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1.
PLoS Biol ; 16(10): e3000038, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30346944

RESUMO

Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many developing nations. A detailed understanding of the MrNV virion structure will inform the development of strategies to control outbreaks. The MrNV capsid has also been engineered to display heterologous antigens, and thus knowledge of its atomic resolution structure will benefit efforts to develop tools based on this platform. Here, we present an atomic-resolution model of the MrNV capsid protein (CP), calculated by cryogenic electron microscopy (cryoEM) of MrNV virus-like particles (VLPs) produced in insect cells, and three-dimensional (3D) image reconstruction at 3.3 Å resolution. CryoEM of MrNV virions purified from infected freshwater prawn post-larvae yielded a 6.6 Å resolution structure, confirming the biological relevance of the VLP structure. Our data revealed that unlike other known nodavirus structures, which have been shown to assemble capsids having trimeric spikes, MrNV assembles a T = 3 capsid with dimeric spikes. We also found a number of surprising similarities between the MrNV capsid structure and that of the Tombusviridae: 1) an extensive network of N-terminal arms (NTAs) lines the capsid interior, forming long-range interactions to lace together asymmetric units; 2) the capsid shell is stabilised by 3 pairs of Ca2+ ions in each asymmetric unit; 3) the protruding spike domain exhibits a very similar fold to that seen in the spikes of the tombusviruses. These structural similarities raise questions concerning the taxonomic classification of MrNV.


Assuntos
Nodaviridae/ultraestrutura , Palaemonidae/virologia , Animais , Proteínas do Capsídeo/química , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/ultraestrutura , Microscopia Crioeletrônica , Imageamento Tridimensional , Modelos Moleculares , Nodaviridae/classificação , Nodaviridae/patogenicidade , Domínios e Motivos de Interação entre Proteínas , Estrutura Quaternária de Proteína , Especificidade da Espécie , Tombusviridae/classificação , Tombusviridae/ultraestrutura , Vírion/ultraestrutura , Montagem de Vírus
2.
Arch Virol ; 166(8): 2321-2324, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34046760

RESUMO

The complete sequence of a new viral RNA from babaco (Vasconcellea × heilbornii) was determined. The genome consisted of 4,584 nucleotides, containing two open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5' terminus, and an unusually long (1,843 nt) NCR at the 3' terminus. The presence of a potential heptameric slippery signal located 12 nt upstream the stop codon of ORF 1 suggests a -1 ribosomal frameshift mechanism for the translation of ORF 2. Sequence comparisons of ORF 2 revealed similarity to the RNA-dependent RNA polymerase (RdRp) of several umbra- and umbra-like viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported in papaya, citrus, opuntia, maize, and sugarcane hosts. Viruses of this clade share a most recent ancestor with the umbraviruses but have different genomic features. The creation of a new genus within the family Tombusviridae is proposed for the classification of these novel viruses.


Assuntos
Caricaceae/virologia , Tombusviridae/classificação , Sequenciamento Completo do Genoma/métodos , Composição de Bases , Tamanho do Genoma , Genoma Viral , Fases de Leitura Aberta , Filogenia , Tombusviridae/genética , Tombusviridae/isolamento & purificação
3.
Arch Virol ; 166(3): 961-965, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33410996

RESUMO

Many viral diseases of sugarcane negatively affect yield. A sugarcane accession originating from South Africa exhibiting mosaic symptoms was processed for high-throughput sequencing. Bioinformatic analysis revealed two known sugarcane viruses and a contig of around 2,800 nucleotides resembling umbra-like viruses of the family Tombusviridae. The sequence of the viral contig was confirmed by cloning and Sanger sequencing, and the ends of the virus sequence were determined. Open reading frame analysis revealed the presence of four ORFs. Phylogenetic analysis of the complete virus sequence showed that this virus clusters with other umbra-like viruses of the family Tombusviridae.


