scholarly journals A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing

2013 ◽  
Vol 42 (4) ◽  
pp. 2538-2554 ◽  
Author(s):  
Jie Yang ◽  
Zhenyun Cheng ◽  
Songliu Zhang ◽  
Wei Xiong ◽  
Hongjie Xia ◽  
...  
Keyword(s):  
Replication Initiation ◽  
Simplified Model ◽  
Divalent Ions ◽  
Direct Role ◽  
Rna Chaperone ◽  
Double Stranded Rna ◽  
The Family ◽  
Dsrna Viruses ◽  
Strand Annealing

Abstract For double-stranded RNA (dsRNA) viruses in the family Reoviridae, their inner capsids function as the machinery for viral RNA (vRNA) replication. Unlike other multishelled reoviruses, cypovirus has a single-layered capsid, thereby representing a simplified model for studying vRNA replication of reoviruses. VP5 is one of the three major cypovirus capsid proteins and functions as a clamp protein to stabilize cypovirus capsid. Here, we expressed VP5 from type 5 Helicoverpa armigera cypovirus (HaCPV-5) in a eukaryotic system and determined that this VP5 possesses RNA chaperone-like activity, which destabilizes RNA helices and accelerates strand annealing independent of ATP. Our further characterization of VP5 revealed that its helix-destabilizing activity is RNA specific, lacks directionality and could be inhibited by divalent ions, such as Mg2+, Mn2+, Ca2+ or Zn2+, to varying degrees. Furthermore, we found that HaCPV-5 VP5 facilitates the replication initiation of an alternative polymerase (i.e. reverse transcriptase) through a panhandle-structured RNA template, which mimics the 5′-3′ cyclization of cypoviral positive-stranded RNA. Given that the replication of negative-stranded vRNA on the positive-stranded vRNA template necessitates the dissociation of the 5′-3′ panhandle, the RNA chaperone activity of VP5 may play a direct role in the initiation of reoviral dsRNA synthesis.

scholarly journals Characterization of a Novel Member of the Family Closteroviridae from Mentha spp.

2005 ◽  
Vol 95 (9) ◽  
pp. 1043-1048 ◽  
Author(s):  
Ioannis E. Tzanetakis ◽  
Joseph D. Postman ◽  
Robert R. Martin
Keyword(s):  
Genetic Diversity ◽  
Virus Genome ◽  
Double Stranded Rna ◽  
Atypical Symptoms ◽  
Molecular Tests ◽  
The Family ◽  
Nursery Plant ◽  
Transmission Studies ◽  
Genomic Regions

While characterizing the agents involved in symptomatology of a variegated mint, Mentha × gracilis ‘Variegata’, a nursery plant with atypical symptoms was examined. This plant, unlike ‘Variegata’, did not exhibit yellow vein banding symptoms but instead had distorted and crinkled leaves. Molecular tests for the three viruses found in ‘Variegata’ clones failed to detect any of these viruses in the plant. Double-stranded RNA was extracted and cloned, disclosing the presence of two unknown viruses. One of the viruses was a novel member of the family Closteroviridae. The complete nucleotide sequence of the virus, designated as Mint virus 1, has been obtained. A detection test was developed, and revealed the presence of the virus in several other mint clones and species. Genomic regions from three additional isolates were examined to investigate the genetic diversity of the virus. Genome and phylogenetic analysis placed Mint virus 1 in the genus Closterovirus and transmission studies have identified the mint aphid, Ovatus crataegarius, as a vector for this new member of the genus Closterovirus.

scholarly journals Characterization of a novel transcript variant of human STAU1 gene.

2008 ◽  
Vol 55 (3) ◽  
pp. 473-478
Author(s):  
Nie Fa-Hui ◽  
Yao Hai-Feng ◽  
Qi Rui-Feng ◽  
Li Xin ◽  
Wu Cai-Bin
Keyword(s):  
Amino Acids ◽  
Rt Pcr ◽  
Double Stranded Rna ◽  
Novel Transcript ◽  
Dsrna Binding ◽  
Immunodeficiency Virus ◽  
The Family ◽  
Hiv 1

Human STAU1 is one member of the family of double-stranded RNA (dsRNA)-binding proteins. It is thought to function in transporting mRNA, controlling translation and eliciting mRNA decay in neurons, and to function in infection of influenza virus and human immunodeficiency virus type 1 (HIV-1). Four transcripts coding two isoforms have been identified before. In this study, we have isolated a novel transcript of STAU1, coding a novel isoform that has six amino acids more (SFPLKQ) than isoform a. In order to examine the tissue distribution of this novel isoform, we have performed RT-PCR experiments and the analysis showed that it was highly expressed in heart, liver, kidney and pancreas.

scholarly journals Phylogenetic evidence for homologous recombination within the family Birnaviridae

