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1.
Nat Commun ; 15(1): 4189, 2024 May 17.
Article En | MEDLINE | ID: mdl-38760379

The viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), while structures corresponding to these activities remain obscure. Here, we resolved two L-P complex conformations from the mumps virus (MuV), a typical member of nsNSVs, via cryogenic-electron microscopy. One conformation presents all five domains of L forming a continuous RNA tunnel to the methyltransferase domain (MTase), preferably as a transcription state. The other conformation has the appendage averaged out, which is inaccessible to MTase. In both conformations, parallel P tetramers are revealed around MuV L, which, together with structures of other nsNSVs, demonstrates the diverse origins of the L-binding X domain of P. Our study links varying structures of nsNSV polymerase complexes with genome replication and transcription and points to a sliding model for polymerase complexes to advance along the RNA templates.


Cryoelectron Microscopy , Mumps virus , Viral Proteins , Mumps virus/genetics , Mumps virus/ultrastructure , Mumps virus/metabolism , Viral Proteins/metabolism , Viral Proteins/ultrastructure , Viral Proteins/chemistry , Viral Proteins/genetics , Models, Molecular , RNA, Viral/metabolism , RNA, Viral/ultrastructure , RNA, Viral/genetics , DNA-Directed RNA Polymerases/metabolism , DNA-Directed RNA Polymerases/ultrastructure , DNA-Directed RNA Polymerases/chemistry , DNA-Directed RNA Polymerases/genetics , Protein Domains , Phosphoproteins/metabolism , Phosphoproteins/chemistry , Phosphoproteins/ultrastructure , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/ultrastructure , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/genetics , Virus Replication , Transcription, Genetic , Protein Conformation
2.
Viruses ; 16(5)2024 Apr 25.
Article En | MEDLINE | ID: mdl-38793558

The cucumber mosaic virus (CMV) 2b protein is a suppressor of plant defenses and a pathogenicity determinant. Amongst the 2b protein's host targets is the RNA silencing factor Argonaute 1 (AGO1), which it binds to and inhibits. In Arabidopsis thaliana, if 2b-induced inhibition of AGO1 is too efficient, it induces reinforcement of antiviral silencing by AGO2 and triggers increased resistance against aphids, CMV's insect vectors. These effects would be deleterious to CMV replication and transmission, respectively, but are moderated by the CMV 1a protein, which sequesters sufficient 2b protein molecules into P-bodies to prevent excessive inhibition of AGO1. Mutant 2b protein variants were generated, and red and green fluorescent protein fusions were used to investigate subcellular colocalization with AGO1 and the 1a protein. The effects of mutations on complex formation with the 1a protein and AGO1 were investigated using bimolecular fluorescence complementation and co-immunoprecipitation assays. Although we found that residues 56-60 influenced the 2b protein's interactions with the 1a protein and AGO1, it appears unlikely that any single residue or sequence domain is solely responsible. In silico predictions of intrinsic disorder within the 2b protein secondary structure were supported by circular dichroism (CD) but not by nuclear magnetic resonance (NMR) spectroscopy. Intrinsic disorder provides a plausible model to explain the 2b protein's ability to interact with AGO1, the 1a protein, and other factors. However, the reasons for the conflicting conclusions provided by CD and NMR must first be resolved.


Arabidopsis Proteins , Arabidopsis , Argonaute Proteins , Cucumovirus , Argonaute Proteins/metabolism , Argonaute Proteins/genetics , Cucumovirus/metabolism , Cucumovirus/genetics , Cucumovirus/physiology , Arabidopsis/metabolism , Arabidopsis/virology , Arabidopsis/genetics , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Protein Binding , Viral Proteins/metabolism , Viral Proteins/genetics , Host-Pathogen Interactions , Viral Replicase Complex Proteins/metabolism , Viral Replicase Complex Proteins/genetics , Plant Diseases/virology , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/chemistry , Methyltransferases
3.
Arch Virol ; 169(6): 126, 2024 May 16.
Article En | MEDLINE | ID: mdl-38753067

