scholarly journals Geometric Mismatches within the Concentric Layers of Rotavirus Particles: a Potential Regulatory Switch of Viral Particle Transcription Activity

2008 ◽  
Vol 82 (6) ◽  
pp. 2844-2852 ◽  
Author(s):  
Sonia Libersou ◽  
Xavier Siebert ◽  
Malika Ouldali ◽  
Leandro F. Estrozi ◽  
Jorge Navaza ◽  
...  
Keyword(s):  
Particle Diameter ◽  
Icosahedral Symmetry ◽  
Internal Layers ◽  
Double Stranded Rna ◽  
Transcription Activity ◽  
Atomic Structures ◽  
Viral Particles ◽  
Functional States ◽  
Triangulation Number ◽  
Icosahedral Capsid

ABSTRACT Rotaviruses are prototypical double-stranded RNA viruses whose triple-layered icosahedral capsid constitutes transcriptional machinery activated by the release of the external layer. To understand the molecular basis of this activation, we studied the structural interplay between the three capsid layers by electron cryo-microscopy and digital image processing. Two viral particles and four virus-like particles containing various combinations of inner (VP2)-, middle (VP6)-, and outer (VP7)-layer proteins were studied. We observed that the absence of the VP2 layer increases the particle diameter and changes the type of quasi-equivalent icosahedral symmetry, as described by the shift in triangulation number (T) of the VP6 layer (from T = 13 to T = 19 or more). By fitting X-ray models of VP6 into each reconstruction, we determined the quasi-atomic structures of the middle layers. These models showed that the VP6 lattices, i.e., curvature and trimer contacts, are characteristic of the particle composition. The different functional states of VP6 thus appear as being characterized by trimers having similar conformations but establishing different intertrimeric contacts. Remarkably, the external protein VP7 reorients the VP6 trimers located around the fivefold axes of the icosahedral capsid, thereby shrinking the channel through which mRNA exits the transcribing rotavirus particle. We conclude that the constraints arising from the different geometries imposed by the external and internal layers of the rotavirus capsid constitute a potential switch regulating the transcription activity of the viral particles.

scholarly journals Resistance of Aerosolized Bacterial Viruses to Relative Humidity and Temperature

2015 ◽  
Vol 81 (20) ◽  
pp. 7305-7311 ◽  
Author(s):  
Daniel Verreault ◽  
Mélissa Marcoux-Voiselle ◽  
Nathalie Turgeon ◽  
Sylvain Moineau ◽  
Caroline Duchaine
Keyword(s):  
Relative Humidity ◽  
Uv Radiation ◽  
Environmental Conditions ◽  
Double Stranded Rna ◽  
Double Stranded Dna ◽  
Viral Particles ◽  
Bacterial Viruses ◽  
Low Levels ◽  
Viral Components ◽  
Uvc Radiation

ABSTRACTThe use of aerosolized bacteriophages as surrogates for hazardous viruses might simplify and accelerate the discovery of links between viral components and their persistence in the airborne state under diverse environmental conditions. In this study, four structurally distinct lytic phages, MS2 (single-stranded RNA [ssRNA]), ϕ6 (double-stranded RNA [dsRNA]), ϕX174 (single-stranded DNA [ssDNA]), and PR772 (double-stranded DNA [dsDNA]), were nebulized into a rotating chamber and exposed to various levels of relative humidity (RH) and temperature as well as to germicidal UV radiation. The aerosolized viral particles were allowed to remain airborne for up to 14 h before being sampled for analysis by plaque assays and quantitative PCRs. Phages ϕ6 and MS2 were the most resistant at low levels of relative humidity, while ϕX174 was more resistant at 80% RH. Phage ϕ6 lost its infectivity immediately after exposure to 30°C and 80% RH. The infectivity of all tested phages rapidly declined as a function of the exposure time to UVC radiation, phage MS2 being the most resistant. Taken altogether, our data indicate that these aerosolized phages behave differently under various environmental conditions and highlight the necessity of carefully selecting viral simulants in bioaerosol studies.

scholarly journals A Novel Partitivirus That Confer Hypovirulence to the Plant Pathogenic Fungus Colletotrichum liriopes

2021 ◽  
Vol 12 ◽  
Author(s):  
Jun Zi Zhu ◽  
Jun Guo ◽  
Zhao Hu ◽  
Xu Tong Zhang ◽  
Xiao Gang Li ◽  
...  
Keyword(s):  
Rna Virus ◽  
Pathogenic Fungus ◽  
Rna Dependent Rna Polymerase ◽  
Virus Elimination ◽  
Double Stranded Rna ◽  
Plant Pathogenic Fungus ◽  
Sequence Identity ◽  
Viral Particles ◽  
Conidia Production ◽  
Significant Amino Acid

