scholarly journals Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 76 ◽  
Author(s):  
Sari Mäntynen ◽  
Lotta-Riina Sundberg ◽  
Hanna Oksanen ◽  
Minna Poranen
Keyword(s):  
Lipid Analysis ◽  
Virus Assembly ◽  
Crop Protection ◽  
Membrane Structures ◽  
Genome Packaging ◽  
Long Distance ◽  
Virus Diversity ◽  
New Concepts ◽  
Ecological Importance ◽  
Original Observation

Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of “viral lineages”, postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.

Chapter 2a: Virology

2021 ◽  
Author(s):  
Daniel Růžek ◽  
Kentaro Yoshii ◽  
Marshall E. Bloom ◽  
Ernest A. Gould
Keyword(s):  
Host Cell ◽  
Secretory Pathway ◽  
Virus Assembly ◽  
Close Association ◽  
Spherical Particles ◽  
Structural Proteins ◽  
Membrane Structures ◽  
Vesicle Membrane ◽  
Reading Frame ◽  
Tbe Virus

TBEV is the most medically important member of the tick-borne serocomplex group within the genus Flavivirus, family Flaviviridae. Three antigenic subtypes of TBEV correspond to the 3 recognized genotypes: European (TBEV-EU), also known as Western, Far Eastern (TBEV-FE), and Siberian (TBEV-SIB). An additional 2 genotypes have been identified in the Irkutsk region of Russia, currently named TBE virus Baikalian subtype (TBEV-BKL) and TBE virus Himalayan subtype (Himalayan and “178-79” group; TBEV-HIM). TBEV virions are small enveloped spherical particles about 50 nm in diameter. The TBEV genome consists of a single-stranded positive sense RNA molecule. The genome encodes one open reading frame (ORF), which is flanked by untranslated (non-coding) regions (UTRs). The 5′-UTR end has a methylated nucleotide cap for canonical cellular translation. The 3′-UTR is not polyadenylated and is characterized by extensive length and sequence heterogeneity. The ORF encodes one large polyprotein, which is co- and post-translationally cleaved into 3 structural proteins (C, prM, and E) and 7 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). TBEV replicates in the cytoplasm of the host cell in close association with virus-induced intracellular membrane structures. Virus assembly occurs in the endoplasmic reticulum. The immature virions are transported to the Golgi complex, and mature virions pass through the host secretory pathway and are finally released from the host cell by fusion of the transport vesicle membrane with the plasma membrane.

scholarly journals Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Rebecca S. Brown ◽  
Dimitrios G. Anastasakis ◽  
Markus Hafner ◽  
Margaret Kielian
Keyword(s):  
Capsid Protein ◽  
Binding Sites ◽  
Semliki Forest Virus ◽  
Virus Assembly ◽  
Genomic Rna ◽  
Packaging Signal ◽  
Genome Packaging ◽  
Genome Recognition ◽  
Infected Cells

Abstract The alphavirus capsid protein (Cp) selectively packages genomic RNA (gRNA) into the viral nucleocapsid to produce infectious virus. Using photoactivatable ribonucleoside crosslinking and an innovative biotinylated Cp retrieval method, here we comprehensively define binding sites for Semliki Forest virus (SFV) Cp on the gRNA. While data in infected cells demonstrate Cp binding to the proposed genome packaging signal (PS), mutagenesis experiments show that PS is not required for production of infectious SFV or Chikungunya virus. Instead, we identify multiple Cp binding sites that are enriched on gRNA-specific regions and promote infectious SFV production and gRNA packaging. Comparisons of binding sites in cytoplasmic vs. viral nucleocapsids demonstrate that budding causes discrete changes in Cp-gRNA interactions. Notably, Cp’s top binding site is maintained throughout virus assembly, and specifically binds and assembles with Cp into core-like particles in vitro. Together our data suggest a model for selective alphavirus genome recognition and assembly.

scholarly journals Sheep gut passage and survival of Mediterranean shrub seeds

2005 ◽  
Vol 15 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Pablo Manzano ◽  
Juan E. Malo ◽  
Begoña Peco
Keyword(s):  
Potential Role ◽  
Central Spain ◽  
Long Distance ◽  
Retama Sphaerocarpa ◽  
Gut Passage ◽  
Lavandula Stoechas ◽  
Significant Difference ◽  
Ecological Importance ◽  
Viable Seeds