A novel mitovirus was identified in Fusarium oxysporum f. sp. melonis strain T-SD3 and designated as "Fusarium oxysporum mitovirus 3" (FoMV3). The virus was isolated from diseased muskmelon plants with the typical symptom of fusarium wilt. The complete genome of FoMV3 is 2269 nt in length with a predicted AU content of 61.40% and contains a single open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF was predicted to encode a polypeptide of 679 amino acids (aa) containing a conserved RNA-dependent RNA polymerase (RdRp) domain with a molecular mass of 77.39 kDa, which contains six conserved motifs with the highly conserved GDD tripeptide in motif IV. The 5'-untranslated region (UTR) and 3'-UTR of FoMV3 were predicted to fold into stem-loop structures. BLASTp analysis revealed that the RdRp of FoMV3 shared the highest aa sequence identity (83.85%) with that of Fusarium asiaticum mitovirus 5 (FaMV5, a member of the family Mitoviridae) infecting F. asiaticum, the causal agent of wheat fusarium head blight. Phylogenetic analysis further suggested that FoMV3 is a new member of the genus Unuamitovirus within the family Mitoviridae. This is the first report of a new mitovirus associated with F. oxysporum f. sp. melonis.


Fungal Viruses , Fusarium , Genome, Viral , Open Reading Frames , Phylogeny , Plant Diseases , Fusarium/virology , Plant Diseases/microbiology , Plant Diseases/virology , Fungal Viruses/genetics , Fungal Viruses/isolation & purification , Fungal Viruses/classification , RNA Viruses/genetics , RNA Viruses/isolation & purification , RNA Viruses/classification , Whole Genome Sequencing , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , Viral Proteins/genetics , Cucumis melo/virology , Cucumis melo/microbiology , Amino Acid Sequence , 5' Untranslated Regions , 3' Untranslated Regions , Base Sequence
4.
Arch Virol ; 169(6): 123, 2024 May 16.
Article En | MEDLINE | ID: mdl-38753216

Chinese bayberry is a fruit that is appreciated for its taste. A novel totivirus associated with rolling, disfiguring, chlorotic and vein-clearing symptoms on the leaf apices of Chinese bayberry was identified by transcriptome sequencing and reverse transcription PCR (RT-PCR). The complete genome of the virus was determined to be 4959 nucleotides long, and it contains two open reading frames (ORFs). Its genomic organization is similar to that of previously reported totiviruses. ORF1 encodes a putative coat protein (CP) of 765 aa, and ORF2 encodes an RNA-dependent RNA polymerase (RdRp) of 815 aa. These two putative proteins share 55.1% and 62.6%, amino acid sequence identity, respectively, with the corresponding proteins of Panax notoginseng virus A, respectively. According to the demarcation criteria for totivirus species established by the International Committee on Taxonomy of Viruses (ICTV), the new virus should be considered a member of a new species in the genus totivirus, family Orthototiviridae, which we have tentatively named ''Myrica rubra-associated totivirus'' (MRaTV).


Genome, Viral , Myrica , Open Reading Frames , Phylogeny , Plant Diseases , Plant Leaves , Totivirus , Whole Genome Sequencing , Genome, Viral/genetics , Plant Diseases/virology , Plant Leaves/virology , Myrica/virology , Myrica/genetics , Totivirus/genetics , Totivirus/isolation & purification , Totivirus/classification , Viral Proteins/genetics , RNA-Dependent RNA Polymerase/genetics , RNA, Viral/genetics
5.
Nat Commun ; 15(1): 4123, 2024 May 15.
Article En | MEDLINE | ID: mdl-38750014

Avian influenza A viruses (IAVs) pose a public health threat, as they are capable of triggering pandemics by crossing species barriers. Replication of avian IAVs in mammalian cells is hindered by species-specific variation in acidic nuclear phosphoprotein 32 (ANP32) proteins, which are essential for viral RNA genome replication. Adaptive mutations enable the IAV RNA polymerase (FluPolA) to surmount this barrier. Here, we present cryo-electron microscopy structures of monomeric and dimeric avian H5N1 FluPolA with human ANP32B. ANP32B interacts with the PA subunit of FluPolA in the monomeric form, at the site used for its docking onto the C-terminal domain of host RNA polymerase II during viral transcription. ANP32B acts as a chaperone, guiding FluPolA towards a ribonucleoprotein-associated FluPolA to form an asymmetric dimer-the replication platform for the viral genome. These findings offer insights into the molecular mechanisms governing IAV genome replication, while enhancing our understanding of the molecular processes underpinning mammalian adaptations in avian-origin FluPolA.