Assuntos
Doenças das Plantas/virologia , Saccharum/virologia , Tombusviridae/classificação , Tombusviridae/genética , Sequenciamento de Nucleotídeos em Larga Escala , Fases de Leitura Aberta/genética , RNA Viral/genética , África do Sul , Tombusviridae/isolamento & purificação
4.
Arch Virol ; 164(10): 2581-2584, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31359148

RESUMO

Maize chlorotic mottle virus (MCMV), an important quarantine virus, causes lethal necrosis in maize when coinfected with a potyvirid, which is seriously threatening the production of maize worldwide. In this study, recombinase polymerase amplification (RPA), a novel isothermal DNA amplification and detection technique, was developed to detect MCMV in maize crops. A pair of specific primers was designed based on the conserved sequences of the MCMV coat protein region. The RT-RPA assay was carried out as an isothermal reaction at 38 °C that was complete within 30 min, and no cross-reactivity was detected with other viruses infecting maize in China. The limit of detection of the RT-RPA assay was tenfold lower than that of ordinary RT-PCR. Moreover, this method was successfully applied to test field-collected samples. The newly developed RT-RPA assay offers a reliable, sensitive and efficient method for rapid detection of MCMV in maize in equipment-limited diagnostic laboratories and on-site facilities.


Assuntos
Técnicas de Diagnóstico Molecular/métodos , Técnicas de Amplificação de Ácido Nucleico/métodos , Doenças das Plantas/virologia , Tombusviridae/isolamento & purificação , Proteínas do Capsídeo/genética , China , Primers do DNA/genética , Sensibilidade e Especificidade , Temperatura , Fatores de Tempo , Tombusviridae/classificação , Tombusviridae/genética
5.
Arch Virol ; 164(9): 2375-2378, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31183555

RESUMO

The complete genomic RNA sequence of a tentative new umbravirus from Patrinia scabiosaefolia, tentatively named "patrinia mild mottle virus" (PatMMoV), was determined. The genome of PatMMoV consists of 4,214 nucleotides and has a typical umbravirus genome organization with four open reading frames. BLAST searches showed that the complete nucleotide sequence of PatMMoV had the highest identity (72%; 50% query coverage) to Ixeridium yellow mottle-associated virus 2 (IxYMaV-2; an unclassified umbravirus). In addition, phylogenetic analysis and pairwise comparisons showed that PatMMoV and IxYMaV-2 were the most closely related and placed in the same clade within a group of umbraviruses. These results suggest that PatMMoV is a putative new member of the genus Umbravirus in the family Tombusviridae.


Assuntos
Genoma Viral , Patrinia/virologia , Doenças das Plantas/virologia , Tombusviridae/genética , Tombusviridae/isolamento & purificação , Sequência de Bases , Dados de Sequência Molecular , Fases de Leitura Aberta , Filogenia , Tombusviridae/classificação , Sequenciamento Completo do Genoma
6.
Arch Virol ; 163(11): 3051-3058, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30069855

RESUMO

Star jasmine (Jasminum multiflorum) plants growing in Hawaii expressing a diverse array of virus-like foliar symptoms were examined for the presence of a causal agent. Symptomatic tissues collected from three locations on the island of Oahu, Hawaii consistently harbored double-stranded (ds)RNAs approximately 4.2 and 1.7 kbp in size. Sanger and high-throughput sequencing approaches revealed these dsRNAs were from two distinct virus species co-infecting the same host plant. One of these two viruses was the recently characterized Jasmine virus H (JaVH), and the second we designated as Jasmine mosaic-associated virus (JMaV). Both viruses were subsequently found, by high-throughput sequencing, in a single angelwing jasmine (J. nitidum) plant exhibiting similar ringspot symptoms and growing at the U.S. National Arboretum in Washington, DC. Phylogenetic placement, genome organization, and sequence comparisons indicate these two viruses are classifiable as members of the genus Pelarspovirus (family Tombusviridae). To determine if either of these viruses were associated with the observed symptoms, a PCR-based detection assay was developed to detect and distinguish these two viruses in several Hawaii-grown plants. All 32 samples collected from four Oahu locations displayed symptoms. All 32 samples were positive for JaVH, and 16 were positive for JMaV. An asymptomatic star jasmine plant from the island of Hawaii was negative for both JaVH and JMaV. Both viruses were also found in a symptomatic J. sambac sample from Maryland while only JMaV was detected in a symptomatic Jasminum sp. sample from California.


