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At least 163 records · Page 9Linked to original sources

PubMed2004

The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation.

The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlavirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fully-sequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.

Capsid Proteins↗

PubMed2004

A novel melon flexivirus transmitted by whitefly.

In recent years, a viral disease on melon plants has become a serious problem in Brazil. Symptoms were principally yellowing and mottling on older leaves. Long filamentous virus particles, resembling those of carlaviruses, were seen in symptomatic leaves. In this study, the 3' terminal region of the virus genome isolated from an infected plant, including the last two ORFs, was cloned and sequenced. The sequence comprised a polyadenilated tail and two ORFs, one exhibiting similarity to potexvirus and carlavirus coat protein gene and the second to a carlavirus protein with potential nucleic acid-binding property. The sequence analysis, the genome organization and the particle morphology indicated that the virus could be classified as a novel whitefly-transmitted flexivirus. The name Melon yellowing-associated virus (MYaV) is tentatively suggested for this virus.

Amino Acid Sequence↗

PubMed2004

Comparison of the complete sequences of three different isolates of Pepino mosaic virus: size variability of the TGBp3 protein between tomato and L. peruvianum isolates.

The complete nucleotide sequence of the genomes of two Spanish isolates (LE-2000 and LE-2002) from tomato and one Peruvian isolate (LP-2001) from Lycopersicon peruvianum of the Pepino mosaic virus (PepMV) were determined. The tomato isolates share identities higher than 99%, while the genome of LP-2001 had mean nucleotide identities of 95.6% to 96.0% with tomato isolates. The predicted amino acid sequences showed similarities ranging between 95.2% and 100% with TGBp3 and TGBp2 and CP proteins, respectively. In LP-2001 two main differences were found with respect to the tomato isolates; (i) the 5' untranslated region (UTR) was 2 nt shorter by deletion at position 12-13 and it had some polymorphims at the putative promoter sequence reported for PepMV tomato isolates and other potexviruses, which could be functionally significant for RNA replication, and (ii) the TGBp3 protein had two extra amino acids in the C-terminal region.

5' Untranslated Regions↗

PubMed1998

Evidence that whitefly-transmitted cowpea mild mottle virus belongs to the genus Carlavirus.

Two strains of whitefly-transmitted cowpea mild mottle virus (CPMMV) causing severe (CPMMV-S) and mild (CPMMV-M) disease symptoms in peanuts were collected from two distinct agro-ecological zones in India. The host-range of these strains was restricted to Leguminosae and Chenopodiaceae, and each could be distinguished on the basis of symptoms incited in different hosts. The 3'-terminal 2500 nucleotide sequence of the genomic RNA of both the strains was 70% identical and contains five open reading frames (ORFs). The first three (P25, P12 and P7) overlap to form a triple gene block of proteins, P32 encodes the coat protein, followed by P12 protein located at the 3' end of the genome. Genome organization and pair-wise comparisons of amino acid sequences of proteins encoded by these ORFs with corresponding proteins of known carlaviruses and potexviruses suggest that CPMMV-S and CPMMV-M are closely related to viruses in the genus Carlavirus. Based on the data, it is concluded that CPMMV is a distinct species in the genus Carlavirus.

Amino Acid Sequence↗

PubMed2000

Molecular characterization of Hop latent virus and phylogenetic relationships among viruses closely related to carlaviruses.

The complete nucleotide sequence of the hop latent virus (HpLV) genome was determined. The viral RNA genome is 8,612 nucleotides long, excluding the poly(A) tail, and contains six open reading frames (ORFs), which encode putative proteins of 224-kDa (ORF 1), 25-kDa (ORF 2), 11-kDa (ORF 3), 7-kDa (ORF 4), 34-kDa (ORF 5), and 12-kDa (ORF 6). ORF 5 encodes the coat protein as demonstrated by N-terminal sequencing of three proteolytic peptides derived from the virus particle. The genome organization of HpLV is similar to that of other species in the genus Carlavirus, and the overall sequence of HpLV is more similar to that of Potato virus M than to sequences of other carlaviruses reported to date. The amino acid sequences of the putative methyltransferase, RNA helicase, and RNA-dependent RNA polymerase encoded in ORF 1 and an 'accessory' helicase encoded in ORF 2 of the HpLV genome were compared with those of viruses in the 'tymo' lineage: the genera Carlavirus, Potexvirus, Allexivirus, Foveavirus, Trichovirus, Capillovirus, Vitivirus, and Tymovirus. The phylogenetic relationships among the viruses in these genera are discussed. This is the first molecular characterization of a carlavirus infecting hop plants.

