells. Additionally, knockdown and rescue studies demonstrated that the RNA helicase DDX6 acts enzymatically to facilitate capsid assembly independent of RNA packaging. Using IEM, we localized the defect in DDX6-depleted cells to Gag multimerization at the plasma membrane. We also confirmed that DDX6 depletion reduces production of infectious HIV-1 from primary human T cells. Thus, we propose that assembling HIV-1 co-opts a preexisting host complex containing cellular facilitators such as DDX6, which the virus uses to catalyze capsid assembly.

scholarly journals H5N8 and H7N9 packaging signals constrain HA reassortment with a seasonal H3N2 influenza A virus

2019 ◽  
Vol 116 (10) ◽  
pp. 4611-4618 ◽  
Author(s):  
Maria C. White ◽  
Hui Tao ◽  
John Steel ◽  
Anice C. Lowen
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Molecular Mechanisms ◽  
H3n2 Virus ◽  
Dependent Manner ◽  
Rna Packaging ◽  
H3n2 Influenza ◽  
Guinea Pig Model ◽  
Packaging Signals

Influenza A virus (IAV) has a segmented genome, which (i) allows for exchange of gene segments in coinfected cells, termed reassortment, and (ii) necessitates a selective packaging mechanism to ensure incorporation of a complete set of segments into virus particles. Packaging signals serve as segment identifiers and enable segment-specific packaging. We have previously shown that packaging signals limit reassortment between heterologous IAV strains in a segment-dependent manner. Here, we evaluated the extent to which packaging signals prevent reassortment events that would raise concern for pandemic emergence. Specifically, we tested the compatibility of hemagglutinin (HA) packaging signals from H5N8 and H7N9 avian IAVs with a human seasonal H3N2 IAV. By evaluating reassortment outcomes, we demonstrate that HA segments carrying H5 or H7 packaging signals are significantly disfavored for incorporation into a human H3N2 virus in both cell culture and a guinea pig model. However, incorporation of the heterologous HAs was not excluded fully, and variants with heterologous HA packaging signals were detected at low levels in vivo, including in naïve contact animals. This work indicates that the likelihood of reassortment between human seasonal IAV and avian IAV is reduced by divergence in the RNA packaging signals of the HA segment. These findings offer important insight into the molecular mechanisms governing IAV emergence and inform efforts to estimate the risks posed by H7N9 and H5N8 subtype avian IAVs.

scholarly journals cis-Acting Elements Important for Retroviral RNA Packaging Specificity

2002 ◽  
Vol 76 (10) ◽  
pp. 4950-4960 ◽  
Author(s):  
Benjamin E. Beasley ◽  
Wei-Shau Hu
Keyword(s):  
Leukemia Virus ◽  
Rna Packaging ◽  
Packaging Signal ◽  
Core Element ◽  
Viral Packaging ◽  
Cis Acting ◽  
Spleen Necrosis ◽  
Flanking Regions ◽  
Packaging Signals

ABSTRACT Spleen necrosis virus (SNV) proteins can package RNA from distantly related murine leukemia virus (MLV), whereas MLV proteins cannot package SNV RNA efficiently. We used this nonreciprocal recognition to investigate regions of packaging signals that influence viral RNA encapsidation specificity. Although the MLV and SNV packaging signals (Ψ and E, respectively) do not contain significant sequence homology, they both contain a pair of hairpins. This hairpin pair was previously proposed to be the core element in MLV Ψ. In the present study, MLV-based vectors were generated to contain chimeric SNV/MLV packaging signals in which the hairpins were replaced with the heterologous counterpart. The interactions between these chimeras and MLV or SNV proteins were examined by virus replication and RNA analyses. SNV proteins recognized all of the chimeras, indicating that these chimeras were functional. We found that replacing the hairpin pair did not drastically alter the ability of MLV proteins to package these chimeras. These results indicate that, despite the important role of the hairpin pair in RNA packaging, it is not the major motif responsible for the ability of MLV proteins to discriminate between the MLV and SNV packaging signals. To determine the role of sequences flanking the hairpins in RNA packaging specificity, vectors with swapped flanking regions were generated and evaluated. SNV proteins packaged all of these chimeras efficiently. In contrast, MLV proteins strongly favored chimeras with the MLV 5′-flanking regions. These data indicated that MLV Gag recognizes multiple elements in the viral packaging signal, including the hairpin structure and flanking regions.

scholarly journals Special issue: Plant viruses. Ambisense RNA genome of rice stripe virus.

Uirusu ◽  
1994 ◽  
Vol 44 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Chika Hamamatsu ◽  
Akira Ishihama
Keyword(s):  
Rice Stripe Virus ◽  
Plant Viruses ◽  
Special Issue ◽  
Rna Genome
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