Here, we report a novel double-stranded RNA virus designated Colletotrichum liriopes partitivirus 1 (ClPV1) from the plant pathogenic fungus C. liriopes. ClPV1 genome has two double stranded RNAs (dsRNAs), named as dsRNA 1 and dsRNA 2, which in the lengths of 1,807 and 1,706 bp, respectively. The dsRNA 1 and dsRNA 2 encoded proteins showing significant amino acid (aa) sequence identity to the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) of partitiviruses, respectively. Phylogenetic analysis using the aa sequences of RdRp and CP indicated that ClPV1 was grouped to members of the putative Epsilonpartitivirus genus in the Partitiviridae family. Spherical viral particles in approximately 35 nm in diameter and packaging the ClPV1 genome were isolated. Virus elimination and virus transfection with purified viral particles, and biological comparison revealed that ClPV1 could reduce the virulence and conidia production of C. liriopes. To the best of our knowledge, this is the first report of mycovirus in C. liriopes fungus.

Suppression of chromosomal mutations affecting M1 virus replication in Saccharomyces cerevisiae by a variant of a viral RNA segment (L-A) that encodes coat protein

1988 ◽  
Vol 8 (2) ◽  
pp. 938-944
Author(s):  
H Uemura ◽  
R B Wickner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Copy Number ◽  
Efficient Production ◽  
Double Stranded Rna ◽  
Transfection Experiment ◽  
Heat Curing ◽  
Viral Particles ◽  
Chromosomal Genes ◽  
Viruslike Particles ◽  
Chromosomal Mutations

For the maintenance of "killer" M1 double-stranded RNA in Saccharomyces cerevisiae, more than 30 chromosomal genes are required. The requirement for some of these genes can be completely suppressed by a cytoplasmic element, [B] (for bypass). We have isolated a mutant unable to maintain [B] (mab) and found that it is allelic to MAK10, one of the three chromosomal MAK genes required for the maintenance of L-A. The heat curing of [B] always coincided with the loss of L-A. To confirm that [B] is located on L-A, we purified viral particles containing either L-A or M1 from strains with or without [B] activity and transfected these purified particles into a strain which did not have either L-A or M1. The transfectants harboring L-A and M1 from a [B] strain showed the [B] phenotype, but the transfectants with L-A and M1 from a [B-o] strain did not show the [B] phenotype. Furthermore, the transfectants having L-A from a [B] strain and M1 from a [B-o] strain also showed the [B] phenotype. Therefore, we concluded that [B] is a property of a variant of L-A. In the transfection experiment, we also proved that the superkiller phenotype of the [B] strain is a property of L-A and that L-A with [B] activity can maintain a higher copy number of M1 regardless of the source of M1 viruslike particles. These data suggest that MAK genes whose mutations are suppressed by [B] are concerned with the protection of M1 (+) single-stranded RNA or the formation of M1 viruslike particles and that an L-A with more efficient production of M1 viruslike particles can completely dispense with the requirement for those MAK genes.

scholarly journals Genome Assembly and Particle Maturation of the Birnavirus Infectious Pancreatic Necrosis Virus

2004 ◽  
Vol 78 (24) ◽  
pp. 13829-13838 ◽  
Author(s):  
Rodrigo A. Villanueva ◽  
José L. Galaz ◽  
Juan A. Valdés ◽  
Matilde M. Jashés ◽  
Ana María Sandino
Keyword(s):  
Pancreatic Necrosis ◽  
Infectious Pancreatic Necrosis Virus ◽  
Necrosis Virus ◽  
Particle Assembly ◽  
Double Stranded Rna ◽  
Viral Particles ◽  
Agarose Electrophoresis ◽  
Electrophoresis System ◽  
Infectious Pancreatic Necrosis ◽  
Pancreatic Necrosis Virus

ABSTRACT In this study, we have analyzed the morphogenesis of the birnavirus infectious pancreatic necrosis virus throughout the infective cycle in CHSE-214 cells by using a native agarose electrophoresis system. Two types of viral particles (designated A and B) were identified, isolated, and characterized both molecularly and biologically. Together, our results are consistent with a model of morphogenesis in which the genomic double-stranded RNA is immediately assembled, after synthesis, into a large (66-nm diameter) and uninfectious particle A, where the capsid is composed of both mature and immature viral polypeptides. Upon maturation, particles A yield particles B through the proteolytic cleavage of most of the remaining viral precursors within the capsid, the compaction of the particle (60-nm diameter), and the acquisition of infectivity. These studies will provide the foundation for further analyses of birnavirus particle assembly and RNA replication.