Cryoelectron Microscopy , Genome, Viral , Influenza A Virus, H5N1 Subtype , Nuclear Proteins , Virus Replication , Humans , Influenza A Virus, H5N1 Subtype/genetics , Virus Replication/genetics , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/chemistry , Animals , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/chemistry , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Viral Proteins/metabolism , Viral Proteins/genetics , Viral Proteins/chemistry , Adaptation, Physiological/genetics , Influenza, Human/virology , RNA, Viral/metabolism , RNA, Viral/genetics , HEK293 Cells , Protein Multimerization , Models, Molecular
6.
Virus Res ; 345: 199387, 2024 Jul.
Article En | MEDLINE | ID: mdl-38719025

Influenza A virus can infect respiratory tracts and may cause severe illness in humans. Proteins encoded by influenza A virus can interact with cellular factors and dysregulate host biological processes to support viral replication and cause pathogenicity. The influenza viral PA protein is not only a subunit of influenza viral polymerase but also a virulence factor involved in pathogenicity during infection. To explore the role of the influenza virus PA protein in regulating host biological processes, we performed immunoprecipitation and LC‒MS/MS to globally identify cellular factors that interact with the PA proteins of the influenza A H1N1, 2009 pandemic H1N1, and H3N2 viruses. The results demonstrated that proteins located in the mitochondrion, proteasome, and nucleus are associated with the PA protein. We further discovered that the PA protein is partly located in mitochondria by immunofluorescence and mitochondrial fractionation and that overexpression of the PA protein reduces mitochondrial respiration. In addition, our results revealed the interaction between PA and the mitochondrial matrix protein PYCR2 and the antiviral role of PYCR2 during influenza A virus replication. Moreover, we found that the PA protein could also trigger autophagy and disrupt mitochondrial homeostasis. Overall, our research revealed the impacts of the influenza A virus PA protein on mitochondrial function and autophagy.


Mitochondria , Viral Proteins , Virus Replication , Humans , Mitochondria/metabolism , Mitochondria/virology , Viral Proteins/metabolism , Viral Proteins/genetics , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , Influenza A virus/physiology , Influenza A virus/genetics , Influenza A virus/pathogenicity , Influenza A virus/metabolism , Host-Pathogen Interactions , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/physiology , Influenza A Virus, H3N2 Subtype/metabolism , Autophagy , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/physiology , Influenza A Virus, H1N1 Subtype/pathogenicity , HEK293 Cells , Influenza, Human/virology , Influenza, Human/metabolism , A549 Cells , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Tandem Mass Spectrometry
7.
Front Cell Infect Microbiol ; 14: 1331755, 2024.
Article En | MEDLINE | ID: mdl-38800833

The mosquito-borne Rift Valley fever virus (RVFV) from the Phenuiviridae family is a single-stranded RNA virus that causes the re-emerging zoonotic disease Rift Valley fever (RVF). Classified as a Category A agent by the NIH, RVFV infection can cause debilitating disease or death in humans and lead to devastating economic impacts by causing abortion storms in pregnant cattle. In a previous study, we showed that the host chaperone protein HSP90 is an RVFV-associated host factor that plays a critical role post viral entry, during the active phase of viral genome replication/transcription. In this study, we have elucidated the molecular mechanisms behind the regulatory effect of HSP90 during infection with RVFV. Our results demonstrate that during the early infection phase, host HSP90 associates with the viral RNA-dependent RNA polymerase (L protein) and prevents its degradation through the proteasome, resulting in increased viral replication.