2008 ◽  
Vol 89 (12) ◽  
pp. 3156-3164 ◽  
Author(s):  
Chung-Chau Hon ◽  
Tommy Tsan-Yuk Lam ◽  
Chi-Wai Yip ◽  
Raymond Tsz-Yeung Wong ◽  
Mang Shi ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Live Attenuated Vaccine ◽  
Double Stranded Rna ◽  
Live Vaccines ◽  
Naturally Occurring ◽  
Wide Range ◽  
The Family ◽  
Bursal Disease ◽  
Comprehensive Survey ◽  
Dsrna Viruses

Birnaviruses are bi-segmented double-stranded RNA (dsRNA) viruses infecting insects, avian species and a wide range of aquatic species. Although homologous recombination is a common phenomenon in positive-sense RNA viruses, recombination in dsRNA viruses is rarely reported. Here we performed a comprehensive survey on homologous recombination in all available sequences (>1800) of the family Birnaviridae based on phylogenetic incongruence. Although inter-species recombination was not evident, potential intra-species recombination events were detected in aquabirnaviruses and infectious bursal disease virus (IBDV). Eight potential recombination events were identified and the possibility that these events were non-naturally occurring was assessed case by case. Five of the eight events were identified in IBDVs and all of these five events involved live attenuated vaccine strains. This finding suggests that homologous recombination between vaccine and wild-type IBDV strains may have occurred; the potential risk of mass vaccination using live vaccines is discussed. This is the first report of evidence for homologous recombination within the family Birnaviridae.

scholarly journals Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1

2016 ◽  
Vol 90 (24) ◽  
pp. 11220-11230 ◽  
Author(s):  
Daniel Luque ◽  
Carlos P. Mata ◽  
Fernando González-Camacho ◽  
José M. González ◽  
Josué Gómez-Blanco ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Molecular Sieves ◽  
Three Dimensional ◽  
Rosellinia Necatrix ◽  
Double Stranded Rna ◽  
Content Type ◽  
Cryo Electron Microscopy ◽  
Wide Range ◽  
The Family ◽  
Dsrna Viruses

ABSTRACTMost double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids help to organize the viral genome and replicative complex(es). They also act as molecular sieves that isolate the virus genome from host defense mechanisms and allow the passage of nucleotides and viral transcripts. Rosellinia necatrix quadrivirus 1 (RnQV1), the type species of the familyQuadriviridae, is a dsRNA fungal virus with a multipartite genome consisting of four monocistronic segments (segments 1 to 4). dsRNA-2 and dsRNA-4 encode two CPs (P2 and P4, respectively), which coassemble into ∼450-Å-diameter capsids. We used three-dimensional cryo-electron microscopy combined with complementary biophysical techniques to determine the structures of RnQV1 virion strains W1075 and W1118. RnQV1 has a quadripartite genome, and the capsid is based on a single-shelled T=1 lattice built of P2-P4 dimers. Whereas the RnQV1-W1118 capsid is built of full-length CP, P2 and P4 of RnQV1-W1075 are cleaved into several polypeptides, maintaining the capsid structural organization. RnQV1 heterodimers have a quaternary organization similar to that of homodimers of reoviruses and other dsRNA mycoviruses. The RnQV1 capsid is the first T=1 capsid with a heterodimer as an asymmetric unit reported to date and follows the architectural principle for dsRNA viruses that a 120-subunit capsid is a conserved assembly that supports dsRNA replication and organization.IMPORTANCEGiven their importance to health, members of the familyReoviridaeare the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of bacterial, protozoal, and fungal dsRNA viruses has improved our understanding of their structure, function, and evolution, as well. Here, we studied a dsRNA virus that infects the fungusRosellinia necatrix, an ascomycete that is pathogenic to a wide range of plants. Using three-dimensional cryo-electron microscopy and analytical ultracentrifugation analysis, we determined the structure and stoichiometry of Rosellinia necatrix quadrivirus 1 (RnQV1). The RnQV1 capsid is a T=1 capsid with 60 heterodimers as the asymmetric units. The large amount of genetic information used by RnQV1 to construct a simple T=1 capsid is probably related to the numerous virus-host and virus-virus interactions that it must face in its life cycle, which lacks an extracellular phase.

scholarly journals Unexpected Genetic Diversity of Two Novel Swine MRVs in Italy

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 574 ◽  
Author(s):  
Lara Cavicchio ◽  
Luca Tassoni ◽  
Gianpiero Zamperin ◽  
Mery Campalto ◽  
Marilena Carrino ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Molecular Characterization ◽  
First Report ◽  
Genetic Relation ◽  
Genetic Groups ◽  
The Family ◽  
Dsrna Viruses ◽  
Unique Amino Acid