Assuntos
Jasminum/virologia , Doenças das Plantas/virologia , Tombusviridae/isolamento & purificação , Genoma Viral , Havaí , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Tombusviridae/classificação , Tombusviridae/genética , Washington
7.
Arch Virol ; 163(3): 731-735, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29214362

RESUMO

Jasmine virus H (JaVH) is a novel virus associated with symptoms of yellow mosaic on jasmine. The JaVH genome is 3,867 nt in length with five open reading frames (ORFs) encoding a 27-kDa protein (ORF 1), an 87-kDa replicase protein (ORF 2), two centrally located movement proteins (ORF 3 and 4), and a 37-kDa capsid protein (ORF 5). Based on genomic and phylogenetic analysis, JaVH is predicted to be a member of the genus Pelarspovirus in the family Tombusviridae.


Assuntos
Genoma Viral , Jasminum/virologia , Filogenia , RNA Viral/genética , Tombusviridae/genética , Sequência de Bases , Proteínas do Capsídeo/genética , Sequenciamento de Nucleotídeos em Larga Escala , Fases de Leitura Aberta , RNA Polimerase Dependente de RNA/genética , Tombusviridae/classificação , Tombusviridae/isolamento & purificação
8.
Arch Virol ; 163(3): 771-776, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29147792

RESUMO

Fungal viruses, also known as mycoviruses, are widespread in all major groups of fungi. Mycoviruses from plant pathogens can reduce the virulence of their host fungus and have therefore potential as biological control agents. This has spurred the identification of novel mycoviruses in plant pathogens, research which is greatly contributing to our understanding of these organisms. In this work, we report the characterization of a novel monopartite mycovirus from Verticillium dahliae, the main causal agent of Verticillium wilt. This novel mycovirus, which we termed Verticillium dahliae RNA virus 1 (VdRV1), was identified in three different isolates of V. dahliae collected in olive growing areas of the Guadalquivir valley, southern Spain. We determined that the VdRV1 genome is a positive (+) single-stranded (ss) RNA, 2631 nucleotides in length, containing two open reading frames. VdRV1 showed few similarities with known mycoviruses, only with a group of unassigned (+) ssRNA mycoviruses which are related to plant viruses classified within the family Tombusviridae. However, phylogenetic analysis revealed that VdRV1 and the unassigned (+) ssRNA mycoviruses have a closer relationship with recently reported invertebrate viruses. This result indicates that as more viral sequences become available, the relationships of mycoviruses with viruses from other hosts should be reexamined. Additionally, the work supports the hypothesis of a heterogeneous origin for mycoviruses.


Assuntos
Micovírus/genética , Genoma Viral , Olea/microbiologia , Filogenia , RNA Viral/genética , Verticillium/virologia , Animais , Micovírus/classificação , Micovírus/isolamento & purificação , Invertebrados/virologia , Fases de Leitura Aberta , Doenças das Plantas/microbiologia , Análise de Sequência de RNA , Espanha , Tombusviridae/classificação , Tombusviridae/genética , Verticillium/patogenicidade , Verticillium/fisiologia
9.
Arch Virol ; 163(6): 1585-1594, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29492653

RESUMO

A novel virus was discovered in a freeze-dried collection held at SASA, UK, originating from potato (Solanum tuberosum) cv. Nadine. The complete sequence of the viral RNA was determined to be 3674 nucleotides in length encoding five predicted proteins. Based on the deduced genome organization and phylogenetic analysis, this virus represents a putative new member of the genus Alphanecrovirus, family Tombusviridae, most closely related to isolates of Olive mild mosaic virus. The virus was easily transmitted to indicator plants with symptoms that were slower to develop and less severe than those of related viruses. To distinguish this virus, the clearest symptom differences occurred with Nicotiana debneyi, Chenopodium amaranticolor and Ch. quinoa. The virus was detected with antisera to the related viruses tobacco necrosis virus A and tobacco necrosis virus D. The close association to the tobacco necrosis viruses would suggest this virus is not a new introduction to potato but in the past has been misidentified as one of these viruses. The virus isolate has been named potato necrosis virus.