HSP90 Heat-Shock Proteins , Proteasome Endopeptidase Complex , Proteolysis , Rift Valley fever virus , Virus Replication , HSP90 Heat-Shock Proteins/metabolism , HSP90 Heat-Shock Proteins/genetics , Rift Valley fever virus/genetics , Rift Valley fever virus/metabolism , Proteasome Endopeptidase Complex/metabolism , Animals , Genome, Viral , Humans , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , Host-Pathogen Interactions , Viral Proteins/metabolism , Viral Proteins/genetics , Transcription, Genetic , Rift Valley Fever/virology , Rift Valley Fever/metabolism , Cell Line
8.
PLoS One ; 19(5): e0303838, 2024.
Article En | MEDLINE | ID: mdl-38753834

This study presents the complete genome sequence of a novel nege-like virus identified in whiteflies (Bemisia tabaci MEAM1), provisionally designated as whitefly negevirus 1 (WfNgV1). The virus possesses a single-stranded RNA genome comprising 11,848 nucleotides, organized into four open reading frames (ORFs). These ORFs encode the putative RNA-dependent-RNA-polymerase (RdRp, ORF 1), a glycoprotein (ORF 2), a structural protein with homology to those in the SP24 family, (ORF 3), and a protein of unknown function (ORF 4). Phylogenetic analysis focusing on RdRp and SP24 amino acid sequences revealed a close relationship between WfNgV1 and Bemisia tabaci negevirus 1, a negevirus sequence recently discovered in whiteflies from Israel. Both viruses form a clade sharing a most recent common ancestor with the proposed nelorpivirus and centivirus taxa. The putative glycoprotein from ORF 2 and SP24 (ORF 3) of WfNgV1 exhibit the characteristic topologies previously reported for negevirus counterparts. This marks the first reported negevirus-like sequence from whiteflies in the Americas.


Genome, Viral , Hemiptera , Open Reading Frames , Phylogeny , Animals , Hemiptera/virology , Hemiptera/genetics , Open Reading Frames/genetics , Viral Proteins/genetics , RNA, Viral/genetics , Amino Acid Sequence , RNA-Dependent RNA Polymerase/genetics
9.
RNA Biol ; 21(1): 1-9, 2024 Jan.
Article En | MEDLINE | ID: mdl-38785360

The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme. Guided by these experiments, we analyse protocellular evolution with an expanded set of reaction pathways made possible through the presence of DNA nucleotides. By encapsulating these reactions inside three different types of protocellular compartments, each subject to distinct modes of selection, we show how protocells containing DNA-encoded replicases in low copy numbers and replicases in high copy numbers can dominate the population. This is facilitated by a reaction that leads to auto-catalytic synthesis of replicase ribozymes from DNA templates encoding the replicase after the chance emergence of a replicase through non-enzymatic reactions. Our work unveils a pathway for the transition from an RNA world to a mixed RNA-DNA world characterized by Darwinian evolution, where DNA sequences encode heritable phenotypes.


DNA , RNA, Catalytic , RNA , DNA/genetics , DNA/metabolism , DNA/chemistry , RNA/genetics , RNA/metabolism , RNA/chemistry , RNA, Catalytic/genetics , RNA, Catalytic/metabolism , Evolution, Molecular , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/metabolism , Artificial Cells/metabolism
10.
Mol Biol Rep ; 51(1): 642, 2024 May 10.
Article En | MEDLINE | ID: mdl-38727866

BACKGROUND: The mitochondrial carrier homolog 2 (MTCH2) is a mitochondrial outer membrane protein regulating mitochondrial metabolism and functions in lipid homeostasis and apoptosis. Experimental data on the interaction of MTCH2 with viral proteins in virus-infected cells are very limited. Here, the interaction of MTCH2 with PA subunit of influenza A virus RdRp and its effects on viral replication was investigated. METHODS: The human MTCH2 protein was identified as the influenza A virus PA-related cellular factor with the Y2H assay. The interaction between GST.MTCH2 and PA protein co-expressed in transfected HEK293 cells was evaluated by GST-pull down. The effect of MTCH2 on virus replication was determined by quantification of viral transcript and/or viral proteins in the cells transfected with MTCH2-encoding plasmid or MTCH2-siRNA. An interaction model of MTCH2 and PA was predicted with protein modeling/docking algorithms. RESULTS: It was observed that PA and GST.MTCH2 proteins expressed in HEK293 cells were co-precipitated by glutathione-agarose beads. The influenza A virus replication was stimulated in HeLa cells whose MTCH2 expression was suppressed with specific siRNA, whereas the increase of MTCH2 in transiently transfected HEK293 cells inhibited viral RdRp activity. The results of a Y2H assay and protein-protein docking analysis suggested that the amino terminal part of the viral PA (nPA) can bind to the cytoplasmic domain comprising amino acid residues 253 to 282 of the MTCH2. CONCLUSION: It is suggested that the host mitochondrial MTCH2 protein is probably involved in the interaction with the viral polymerase protein PA to cause negative regulatory effect on influenza A virus replication in infected cells.