Mammalian Orthoreoviruses (MRV) are segmented dsRNA viruses in the family Reoviridae. MRVs infect mammals and cause asymptomatic respiratory, gastro-enteric and, rarely, encephalic infections. MRVs are divided into at least three serotypes: MRV1, MRV2 and MRV3. In Europe, swine MRV (swMRV) was first isolated in Austria in 1998 and subsequently reported more than fifteen years later in Italy. In the present study, we characterized two novel reassortant swMRVs identified in one same Italian farm over two years. The two viruses shared the same genetic backbone but showed evidence of reassortment in the S1, S4, M2 segments and were therefore classified into two serotypes: MRV3 in 2016 and MRV2 in 2018. A genetic relation to pig, bat and human MRVs and other unknown sources was identified. A considerable genetic diversity was observed in the Italian MRV3 and MRV2 compared to other available swMRVs. The S1 protein presented unique amino acid signatures in both swMRVs, with unexpected frequencies for MRV2. The remaining genes formed distinct and novel genetic groups that revealed a geographically related evolution of swMRVs in Italy. This is the first report of the complete molecular characterization of novel reassortant swMRVs in Italy and Europe, which suggests a greater genetic diversity of swMRVs never identified before.

scholarly journals Purified Recombinant Bluetongue Virus VP1 Exhibits RNA Replicase Activity

2004 ◽  
Vol 78 (8) ◽  
pp. 3994-4002 ◽  
Author(s):  
Mark Boyce ◽  
Josa Wehrfritz ◽  
Rob Noad ◽  
Polly Roy
Keyword(s):  
Viral Genome ◽  
Bluetongue Virus ◽  
De Novo ◽  
Surveillance Systems ◽  
Sequence Specificity ◽  
Core Particle ◽  
Double Stranded Rna ◽  
The Family ◽  
Capping Enzyme ◽  
Dsrna Viruses

ABSTRACT The polymerase protein of all known double-stranded RNA (dsRNA) viruses is located within a complex subviral core particle that is responsible for transcription of the viral genome. For members of the family Reoviridae, this particle allows messenger sense RNA synthesis while sequestering the viral genome away from cellular dsRNA surveillance systems during infection of eukaryotic cells. The core particle of bluetongue virus (BTV) consists of the major structural proteins VP3 and VP7 and the minor enzymatic proteins VP1 (polymerase), VP4 (capping enzyme), and VP6 (helicase). In this report we have characterized fully processive dsRNA synthesis by VP1 from a viral plus-strand RNA template in the absence of the other proteins of the BTV core. This replicase activity consists of de novo initiation of synthesis, followed by elongation of the minus strand. Purified VP1 exhibits little sequence specificity for BTV plus-strand template, suggesting that the choice of viral over nonviral RNA template comes from its association with other proteins within the viral core.

scholarly journals Molecular Characterization of the First Alternavirus Identified in Fusarium oxysporum

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2026
Author(s):  
Caiyi Wen ◽  
Xinru Wan ◽  
Yuanyuan Zhang ◽  
Hongyan Du ◽  
Chenxing Wei ◽  
...  
Keyword(s):  
Biological Control ◽  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
Hypothetical Proteins ◽  
Rna Dependent Rna Polymerase ◽  
Double Stranded Rna ◽  
Blast Search ◽  
Multiple Alignments ◽  
The Family

A novel mycovirus named Fusarium oxysporum alternavirus 1(FoAV1) was identified as infecting Fusarium oxysporum strain BH19, which was isolated from a fusarium wilt diseased stem of Lilium brownii. The genome of FoAV1 contains four double-stranded RNA (dsRNA) segments (dsRNA1, dsRNA 2, dsRNA 3 and dsRNA 4, with lengths of 3.3, 2.6, 2.3 and 1.8 kbp, respectively). Additionally, dsRNA1 encodes RNA-dependent RNA polymerase (RdRp), and dsRNA2- dsRNA3- and dsRNA4-encoded hypothetical proteins (ORF2, ORF3 and ORF4), respectively. A homology BLAST search, along with multiple alignments based on RdRp, ORF2 and ORF3 sequences, identified FoAV1 as a novel member of the proposed family “Alternaviridae”. Evolutionary relation analyses indicated that FoAV1 may be related to alternaviruses, thus dividing the family “Alternaviridae” members into four clades. In addition, we determined that dsRNA4 was dispensable for replication and may be a satellite-like RNA of FoAV1—and could perhaps play a role in the evolution of alternaviruses. Our results provided evidence for potential genera establishment within the proposed family “Alternaviridae”. Additionally, FoAV1 exhibited biological control of Fusarium wilt. Our results also laid the foundations for the further study of mycoviruses within the family “Alternaviridae”, and provide a potential agent for the biocontrol of diseases caused by F. oxysporum.

scholarly journals Comparison of Polymerase Subunits from Double-Stranded RNA Bacteriophages