Although viable seeds of Mediterranean dry-fruited shrubs are found in herbivore dung, the ecological importance of this observation is still not well understood. We analysed seed retrieval percentages, defecation time and germinability after sheep gut passage for the five most common shrub species of an area in central Spain (Retama sphaerocarpa, Cytisus scoparius, Halimium umbellatum subsp. viscosum, Cistus ladanifer and Lavandula stoechas subsp. pedunculata). Five ewes were fed seeds, and their dung was collected regularly during the following week. Seeds were hand-sorted from dung subsamples and tested for germinability. The defecated seeds were clustered in time, with a majority retrieved in the 24–40 h period, although over 1% of the seeds were retained in the gut for more than 72 h. Data suggested a possible link between seed size and retrieval, with medium-sized seeds less damaged (16–23%) than larger and smaller seeds (10–12%), although only a small number of species were studied. Germination results showed an increased percentage of germination after gut passage for H. umbellatum (x2 test, P<0.05) and a marginally significant difference for C. scoparius (P<0.1). Soft-seeded L. stoechas did not germinate after gut passage. The results indicate a potential role of herbivore endozoochory for the long-distance dispersal of dry-fruited shrubs and their potential colonization of distant sites.

scholarly journals Pollination by hoverflies in the Anthropocene

2020 ◽  
Vol 287 (1927) ◽  
pp. 20200508 ◽  
Author(s):  
Toby Doyle ◽  
Will L. S. Hawkes ◽  
Richard Massy ◽  
Gary D. Powney ◽  
Myles H. M. Menz ◽  
...  
Keyword(s):  
Crop Protection ◽  
Ecosystem Functions ◽  
Anthropogenic Change ◽  
Migratory Species ◽  
Long Distance ◽  
Pollination Services ◽  
Relative Contribution ◽  
Or Groups ◽  
Large Populations ◽  
Global Food

Pollinator declines, changes in land use and climate-induced shifts in phenology have the potential to seriously affect ecosystem function and food security by disrupting pollination services provided by insects. Much of the current research focuses on bees, or groups other insects together as ‘non-bee pollinators’, obscuring the relative contribution of this diverse group of organisms. Prominent among the ‘non-bee pollinators’ are the hoverflies, known to visit at least 72% of global food crops, which we estimate to be worth around US$300 billion per year, together with over 70% of animal pollinated wildflowers. In addition, hoverflies provide ecosystem functions not seen in bees, such as crop protection from pests, recycling of organic matter and long-distance pollen transfer. Migratory species, in particular, can be hugely abundant and unlike many insect pollinators, do not yet appear to be in serious decline. In this review, we contrast the roles of hoverflies and bees as pollinators, discuss the need for research and monitoring of different pollinator responses to anthropogenic change and examine emerging research into large populations of migratory hoverflies, the threats they face and how they might be used to improve sustainable agriculture.

scholarly journals The Roles of Pol and Env in the Assembly Pathway of Human Foamy Virus

1998 ◽  
Vol 72 (5) ◽  
pp. 3658-3665 ◽  
Author(s):  
David N. Baldwin ◽  
Maxine L. Linial
Keyword(s):  
Virus Assembly ◽  
Foamy Virus ◽  
Surface Glycoprotein ◽  
Human Foamy Virus ◽  
Structural Protein ◽  
Genome Packaging ◽  
Particle Assembly ◽  
P Protein ◽  
Assembly Pathway ◽  
B Virus

ABSTRACT Human foamy virus (HFV) is the prototype of theSpumavirus genus of retroviruses. These viruses have a genomic organization close to that of other complex retroviruses but have similarities to hepadnaviruses such as human hepatitis B virus (HBV). Both HFV and HBV express their Pol protein independently of their structural proteins. Retroviruses and hepadnaviruses differ in their requirements for particle assembly and genome packaging. Assembly of retroviral particles containing RNA genomes requires only the Gag structural protein. The Pol protein is not required for capsid assembly, and the Env surface glycoprotein is not required for release of virions from the cell. In contrast, assembly of extracellular HBV particles containing DNA requires core structural protein and polymerase (P protein) for assembly of nucleocapsids and requires surface glycoproteins for release from the cell. We investigated the requirements for synthesis of extracellular HFV particles by constructing mutants with either the pol or envgene deleted. We found that the Pol protein is dispensable for production of extracellular particles containing viral nucleic acid. In the absence of Env, intracellular particles are synthesized but few or no extracellular particles could be detected. Thus, foamy virus assembly is distinct from that of other reverse transcriptase-encoding mammalian viruses.