Influenza A virus , Virus Replication , Humans , Virus Replication/genetics , HEK293 Cells , Influenza A virus/physiology , Influenza A virus/genetics , HeLa Cells , Down-Regulation , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Viral Proteins/metabolism , Viral Proteins/genetics , Protein Binding , Mitochondria/metabolism , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics
11.
Methods Mol Biol ; 2808: 19-33, 2024.
Article En | MEDLINE | ID: mdl-38743360

Morbilliviruses such as measles virus (MeV) are responsible for major morbidity and mortality worldwide, despite the availability of an effective vaccine and global vaccination campaigns. MeV belongs to the mononegavirus order of viral pathogens that store their genetic information in non-segmented negative polarity RNA genomes. Genome replication and viral gene expression are carried out by a virus-encoded RNA-dependent RNA polymerase (RdRP) complex that has no immediate host cell analog. To better understand the organization and regulation of the viral RdRP and mechanistically characterize antiviral candidates, biochemical RdRP assays have been developed that employ purified recombinant polymerase complexes and synthetic RNA templates to monitor the initiation of RNA synthesis and RNA elongation in vitro. In this article, we will discuss strategies for the efficient expression and preparation of mononegavirus polymerase complexes, provide detailed protocols for the execution and optimization of RdRP assays, evaluate alternative options for the choice of template and detection system, and describe the application of the assay for the characterization of inhibitor candidates. Although MeV RdRP assays are the focus of this article, the general strategies and experimental approaches are readily transferable to related viruses in the mononegavirus order.


Measles virus , RNA-Dependent RNA Polymerase , Virus Replication , Measles virus/genetics , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , RNA, Viral/genetics , Mononegavirales/genetics , Animals , Viral Proteins/metabolism , Viral Proteins/genetics , Humans
12.
Arch Virol ; 169(5): 105, 2024 Apr 18.
Article En | MEDLINE | ID: mdl-38637359

In this study, we identified a novel double-strand RNA (dsRNA) mycovirus in Pyricularia oryzae, designated "Magnaporthe oryzae partitivirus 4" (MoPV4). The genome of MoPV4 consists of a dsRNA-1 segment encoding an RNA-dependent RNA polymerase (RdRP) and a dsRNA-2 segment encoding a capsid protein (CP). Phylogenetic analysis indicated that MoPV4 belongs to the genus Gammapartitivirus within family Partitiviridae. The particles of MoPV4 are isometric with a diameter of about 32.4 nm. Three-dimensional structure predictions indicated that the RdRP of MoPV4 forms a classical right-handed conformation, while the CP has a reclining-V shape.


Ascomycota , Fungal Viruses , RNA Viruses , RNA, Viral/genetics , Phylogeny , RNA Viruses/genetics , Capsid Proteins/genetics , RNA-Dependent RNA Polymerase/genetics , Genome, Viral , Fungal Viruses/genetics , RNA, Double-Stranded/genetics , Open Reading Frames
13.
Antiviral Res ; 226: 105895, 2024 Jun.
Article En | MEDLINE | ID: mdl-38679165