scholarly journals The RNA-Binding Protein of a Double-Stranded RNA Virus Acts like a Scaffold Protein

2018 ◽  
Vol 92 (19) ◽  
Author(s):  
Carlos P. Mata ◽  
Johann Mertens ◽  
Juan Fontana ◽  
Daniel Luque ◽  
Carolina Allende-Ballestero ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Rna Virus ◽  
Scaffold Protein ◽  
Double Stranded Rna ◽  
Force Microscopy ◽  
Ribonucleoprotein Complexes ◽  
Atomic Force ◽  
Bursal Disease ◽  
Dsdna Viruses ◽  
Icosahedral Capsid

ABSTRACTInfectious bursal disease virus (IBDV), a nonenveloped, double-stranded RNA (dsRNA) virus with a T=13 icosahedral capsid, has a virion assembly strategy that initiates with a precursor particle based on an internal scaffold shell similar to that of tailed double-stranded DNA (dsDNA) viruses. In IBDV-infected cells, the assembly pathway results mainly in mature virions that package four dsRNA segments, although minor viral populations ranging from zero to three dsRNA segments also form. We used cryo-electron microscopy (cryo-EM), cryo-electron tomography, and atomic force microscopy to characterize these IBDV populations. The VP3 protein was found to act as a scaffold protein by building an irregular, ∼40-Å-thick internal shell without icosahedral symmetry, which facilitates formation of a precursor particle, the procapsid. Analysis of IBDV procapsid mechanical properties indicated a VP3 layer beneath the icosahedral shell, which increased the effective capsid thickness. Whereas scaffolding proteins are discharged in tailed dsDNA viruses, VP3 is a multifunctional protein. In mature virions, VP3 is bound to the dsRNA genome, which is organized as ribonucleoprotein complexes. IBDV is an amalgam of dsRNA viral ancestors and traits from dsDNA and single-stranded RNA (ssRNA) viruses.IMPORTANCEStructural analyses highlight the constraint of virus evolution to a limited number of capsid protein folds and assembly strategies that result in a functional virion. We report the cryo-EM and cryo-electron tomography structures and the results of atomic force microscopy studies of the infectious bursal disease virus (IBDV), a double-stranded RNA virus with an icosahedral capsid. We found evidence of a new inner shell that might act as an internal scaffold during IBDV assembly. The use of an internal scaffold is reminiscent of tailed dsDNA viruses, which constitute the most successful self-replicating system on Earth. The IBDV scaffold protein is multifunctional and, after capsid maturation, is genome bound to form ribonucleoprotein complexes. IBDV encompasses numerous functional and structural characteristics of RNA and DNA viruses; we suggest that IBDV is a modern descendant of ancestral viruses and comprises different features of current viral lineages.

scholarly journals Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors

2017 ◽  
Author(s):  
Anton V. Sinitskiy ◽  
Vijay S. Pande
Keyword(s):  
Nmda Receptors ◽  
Computer Simulations ◽  
Functional State ◽  
Structural Heterogeneity ◽  
Atomic Structures ◽  
The Past ◽  
Electrophysiological Recordings ◽  
Functional States

AbstractIt is unclear how the known atomic structures of neuronal NMDA receptors (NMDARs) relate to the functional states of NMDARs inferred from electrophysiological recordings. We address this problem by all-atom computer simulations, a method successfully applied in the past to much smaller biomolecules. Our simulations predict that four ‘non-active’ cryoEM structures of NMDARs rapidly interconvert on submicrosecond timescales, and therefore, correspond to the same functional state of the receptor.

scholarly journals Irregular and Semi-Regular Polyhedral Models for Rous Sarcoma Virus Cores

2008 ◽  
Vol 9 (3-4) ◽  
pp. 197-210 ◽  
Author(s):  
J. Bernard Heymann ◽  
Carmen Butan ◽  
Dennis C. Winkler ◽  
Rebecca C. Craven ◽  
Alasdair C. Steven
Keyword(s):  
Rous Sarcoma Virus ◽  
Size Range ◽  
Electron Tomography ◽  
Graphical Methods ◽  
Icosahedral Symmetry ◽  
Rous Sarcoma ◽  
Cryo Electron Tomography ◽  
Icosahedral Viruses ◽  
Sarcoma Virus ◽  
Triangulation Number