Assuntos
Genoma Viral , Filogenia , RNA Viral/genética , Solanum tuberosum/virologia , Tombusviridae/genética , Chenopodium/virologia , Chenopodium quinoa/virologia , Efeito Fundador , Fases de Leitura Aberta , Doenças das Plantas/virologia , Nicotiana/virologia , Tombusviridae/classificação , Tombusviridae/isolamento & purificação , Tombusviridae/patogenicidade , Reino Unido
10.
Arch Virol ; 162(4): 1099-1102, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27995336

RESUMO

Bermuda grass samples were examined by transmission electron microscopy and 28-30 nm spherical virus particles were observed. Total RNA from these plants was subjected to high-throughput sequencing (HTS). The nearly full genome sequence of a panicovirus was identified from one HTS scaffold. Sanger sequencing was used to confirm the HTS results and complete the genome sequence of 4404 nt. This virus was provisionally named Bermuda grass latent virus (BGLV). Its predicted open reading frames follow the typical arrangement of the genus Panicovirus. Based on sequence comparisons and phylogenetic analyses BGLV differs from other viruses and therefore taxonomically it is a new member of the genus Panicovirus, family Tombusviridae.


Assuntos
Genoma Viral , Poaceae/virologia , Tombusviridae/genética , Sequência de Bases , Sequenciamento de Nucleotídeos em Larga Escala , Dados de Sequência Molecular , Fases de Leitura Aberta , Filogenia , Doenças das Plantas/virologia , RNA Viral , Tombusviridae/classificação , Tombusviridae/isolamento & purificação , Proteínas Virais/genética
11.
Arch Virol ; 162(12): 3893-3897, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28905257

RESUMO

Two novel viruses, isolated in Bonghwa, Republic of Korea, from an Ixeridium dentatum plant with yellowing mottle symptoms, have been provisionally named Ixeridium yellow mottle-associated virus 1 (IxYMaV-1) and Ixeridium yellow mottle-associated virus 2 (IxYMaV-2). IxYMaV-1 has a genome of 6,017 nucleotides sharing a 56.4% sequence identity with that of cucurbit aphid-borne yellows virus (genus Polerovirus). The IxYMaV-2 genome of 4,196 nucleotides has a sequence identity of less than 48.3% with e other species classified within the genus Umbravirus. Genome properties and phylogenetic analysis suggested that IxYMaV-1 and -2 are representative isolates of new species classifiable within the genus Polerovirus and Umbravirus, respectively.


Assuntos
Asteraceae/virologia , Genoma Viral , Luteoviridae/classificação , Luteoviridae/isolamento & purificação , Tombusviridae/classificação , Tombusviridae/isolamento & purificação , Luteoviridae/genética , Filogenia , Doenças das Plantas/virologia , República da Coreia , Análise de Sequência de DNA , Homologia de Sequência , Tombusviridae/genética
12.
Arch Virol ; 162(5): 1319-1324, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28155196

RESUMO

Plasmopara halstedii virus (PhV) is one of the few characterized oomycete viruses. Although it is fully sequenced and well-studied in its genetic diversity, the exact classification and phylogenetic relationships of PhV remain uncertain. The only known virus with characteristics similar to PhV is the Sclerophthora macrospora Virus A (SmV-A). Both viruses infect obligate biotrophic oomycetes. While RNA-dependent RNA polymerases (RdRp) of oomycetes viruses have high similarity to the corresponding enzymes from viruses classified in the family Nodaviridae, the coat proteins (CP) seem to be completely different from those of other viruses of this family. In contrast, the coat proteins of PhV and SmV-A have high similarity to viruses classified in the Tombusviridae, Circoviridae and a new group of hybrid DNA-RNA viruses (so-called chimeric viruses or cruciviruses). Because phylogenetic analyses based on the sequences of either RdRp or CP result in different affinities, an alternative, genome-based approach combining the sequences of both proteins was used. This analysis placed the two oomycete viruses together with Tombunodavirus UC1 in a new, independent group between families Nodaviridae and Tombusviridae.