Rift Valley fever virus (RVFV) is an arbovirus in the Phenuiviridae family identified initially by the large 'abortion storms' observed among ruminants; RVFV can also infect humans. In humans, there is a wide variation of clinical symptoms ranging from subclinical to mild febrile illness to hepatitis, retinitis, delayed-onset encephalitis, or even hemorrhagic fever. The RVFV is a tri-segmented negative-sense RNA virus consisting of S, M, and L segments. The L segment encodes the RNA-dependent RNA polymerase (RdRp), termed the L protein, which is responsible for both viral mRNA synthesis and genome replication. Phosphorylation of viral RdRps is known to regulate viral replication. This study shows that RVFV L protein is serine phosphorylated and identified Casein Kinase 1 alpha (CK1α) and protein phosphatase 1 alpha (PP1α) as L protein binding partners. Inhibition of CK1 and PP1 through small molecule inhibitor treatment, D4476 and 1E7-03, respectively, caused a change in the phosphorylated status of the L protein. Inhibition of PP1α resulted in increased L protein phosphorylation whereas inhibition of CK1α decreased L protein phosphorylation. It was also found that in RVFV infected cells, PP1α localized to the cytoplasmic compartment. Treatment of RVFV infected cells with CK1 inhibitors reduced virus production in both mammalian and mosquito cells. Lastly, inhibition of either CK1 or PP1 reduced viral genomic RNA levels. These data indicate that L protein is phosphorylated and that CK1 and PP1 play a crucial role in regulating the L protein phosphorylation cycle, which is critical to viral RNA production and viral replication.


Protein Phosphatase 1 , Rift Valley fever virus , Virus Replication , Rift Valley fever virus/physiology , Rift Valley fever virus/genetics , Phosphorylation , Humans , Animals , Protein Phosphatase 1/metabolism , Protein Phosphatase 1/genetics , Genome, Viral , Viral Proteins/metabolism , Viral Proteins/genetics , Casein Kinase Ialpha/metabolism , Casein Kinase Ialpha/genetics , Chlorocebus aethiops , Cell Line , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , Vero Cells , RNA, Viral/genetics , RNA, Viral/metabolism , Rift Valley Fever/virology
14.
J Gen Virol ; 105(4)2024 Apr.
Article En | MEDLINE | ID: mdl-38687001

Nairoviridae is a family for negative-sense RNA viruses with genomes of about 17.2-21.1 kb. These viruses are maintained in and/or transmitted by arthropods among birds, reptiles and mammals. Norwaviruses and orthonairoviruses can cause febrile illness in humans. Several orthonairoviruses can infect mammals, causing mild, severe and sometimes, fatal diseases. Nairovirids produce enveloped virions containing two or three single-stranded RNA segments with open reading frames that encode a nucleoprotein (N), sometimes a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Nairoviridae, which is available at www.ictv.global/report/nairoviridae.


Genome, Viral , Animals , Humans , Open Reading Frames , Viral Proteins/genetics , Nairovirus/genetics , Nairovirus/classification , Nairovirus/isolation & purification , RNA, Viral/genetics , Phylogeny , Virion/ultrastructure , RNA-Dependent RNA Polymerase/genetics
15.
Vet Res ; 55(1): 40, 2024 Mar 26.
Article En | MEDLINE | ID: mdl-38532469

The interaction between viral components and cellular proteins plays a crucial role in viral replication. In a previous study, we showed that the 3'-untranslated region (3'-UTR) is an essential element for the replication of duck hepatitis A virus type 1 (DHAV-1). However, the underlying mechanism is still unclear. To gain a deeper understanding of this mechanism, we used an RNA pull-down and a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assay to identify new host factors that interact with the 3'-UTR. We selected interleukin-2 enhancer binding factor 2 (ILF2) for further analysis. We showed that ILF2 interacts specifically with both the 3'-UTR and the 3D polymerase (3Dpol) of DHAV-1 through in vitro RNA pull-down and co-immunoprecipitation assays, respectively. We showed that ILF2 negatively regulates viral replication in duck embryo fibroblasts (DEFs), and that its overexpression in DEFs markedly suppresses DHAV-1 replication. Conversely, ILF2 silencing resulted in a significant increase in viral replication. In addition, the RNA-dependent RNA polymerase (RdRP) activity of 3Dpol facilitated viral replication by enhancing viral RNA translation efficiency, whereas ILF2 disrupted the role of RdRP in viral RNA translation efficiency to suppress DHAV-1 replication. At last, DHAV-1 replication markedly suppressed the expression of ILF2 in DEFs, duck embryo hepatocytes, and different tissues of 1 day-old ducklings. A negative correlation was observed between ILF2 expression and the viral load in primary cells and different organs of young ducklings, suggesting that ILF2 may affect the viral load both in vitro and in vivo.