scholarly journals C. Elegans Fatty Acid Two-Hydroxylase Regulates Intestinal Homeostasis by Affecting Heptadecenoic Acid Production

2018 ◽  
Vol 49 (3) ◽  
pp. 947-960 ◽  
Author(s):  
Yuanbao Li ◽  
Chunxia Wang ◽  
Yikai Huang ◽  
Rong Fu ◽  
Hanxi Zheng ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Click Chemistry ◽  
Protein Transport ◽  
Lipid Analysis ◽  
Fatty Acyl ◽  
Intestinal Cells ◽  
Membrane Structures ◽  
C Elegans ◽  
Apical Side

Background/Aims: The hydroxylation of fatty acids at the C-2 position is the first step of fatty acid α-oxidation and generates sphingolipids containing 2-hydroxy fatty acyl moieties. Fatty acid 2-hydroxylation is catalyzed by Fatty acid 2-hydroxylase (FA2H) enzyme. However, the precise roles of FA2H and fatty acid 2-hydroxylation in whole cell homeostasis still remain unclear. Methods: Here we utilize Caenorhabditis elegans as the model and systemically investigate the physiological functions of FATH-1/C25A1.5, the highly conserved worm homolog for mammalian FA2H enzyme. Immunostaining, dye-staining and translational fusion reporters were used to visualize FATH-1 protein and a variety of subcellular structures. The “click chemistry” method was employed to label 2-OH fatty acid in vivo. Global and tissue-specific RNAi knockdown experiments were performed to inactivate FATH-1 function. Lipid analysis of the fath-1 deficient mutants was achieved by mass spectrometry. Results: C. elegans FATH-1 is expressed at most developmental stages and in most tissues. Loss of fath-1 expression results in severe growth retardation and shortened lifespan. FATH-1 function is crucially required in the intestine but not the epidermis with stereospecificity. The “click chemistry” labeling technique showed that the FATH-1 metabolites are mainly enriched in membrane structures preferable to the apical side of the intestinal cells. At the subcellular level, we found that loss of fath-1 expression inhibits lipid droplets formation, as well as selectively disrupts peroxisomes and apical endosomes. Lipid analysis of the fath-1 deficient animals revealed a significant reduction in the content of heptadecenoic acid, while other major FAs remain unaffected. Feeding of exogenous heptadecenoic acid (C17: 1), but not oleic acid (C18: 1), rescues the global and subcellular defects of fath-1 knockdown worms. Conclusion: Our study revealed that FATH-1 and its catalytic products are highly specific in the context of chirality, C-chain length, spatial distribution, as well as the types of cellular organelles they affect. Such an unexpected degree of specificity for the synthesis and functions of hydroxylated FAs helps to regulate protein transport and fat metabolism, therefore maintaining the cellular homeostasis of the intestinal cells. These findings may help our understanding of FA2H functions across species, and offer potential therapeutical targets for treating FA2H-related diseases.

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.

scholarly journals Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging

2016 ◽  
Vol 90 (9) ◽  
pp. 4593-4603 ◽  
Author(s):  
Tibor Füzik ◽  
Růžena Píchalová ◽  
Florian K. M. Schur ◽  
Karolína Strohalmová ◽  
Ivana Křížová ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Protein Interactions ◽  
Viral Genome ◽  
Virus Assembly ◽  
Protein Protein Interactions ◽  
Genome Packaging ◽  
Particle Assembly ◽  
Nuclear Trafficking ◽  
Virus Particles ◽  
Gag Polyprotein