Amino Acid Sequence↗

PubMed2001

Molecular characterisation of Banana mild mosaic virus, a new filamentous virus in Musa spp..

Banana mild mosaic virus (BanMMV) is a previously undescribed filamentous virus infecting Musa spp. The complete genome has been sequenced from PCR clones and consists of 7352 nucleotides, encoding five open reading frames (ORFs) of 205, 25.5, 12.4, 8.0 and 26.8 kDa, respectively. BanMMV was most closely related to fovea- and carlaviruses, based on phylogenetic analysis using a portion of the viral replicase. Analysis of other parts of the genome revealed similarities with fovea-, carla- and potexviruses, but the virus was not clearly aligned to any previously recognised genus.

3' Untranslated Regions↗

PubMed2006

Molecular characterization of two Pepino mosaic virus variants from imported tomato seed reveals high levels of sequence identity between Chilean and US isolates.

Pepino mosaic virus (PepMV), a member of the genus Potexvirus, was first described in South America on pepino (Solanum muricatum A.). Only in recent years, it was reported to infect greenhouse-grown tomatoes. Genome nucleotide sequences from several European isolates showed extensive sequence identity (>99%). Recent genome nucleotide sequences from two US isolates (US1 and US2) however showed much greater sequence divergence from that of the European PepMV isolates. My interest in characterizing virus isolates from South America was due to an active commercial tomato seed production in Chile. Through genome sequence comparison and phylogenetic analyses, we may be able to understand the source of virus infection and control this devastating disease from further spreading into new tomato growing regions of the world. Complete genome nucleotide sequences from two PepMV variants (designated as Ch1 and Ch2) were determined from a virus isolate obtained from a commercial tomato seed lot produced in Chile. Using RT-PCR-based genome walking strategy, complete genome sequences from these two variants were determined. Excluding poly (A) tails, the genomes of PepMV Ch1 and Ch2 were 6414 and 6412 nucleotides (nt), respectively. Pairwise comparisons of PepMV Ch1 and Ch2 genomes with other PepMV isolates showed that the highest nucleotide sequence identity was with two US isolates, 98.7% between PepMV Ch1 and US1, and 90.7% between Ch2 and US2. Similar to PepMV US1 and US2, the two Chilean variants were the most divergent from one another (78% nt identity). These two Chilean PepMV variants also shared only 78-86% nucleotide sequence identity to that of five European isolates. The high level of nucleotide sequence identity between Chilean and US isolates suggests a common origin. Phylogenetic analyses with various gene products generated three distinct sequence clusters (or strains): US1 and Ch1 in the first group, US2 and Ch2 in the second, and the European tomato isolates in the third. Based on the host specificity, it was previously suggested that the original pepino isolate should be considered a distinct strain from that of the tomato isolates.

Chile↗

PubMed1988

Organization and interviral homologies of the coat protein gene of white clover mosaic virus.

The sequence of 1612 nucleotides of the 3'-terminal region of white clover mosaic virus (WCIMV) has been determined from cDNA clones. The viral sense RNA contains four open reading frames of Mr 20,684, Mr 7219, Mr 12,989, and at least Mr 17,000. The latter begins 5' to the sequence determined. The amino acid sequence of the open reading frame encoding the 20,684 polypeptide shows marked homology to the coat proteins of three other potexviruses. The putative coat protein gene was subcloned in a T7 transcription plasmid and RNAs produced by in vitro transcription were translated in the rabbit reticulocyte lysate system. The polypeptide products comigrated on SDS-polyacrylamide gels with one of those synthesized by the in vitro translation of viral RNA, and were immunoprecipitable with antiserum raised against WCIMV, confirming the location of the coat protein gene.

Amino Acid Sequence↗

PubMed1990

Control and expression of 3' open reading frames in clover yellow mosaic virus.

The genomic RNA of clover yellow mosaic virus (CYMV) contains at least seven open reading frames (ORFs) which are organized in a more elaborate array than in other sequenced members of the potexvirus group. We have investigated the strategy by which ORFs located in the 3' region of CYMV's genomic RNA are differentially expressed by correlating the location of the 5' termini of the two abundant viral subgenomic RNAs with their coding potential. We have mapped the 5' termini of the subgenomic RNAs precisely to the nucleotide level and have shown that both are capped. The larger 2.1-kb subgenomic RNA encodes as its 5' ORF a 25-kDa polypeptide, whose function is unknown. The smaller 1.0-kb subgenomic RNA can encode only the 23-kDa coat protein. All four ORFs in the 3' 1095 residues of CYMV are efficiently expressed in vitro, but of these only coat protein, which can be expressed from a subgenomic RNA, is detectable in CYMV infected tissue. For this reason, we believe that expression of ORFs in the 3' one-third of CYMV RNA are controlled at the transcriptional level.