Hepatitis Virus, Duck , Hepatitis, Viral, Animal , Picornaviridae Infections , Poultry Diseases , Animals , Interleukin-2/genetics , RNA-Dependent RNA Polymerase/genetics , Gene Expression Regulation , RNA, Viral/genetics , Ducks/genetics , Picornaviridae Infections/veterinary
16.
Arch Virol ; 169(4): 75, 2024 Mar 16.
Article En | MEDLINE | ID: mdl-38492088

Fusarium oxysporum is a widespread plant pathogen that causes fusarium wilt and fusarium root rot in many economically significant crops. Here, a novel dsRNA virus tentatively named "Fusarium oxysporum virus 1" (FoV1) was identified in F. oxysporum strain 3S-18. The genome of FoV1 is 2,944 nucleotides (nt) in length and contains two non-overlapping open reading frames (ORF1 and 2). The larger of these, ORF2, encodes an RNA-dependent RNA polymerase (RdRp) of 590 amino acids with a molecular mass of 67.52 kDa. ORF1 encodes a putative nucleocapsid protein consisting of 134 amino acids with a molecular mass of 34.25 kDa. The RdRp domain of FoV1 shares 60.00% to 84.24% sequence identity with non-segmented dsRNA viruses. Phylogenetic analysis further suggested that FoV1 is a new member of the proposed genus "Unirnavirus" accommodating unclassified monopartite dsRNA viruses.


Fungal Viruses , Fusarium , RNA Viruses , Fusarium/genetics , Double Stranded RNA Viruses/genetics , Phylogeny , Genome, Viral , Fungal Viruses/genetics , RNA-Dependent RNA Polymerase/genetics , Open Reading Frames , Fungi , Amino Acids/genetics , RNA Viruses/genetics , RNA, Double-Stranded/genetics , RNA, Viral/genetics
17.
Arch Virol ; 169(4): 78, 2024 Mar 22.
Article En | MEDLINE | ID: mdl-38517587

Mycoviruses are viruses that infect fungi and oomycetes. They are widespread in all major groups of plant-pathogenic fungi and oomycetes. To date, only the full genome of dsRNA mycoviruses and the contigs of positive-sense single-stranded RNA (+ssRNA) mycoviruses have been reported in Ustilaginoidea virens, which is the notorious causal agent of rice false smut (RFS). Here, we report the molecular characterization of a novel +ssRNA mycovirus, Ustilaginoidea virens narnavirus 4 (UvNV4), isolated from U. virens strain Uv418. UvNV4 has a genome of 3,131 nucleotides (nt) and possesses an open reading frame (ORF) predicted to encode an RNA-dependent RNA polymerase (RdRp) of 1,017 amino acids (aa) sequence with a molecular mass of 116.6 kDa. BLASTp analysis revealed that the RdRp showed 50.34% aa sequence identity to that of the previously described Zhangzhou Narna tick virus 1. Phylogenetic analysis indicated that UvNV4 is closely related to members of the family Narnaviridae. Taken together, these results clearly demonstrate that UvNV4 is a novel +ssRNA virus infecting U. virens.


Fungal Viruses , Hypocreales , RNA Viruses , Phylogeny , Genome, Viral , Hypocreales/genetics , RNA-Dependent RNA Polymerase/genetics , Open Reading Frames , RNA, Viral/genetics , Plant Diseases/microbiology
18.
Curr Protoc ; 4(3): e1007, 2024 Mar.
Article En | MEDLINE | ID: mdl-38511495