ABSTRACTThe Gag polyprotein of retroviruses drives immature virus assembly by forming hexameric protein lattices. The assembly is primarily mediated by protein-protein interactions between capsid (CA) domains and by interactions between nucleocapsid (NC) domains and RNA. Specific interactions between NC and the viral RNA are required for genome packaging. Previously reported cryoelectron microscopy analysis of immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region (residues RKK) in CA may serve as an additional binding site for nucleic acids. Here, we have introduced mutations into the RKK region in both bacterial and proviral M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA binding, budding/release, nuclear trafficking, and infectivity usingin vitroandin vivosystems. Our data indicate that the RKK region binds and structures nucleic acid that serves to promote virus particle assembly in the cytoplasm. Moreover, the RKK region appears to be important for recruitment of viral genomic RNA into Gag particles, and this function could be linked to changes in nuclear trafficking. Together these observations suggest that in M-PMV, direct interactions between CA and nucleic acid play important functions in the late stages of the viral life cycle.IMPORTANCEAssembly of retrovirus particles is driven by the Gag polyprotein, which can self-assemble to form virus particles and interact with RNA to recruit the viral genome into the particles. Generally, the capsid domains of Gag contribute to essential protein-protein interactions during assembly, while the nucleocapsid domain interacts with RNA. The interactions between the nucleocapsid domain and RNA are important both for identifying the genome and for self-assembly of Gag molecules. Here, we show that a region of basic residues in the capsid protein of the betaretrovirus Mason-Pfizer monkey virus (M-PMV) contributes to interaction of Gag with nucleic acid. This interaction appears to provide a critical scaffolding function that promotes assembly of virus particles in the cytoplasm. It is also crucial for packaging the viral genome and thus for infectivity. These data indicate that, surprisingly, interactions between the capsid domain and RNA play an important role in the assembly of M-PMV.

scholarly journals Metagenomic analysis of virus diversity and relative abundance in a eutrophic freshwater harbour

2019 ◽  
Author(s):  
Christine N. Palermo ◽  
Roberta R. Fulthorpe ◽  
Rosemary Saati ◽  
Steven M. Short
Keyword(s):  
Algal Biomass ◽  
Spatial Scales ◽  
Illumina Hiseq ◽  
The Past ◽  
Virus Diversity ◽  
Illumina Hiseq Platform ◽  
Ecological Importance ◽  
Virus Communities ◽  
Virus Community ◽  
Freshwater Environments

ABSTRACTAquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize particle-associated virus communities seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus families Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Diverse Mimiviridae contigs were detected in the samples, but the two sites contained distinct Mimiviridae communities. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Caudovirales were present at low abundances in most samples, contrasting other studies of freshwater environments. Similarly, Phycodnaviridae abundances were surprisingly low in all samples despite the harbour’s capacity to support high algal biomass during the summer and autumn months, suggesting that Mimiviridae are the dominant algae-infecting viruses in this system. Overall, our findings provided insights into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales.

scholarly journals Multiple Capsid Protein Binding Sites Mediate Selective Packaging of the Alphavirus Genomic RNA

2020 ◽  
Author(s):  
Rebecca S. Brown ◽  
Dimitrios G. Anastasakis ◽  
Markus Hafner ◽  
Margaret Kielian
Keyword(s):  
Capsid Protein ◽  
Binding Sites ◽  
Semliki Forest Virus ◽  
Virus Assembly ◽  
Genomic Rna ◽  
Packaging Signal ◽  
Genome Packaging ◽  
Genome Recognition ◽  
Infected Cells

ABSTRACTThe alphavirus capsid protein (Cp) selectively packages genomic RNA (gRNA) into the viral nucleocapsid to produce infectious virus. Using photoactivatable ribonucleoside crosslinking and an innovative biotinylated Cp retrieval method, we comprehensively defined binding sites for Semliki Forest virus (SFV) Cp on the gRNA. While data in infected cells demonstrated Cp binding to the proposed genome packaging signal (PS), mutagenesis experiments showed that PS was not required for production of infectious SFV or Chikungunya virus. Instead, we identified multiple novel Cp binding sites that were enriched on gRNA-specific regions and promoted infectious SFV production and gRNA packaging. Comparisons of binding sites in cytoplasmic vs. viral nucleocapsids demonstrated that budding caused discrete changes in Cp-gRNA interactions. Notably, Cp’s top binding site was maintained throughout virus assembly, and specifically bound and assembled with Cp into core-like particles in vitro. Together our data suggest a new model for selective alphavirus genome recognition and assembly.

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