Assuntos
Proteínas do Capsídeo/genética , Genoma Viral/genética , Nodaviridae/genética , Oomicetos/virologia , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética , Tombusviridae/genética , Sequência de Aminoácidos , Sequência de Bases , Variação Genética , Nodaviridae/classificação , Alinhamento de Sequência , Análise de Sequência de RNA , Tombusviridae/classificação
13.
Arch Virol ; 162(5): 1373-1379, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28138775

RESUMO

Clematis chlorotic mottle virus (ClCMV) is a previously undescribed virus associated with symptoms of yellow mottling and veining, chlorotic ring spots, line pattern mosaics, and flower distortion and discoloration on ornamental Clematis. The ClCMV genome is 3,880 nt in length with five open reading frames (ORFs) encoding a 27-kDa protein (ORF 1), an 87-kDa replicase protein (ORF 2), two centrally located movement proteins (ORF 3 and 4), and a 37-kDa capsid protein (ORF 5). Based on morphological, genomic, and phylogenetic analysis, ClCMV is predicted to be a member of the genus Pelarspovirus in the family Tombusviridae.


Assuntos
Proteínas do Capsídeo/genética , Clematis/virologia , RNA Polimerase Dependente de RNA/genética , Tombusviridae/classificação , Tombusviridae/genética , Sequência de Bases , Genoma Viral , Fases de Leitura Aberta/genética , Filogenia , RNA Viral/genética , Análise de Sequência de RNA
14.
Arch Virol ; 161(10): 2893-8, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27456427

RESUMO

As part of an investigation into viruses of wild plants in Australia, a contiguous sequence of 3935 nucleotides was obtained after shotgun sequencing of RNA isolated from an asymptomatic wild legume, Gompholobium preissii. Phylogenetic analysis of the sequence revealed that it most closely resembled that of Trailing lespedeza virus 1 (TLV1), a virus isolated from a wild legume in America. The proposed virus, named Gompholobium virus A, and TLV1 are genetically closest to viruses in the genera Alphacarmovirus and Pelarspovirus, family Tombusviridae, but they share features distinguishing them from both groups.


Assuntos
Fabaceae/virologia , Tombusviridae/classificação , Tombusviridae/isolamento & purificação , Austrália , Análise por Conglomerados , Filogenia , RNA Viral/genética , RNA Viral/isolamento & purificação , Análise de Sequência de DNA , Homologia de Sequência , Tombusviridae/genética
15.
Virol J ; 12: 111, 2015 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-26209518

RESUMO

BACKGROUND: During the past decade, tobacco bushy top disease, which is mainly caused by a combination of Tobacco bushy top virus (TBTV) and Tobacco vein-distorting virus (TVDV), underwent a sudden appearance, extreme virulence and degeneration of the epidemic in the Yunnan province of China. In addition to integrative control of its aphid vector, it is of interest to examine diversity and evolution among different TBTV isolates. METHODS: 5' and 3' RACE, combined with one step full-length RT-PCR, were used to clone the full-length genome of three new isolates of TBTV that exhibited mild pathogenicity in Chinese fields. Nucleotide and amino acid sequences for the TBTV isolates were analyzed by DNAMAN. MEGA 5.0 was used to construct phylogenetic trees. RDP4 was used to detect recombination events during evolution of these isolates. RESULTS: The genomes of three isolates, termed TBTV-JC, TBTV-MD-I and TBTV-MD-II, were 4152 nt in length and included one distinctive difference from previously reported TBTV isolates: the first nucleotide of the genome was a guanylate instead of an adenylate. Diversity and phylogenetic analyses among these three new TBTV isolates and five other available isolates suggest that ORFs and 3'UTRs of TBTV may have evolved separately. Moreover, the RdRp-coding region was the most variable. Recombination analysis detected a total of 29 recombination events in the 8 TBTV isolates, in which 24 events are highly likely and 5 events have low-level likelihood based on their correlation with the phylogenetic trees. The three new TBTV isolates have individual recombination patterns with subtle divergences in parents and locations. CONCLUSIONS: The genome sizes of TBTV isolates were constant while different ORF-coding regions and 3'UTRs may have evolved separately. The RdRp-coding region was the most variable. Frequent recombination occurred among TBTV isolates. Three new TBTV isolates have individual recombination patterns and may have different progenitors.