2001 ◽  
Vol 75 (22) ◽  
pp. 11088-11095 ◽  
Author(s):  
Hongyan Yang ◽  
Eugene V. Makeyev ◽  
Dennis H. Bamford
Keyword(s):  
Molecular Basis ◽  
Rna Synthesis ◽  
Regulatory Mechanism ◽  
Biochemical Properties ◽  
Double Stranded Rna ◽  
The Family ◽  
Dsrna Viruses ◽  
Template Specificity

ABSTRACT The family Cystoviridae comprises several bacteriophages with double-stranded RNA (dsRNA) genomes. We have previously purified the catalytic polymerase subunit (Pol) of one of the Cystoviridae members, bacteriophage φ6, and shown that the protein can catalyze RNA synthesis in vitro. In this reaction, both bacteriophage-specific and heterologous RNAs can serve as templates, but those containing 3′ termini from the φ6 minus strands are favored. This provides a molecular basis for the observation that only plus strands, not minus strands, are transcribed from φ6 dsRNA segments in vivo. To test whether such a regulatory mechanism is also found in other dsRNA viruses, we purified recombinant Pol subunits from the φ6-related bacteriophages φ8 and φ13 and assayed their polymerase activities in vitro. The enzymes catalyze template-dependent RNA synthesis using both single-stranded-RNA (ssRNA) and dsRNA templates. However, they differ from each other as well as from φ6 Pol in certain biochemical properties. Notably, each polymerase demonstrates a distinct preference for ssRNAs bearing short 3′-terminal sequences from the virus-specific minus strands. This suggests that, in addition to other factors, RNA transcription inCystoviridae is controlled by the template specificity of the polymerase subunit.

scholarly journals Identification and Molecular Characterization of a Novel Partitivirus from Trichoderma atroviride NFCF394

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 578 ◽  
Author(s):  
Jeesun Chun ◽  
Han-Eul Yang ◽  
Dae-Hyuk Kim
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Molecular Characteristics ◽  
Trichoderma Atroviride ◽  
Double Stranded Rna ◽  
Reading Frame ◽  
Viral Particles ◽  
The Family ◽  
Isogenic Strains

An increasing number of novel mycoviruses have been described in fungi. Here, we report the molecular characteristics of a novel bisegmented double-stranded RNA (dsRNA) virus from the fungus Trichoderma atroviride NFCF394. We designated this mycovirus as Trichoderma atroviride partitivirus 1 (TaPV1). Electron micrographs of negatively stained, purified viral particles showed an isometric structure approximately of 30 nm in diameter. The larger segment (dsRNA1) of the TaPV1 genome comprised 2023 bp and contained a single open reading frame (ORF) encoding 614 amino acid (AA) residues of RNA-dependent RNA polymerase (RdRp). The smaller segment (dsRNA2) consisted of 2012 bp with a single ORF encoding 577 AA residues of capsid protein (CP). The phylogenetic analysis, based on deduced amino acid sequences of RdRp and CP, indicated that TaPV1 is a new member of the genus Alphapartitivirus in the family Partitiviridae. Virus-cured isogenic strains did not show significant changes in colony morphology. In addition, no changes in the enzymatic activities of β-1,3-glucanase and chitinase were observed in virus-cured strains. To the best of our knowledge, this is the first report of an Alphapartitivirus in T. atroviride.

Towards Understanding the Structural Requirements for Endogenous Transcription in Rotavirus

1998 ◽  
Vol 4 (S2) ◽  
pp. 1050-1051
Author(s):  
J. A. Lawton ◽  
M. K. Estes ◽  
B. V. Venkataram Prasad
Keyword(s):  
Structural Integrity ◽  
Structural Complexity ◽  
Cell Entry ◽  
Structural Studies ◽  
Double Stranded Rna ◽  
Severe Diarrhea ◽  
The Family ◽  
Causative Agents ◽  
Icosahedral Viruses ◽  
Dsrna Viruses

Rotaviruses are complex, relatively large (1000 Å) nonenveloped icosahedral viruses. They are the major causative agents of severe diarrhea in children and animals. Annually an estimated 1 million children die from rotavirus-induced gastroenteritis worldwide. Medical relevance, intriguing structural complexity, and several unique strategies in the morphogenesis and replication have provoked extensive molecular biological and structural studies on rotaviruses in recent years.Rotaviruses are double-stranded RNA (dsRNA) viruses belonging to the family Reoviridae. Each of the 11 segments codes for one protein. Of the eleven proteins encoded by the genomic RNA, six are structural and five are non-structural. Structural studies have shown that mature rotaviruses are triple-layered particles (TLPs). During the process of cell entry the outer-most layer consisting of VP7 and the spike protein VP4 is lost and the resulting double layered particles (DLPs) become transcriptionally active (Fig. 1 A). During the process of transcription, the DLPs maintain their structural Integrity.

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