An optimized protocol has been developed to express and purify the core RNA-dependent RNA polymerase (RdRP) complex from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The expression and purification of active core SARS-CoV-2 RdRp complex is challenging due to the complex multidomain fold of nsp12, and the assembly of the multimeric complex involving nsp7, nsp8, and nsp12. Our approach adapts a previously published method to express the core SARS-CoV-2 RdRP complex in Escherichia coli and combines it with a procedure to express the nsp12 fusion with maltose-binding protein in insect cells to promote the efficient assembly and purification of an enzymatically active core polymerase complex. The resulting method provides a reliable platform to produce milligram amounts of the polymerase complex with the expected 1:2:1 stoichiometry for nsp7, nsp8, and nsp12, respectively, following the removal of all affinity tags. This approach addresses some of the limitations of previously reported methods to provide a reliable source of the active polymerase complex for structure, function, and inhibition studies of the SARS-CoV-2 RdRP complex using recombinant plasmid constructs that have been deposited in the widely accessible Addgene repository. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Expression and production of SARS-CoV-2 nsp7, nsp8, and nsp12 in E. coli cells Support Protocol: Establishment and maintenance of insect cell cultures Basic Protocol 2: Generation of recombinant baculovirus in Sf9 cells and production of nsp12 fusion protein in T. ni cells Basic Protocol 3: Purification of the SARS-CoV-2 core polymerase complex.


COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Escherichia coli/genetics , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/metabolism
19.
Arch Virol ; 169(3): 60, 2024 Mar 02.
Article En | MEDLINE | ID: mdl-38430446

A novel partitivirus, Fusarium commune partitivirus 1 (FcoPV1), was identified in Fusarium commune strain CP-SX-3 isolated from diseased roots of strawberry with symptoms of root rot. The complete genome of FcoPV1 comprises three double-stranded RNAs (dsRNAs): dsRNA1 (1,825 nt), dsRNA2 (1,592 nt), and dsRNA3 (1,421 nt). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), and dsRNA2 contains a single ORF (ORF2) encoding a coat protein (CP). dsRNA3 is a possible satellite RNA that does not appear to encode a known protein. BLASTp analysis revealed that RdRp (86.59%) and CP (74.13%) encoded by the two ORFs (ORF1 and ORF2) had the highest sequence similarity to their counterparts in Fusarium equiseti partitivirus 1 (FePV1). Phylogenetic analysis based on the complete amino acid sequence of RdRp suggested that FcoPV1 should be considered a member of a new species in the proposed genus "Zetapartitivirus" within the family Partitiviridae. To the best of our knowledge, this is the first report of a zetapartitivirus infecting phytopathogenic F. commune.


Fragaria , Fusarium , Phylogeny , Genome, Viral , RNA-Dependent RNA Polymerase/genetics
20.
PLoS Pathog ; 20(3): e1012110, 2024 Mar.
Article En | MEDLINE | ID: mdl-38498560

The interaction between influenza A virus (IAV) and host proteins is an important process that greatly influences viral replication and pathogenicity. PB2 protein is a subunit of viral ribonucleoprotein (vRNP) complex playing distinct roles in viral transcription and replication. BAG6 (BCL2-associated athanogene 6) as a multifunctional host protein participates in physiological and pathological processes. Here, we identify BAG6 as a new restriction factor for IAV replication through targeting PB2. For both avian and human influenza viruses, overexpression of BAG6 reduced viral protein expression and virus titers, whereas deletion of BAG6 significantly enhanced virus replication. Moreover, BAG6-knockdown mice developed more severe clinical symptoms and higher viral loads upon IAV infection. Mechanistically, BAG6 restricted IAV transcription and replication by inhibiting the activity of viral RNA-dependent RNA polymerase (RdRp). The co-immunoprecipitation assays showed BAG6 specifically interacted with the N-terminus of PB2 and competed with PB1 for RdRp complex assembly. The ubiquitination assay indicated that BAG6 promoted PB2 ubiquitination at K189 residue and targeted PB2 for K48-linked ubiquitination degradation. The antiviral effect of BAG6 necessitated its N-terminal region containing a ubiquitin-like (UBL) domain (17-92aa) and a PB2-binding domain (124-186aa), which are synergistically responsible for viral polymerase subunit PB2 degradation and perturbing RdRp complex assembly. These findings unravel a novel antiviral mechanism via the interaction of viral PB2 and host protein BAG6 during avian or human influenza virus infection and highlight a potential application of BAG6 for antiviral drug development.


Influenza A virus , Influenza, Human , Animals , Humans , Mice , Antiviral Agents/metabolism , Influenza A virus/genetics , Molecular Chaperones/metabolism , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/metabolism , Viral Proteins/genetics , Viral Proteins/metabolism , Virus Replication/genetics
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