Assuntos
Nicotiana/virologia , Filogenia , RNA Viral/genética , Recombinação Genética , Tombusviridae/classificação , Tombusviridae/genética , China , Clonagem Molecular , Análise por Conglomerados , Evolução Molecular , Genoma Viral , Dados de Sequência Molecular , Fases de Leitura Aberta , Análise de Sequência de DNA , Homologia de Sequência , Tombusviridae/isolamento & purificação
16.
Arch Virol ; 160(9): 2385-93, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26149249

RESUMO

Currently, the family Tombusviridae encompasses thirteen viral genera that contain single-stranded, positive-sense RNA genomes and isometric virions; the exception being the genus Umbravirus, whose members do not encode a coat protein (CP). A new genus, tentatively named Pelarspovirus, is proposed to be added to this family and would include five members, with Pelargonium line pattern virus recommended as the type species. Viruses assigned to this proposed genus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal CP that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. Distinguishing characteristics of these viruses include i) production of a single, tricistronic subgenomic RNA for expression of MP and CP genes, ii) presence of a non-AUG start codon (CUG or GUG) initiating the MP2 ORF, iii) absence of AUG codons in any frame between the AUG initiation codons of MP1 and CP genes, and iv) sequence-based phylogenetic clustering of all encoded proteins in separate clades from those of other family members.


Assuntos
Tombusviridae/classificação , Tombusviridae/genética , Proteínas do Capsídeo/genética , Análise por Conglomerados , Códon de Iniciação , Ordem dos Genes , Genoma Viral , Filogenia , Proteínas do Movimento Viral em Plantas/genética , RNA Polimerase Dependente de RNA/genética , Homologia de Sequência
17.
Arch Virol ; 159(10): 2795-8, 2014 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-24838852

RESUMO

The genome of the rose yellow leaf virus (RYLV) has been determined to be 3918 nucleotides long and to contain seven open reading frames (ORFs). ORF1 encodes a 27-kDa peptide (p27). ORF2 shares a common start codon with ORF1 and continues through the amber stop codon of p27 to encode an 87-kDa (p87) protein that has amino acid similarity to the RNA-dependent RNA polymerase (RdRp) of members of the family Tombusviridae. ORFs 3 and 4 have no significant amino acid similarity to known functional viral ORFs. ORF5 encodes a 6-kDa (p6) protein that has similarity to movement proteins of members of the Tombusviridae. ORF5A has no conventional start codon and overlaps with p6. A putative +1 frameshift mechanism allows p6 translation to continue through the stop codon and results in a 12-kDa protein that has high homology to the carmovirus p13 movement protein. The 37-kDa protein encoded by ORF6 has amino acid sequence similarity to coat proteins (CP) of members of the Tombusviridae. ORF7 has no significant amino acid similarity to known viral ORFs. Phylogenetic analysis of the RdRp amino acid sequences grouped RYLV together with the unclassified Rosa rugosa leaf distortion virus (RrLDV), pelargonium line pattern virus (PLPV), and pelargonium chlorotic ring pattern virus (PCRPV) in a distinct subgroup of the family Tombusviridae.