Whereas many viruses have capsids of uniquely defined sizes that observe icosahedral symmetry, retrovirus capsids are highly polymorphic. Nevertheless, they may also be described as polyhedral foldings of a fullerene lattice on which the capsid protein (CA) is arrayed. Lacking the high order of symmetry that facilitates the reconstruction of icosahedral capsids from cryo-electron micrographs, the 3D structures of individual retrovirus capsids may be determined by cryo-electron tomography, albeit at lower resolution. Here, we describe computational and graphical methods used to construct polyhedral models that match in size and shape, capsids of Rous sarcoma virus (RSV) observed within intact virions. The capsids fall into several shape classes, including tubes, ‘lozenges’ and ‘coffins’. The extent to which a capsid departs from icosahedral symmetry reflects the irregularity of the distribution of pentamers, which are always 12 in number for a closed polyhedral capsid. The number of geometrically distinct polyhedra grows rapidly with increasing quotas of hexamers, and ranks in the millions for particles in the size range of RSV capsids, which typically have 150–300 hexamers. Unlike the CAs of icosahedral viruses that assume a minimal number of quasi-equivalent conformations equal to the triangulation number (T), retroviral CAs exhibit a near-continuum of quasi-equivalent conformations – a property that may be attributed to the flexible hinge linking the N- and C-terminal domains.

scholarly journals New Insights into Viral Architecture via Affine Extended Symmetry Groups

2008 ◽  
Vol 9 (3-4) ◽  
pp. 221-229 ◽  
Author(s):  
T. Keef ◽  
R. Twarock
Keyword(s):  
Viral Genome ◽  
3D Structure ◽  
Icosahedral Symmetry ◽  
Mathematical Framework ◽  
Tertiary Structures ◽  
Virus Structure ◽  
Viral Capsids ◽  
Virus Particles ◽  
Viral Particles ◽  
The Family

Since the seminal work of Caspar and Klug on the structure of the protein containers that encapsulate and hence protect the viral genome, it has been recognized that icosahedral symmetry is crucial for the structural organization of viruses. In particular, icosahedral symmetry has been invoked in order to predict the surface structures of viral capsids in terms of tessellations or tilings that schematically encode the locations of the protein subunits in the capsids. Whilst this approach is capable of predicting the relative locations of the proteins in the capsids, a prediction on the relative sizes of different virus particles in a family cannot be made. Moreover, information on the full 3D structure of viral particles, including the tertiary structures of the capsid proteins and the organization of the viral genome within the capsid are inaccessible with their approach. We develop here a mathematical framework based on affine extensions of the icosahedral group that allows us to address these issues. In particular, we show that the relative radii of viruses in the family of Polyomaviridae and the material boundaries in simple RNA viruses can be determined with our approach. The results complement Caspar and Klug's theory of quasi-equivalence and provide details on virus structure that have not been accessible with previous methods, implying that icosahedral symmetry is more important for virus architecture than previously appreciated.

scholarly journals Molecular basis of Coxsackievirus A10 entry using the two-in-one attachment and uncoating receptor KRM1

2020 ◽  
Vol 117 (31) ◽  
pp. 18711-18718
Author(s):  
Yingzi Cui ◽  
Ruchao Peng ◽  
Hao Song ◽  
Zhou Tong ◽  
Xiao Qu ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Viral Entry ◽  
Foot And Mouth Disease ◽  
Atomic Structures ◽  
Viral Particles ◽  
Acidic Conditions ◽  
Underlying Mechanisms ◽  
Viral Protein 1 ◽  
Key Residues

KREMEN1 (KRM1) has been identified as a functional receptor for Coxsackievirus A10 (CV-A10), a causative agent of hand-foot-and-mouth disease (HFMD), which poses a great threat to infants globally. However, the underlying mechanisms for the viral entry process are not well understood. Here we determined the atomic structures of different forms of CV-A10 viral particles and its complex with KRM1 in both neutral and acidic conditions. These structures reveal that KRM1 selectively binds to the mature viral particle above the canyon of the viral protein 1 (VP1) subunit and contacts across two adjacent asymmetry units. The key residues for receptor binding are conserved among most KRM1-dependent enteroviruses, suggesting a uniform mechanism for receptor binding. Moreover, the binding of KRM1 induces the release of pocket factor, a process accelerated under acidic conditions. Further biochemical studies confirmed that receptor binding at acidic pH enabled CV-A10 virion uncoating in vitro. Taken together, these findings provide high-resolution snapshots of CV-A10 entry and identify KRM1 as a two-in-one receptor for enterovirus infection.

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