Assuntos
Genoma Viral/genética , Rosa/virologia , Tombusviridae/classificação , Tombusviridae/genética , Sequência de Aminoácidos , Sequência de Bases , Códon de Iniciação , Variação Genética , Fases de Leitura Aberta/genética , Doenças das Plantas/virologia , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética , Análise de Sequência de RNA , Homologia de Sequência de Aminoácidos , Proteínas Virais/genética
18.
Arch Virol ; 159(6): 1351-7, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24352437

RESUMO

The CP gene variability among 21 olive latent virus 1 (OLV-1) isolates obtained from different hosts and locations and at different times was assessed. Amplicons obtained by RT-PCR were cloned, and at least 10 sequences from each isolate were analyzed and compared. OLV-1 sequences available in GenBank were included. The encoded CPs consisted of 270 amino acids, except those of isolates G1S and C7 (269 aa) and G6 (271 aa). Comparison of CP genomic sequences of the isolates under study showed very low values of nucleotide diversity, 0.02, and maximum nucleotide distances between (0.087) or within isolates (0.001). Although very few nucleotide sequence differences were observed among the isolates, olive isolates exhibited lower diversity (0.012). In addition, at position 158 (157 in C7 and G1S and 159 in G6) of the deduced aa sequences, an alanine residue was found to be conserved among the olive isolates. In citrus and tulip isolates, a threonine residue was present at position 158, whereas a valine was present at this same position in tomato isolates. Phylogenetic analysis indicated that OLV-1 isolates clustered in five groups according to original host. However, G6, originally recovered from olive but repeatedly inoculated and maintained in N. benthamiana plants for 8 years in our laboratory, was separated from other isolates. This may be attributable to adaptation to the experimental host over time. There was no correlation of phylogenetic grouping of isolates based on geographical location or year of collection. Strong negative selection may have contributed to the low diversity among the OLV-1 CP isolates.


Assuntos
Proteínas do Capsídeo/genética , Variação Genética , Tombusviridae/classificação , Tombusviridae/genética , Clonagem Molecular , Análise por Conglomerados , Dados de Sequência Molecular , Filogenia , Plantas/virologia , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Seleção Genética , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Tombusviridae/isolamento & purificação
19.
Nat Commun ; 13(1): 716, 2022 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-35132090

RESUMO

Mitogen-activated protein kinase (MAPK) cascades play an important role in innate immunity against various pathogens in plants and animals. However, we know very little about the importance of MAPK cascades in plant defense against viral pathogens. Here, we used a positive-strand RNA necrovirus, beet black scorch virus (BBSV), as a model to investigate the relationship between MAPK signaling and virus infection. Our findings showed that BBSV infection activates MAPK signaling, whereas viral coat protein (CP) counteracts MAPKKKα-mediated antiviral defense. CP does not directly target MAPKKKα, instead it competitively interferes with the binding of 14-3-3a to MAPKKKα in a dose-dependent manner. This results in the instability of MAPKKKα and subversion of MAPKKKα-mediated antiviral defense. Considering the conservation of 14-3-3-binding sites in the CPs of diverse plant viruses, we provide evidence that 14-3-3-MAPKKKα defense signaling module is a target of viral effectors in the ongoing arms race of defense and viral counter-defense.


Assuntos
Proteínas 14-3-3/imunologia , Proteínas do Capsídeo/imunologia , MAP Quinase Quinase Quinases/imunologia , Imunidade Vegetal/genética , Tombusviridae/patogenicidade , Proteínas 14-3-3/genética , Morte Celular , Regulação da Expressão Gênica de Plantas , Interações Hospedeiro-Patógeno , Evasão da Resposta Imune , MAP Quinase Quinase Quinases/genética , Sistema de Sinalização das MAP Quinases , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Doenças das Plantas/virologia , Folhas de Planta/genética , Folhas de Planta/imunologia , Folhas de Planta/virologia , Ligação Proteica , Nicotiana/genética , Nicotiana/imunologia , Nicotiana/virologia , Tombusviridae/classificação , Tombusviridae/metabolismo
20.
mBio ; 11(5)2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873755

RESUMO

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.IMPORTANCE Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.


Assuntos
Vírus de DNA/classificação , Mineração de Dados , Genoma Viral , Metagenoma , Proteínas do Capsídeo/genética , Vírus de DNA/genética , Metagenômica , Vírus de RNA/classificação , Vírus de RNA/genética , Tombusviridae/classificação , Tombusviridae/genética
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