Base Sequence↗

PubMed1991

Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products.

A small group of 1.2-kb RNAs present on polyribosomes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Some features of these RNAs suggest that they are similar to defective interfering (DI) RNAs, and would be the first to be reported for the potexvirus group. The prototype 1.2-kb RNA is 1172 nucleotides in length excluding a probable poly(A) tail and is composed of two noncontiguous regions corresponding to 757 nucleotides of the 5' and 415 nucleotides of the 3' termini of CYMV's gRNA. The sequence of the prototype 1.2-kb RNA reveals that the two terminal gRNA regions present in this RNA encode a single open reading frame (ORF) joining the N-terminus of the 191-kDa nonstructural product and the C-terminus of the coat protein to form a 35-kDa 191-kDa/coat protein fusion product. The coding properties of this prototype RNA have been confirmed by translation in vitro of native and synthetic transcripts of the 1.2-kb RNAs, both of which direct the synthesis of the anticipated 35-kDa product which reacts with anti-CYMV antiserum. Three additional 1.2-kb RNA species, each of which contains a unique junction site, have been characterized. In all cases, a fusion ORF encoding a 191-kDa/coat protein fusion product is encoded on the RNA. The presence of a fusion ORF in all members of the 1.2-kb RNA species analyzed suggests that maintenance of this ORF may be important for the survival of this class of RNA within the plant. This coding strategy represents a novel property of plant virus defective RNAs.

Amino Acid Sequence↗

PubMed1992

The nucleotide sequence of apple stem grooving capillovirus genome.

The complete nucleotide sequence of apple stem grooving virus (ASGV) genome has been determined. The genome is 6496 nucleotides in length excluding a 3'-terminal poly(A) tail and contains two overlapping open reading frames (ORFs). ORF1 begins at nucleotide position 37 and is terminated at position 6341, encoding a protein with a molecular weight of 241 kDa. ORF2, which is in a different reading frame within ORF1, begins at position 4788 and can encode a 36-kDa protein. The 241-kDa protein contains two consensus sequences associated with the RNA-dependent RNA polymerase and the NTP-binding helicase. Comparisons of amino acid sequences around these conserved motifs with other RNA viruses revealed that ASGV has extensive similarities with apple chlorotic leaf spot, tymo-, carla-, and potexviruses, and is a member of the sindbis-like supergroup. ASGV coat protein is found to be located in the C-terminal region of the 241-kDa polyprotein. The 36-kDa protein encoded by ORF2 contains the consensus sequence Gly-Asp-Ser-Gly found in the active site of several cellular and viral serine proteases.

Amino Acid Sequence↗

PubMed1992

Efficient cell-to-cell movement of beet necrotic yellow vein virus requires 3' proximal genes located on RNA 2.

RNA 2 of beet necrotic yellow vein virus (BNYVV) carries six open reading frames. The four 3' proximal frames encode the proteins P42, P13, P15, and P14. The first three species present homologies to proteins encoded by three overlapping open reading frames (the triple gene block) in potexviruses, carlaviruses, and barley stripe mosaic virus. P14 does not display homology with other known plant viral proteins. The functions of P42, P13, P15, and P14 were investigated by site-directed mutagenesis. Full-length transcripts of wild-type BNYVV RNAs 1 and 2 were infectious when coinoculated to protoplasts or leaves of Chenopodium quinoa. RNA 2 transcripts in which P42, P13, and P15 were prematurely terminated by frameshift mutations replicated in protoplasts (when inoculated with wild-type RNA 1) but were not infectious to leaves, indicating that the triple gene block proteins of BNYVV are essential for viral cell-to-cell spread. Mutations in P14 were not lethal in leaf infections but smaller local lesions and lesser amounts of viral RNA were produced. RNA 2-related subgenomic RNA species of 2.6, 1.4, and 0.7 kb were detected; they presumably direct synthesis of P42, P13, and P14. No species of the length predicted for a P15-specific subgenomic RNA was detected.

Base Sequence↗

PubMed1993

Rapid detection of cymbidium mosaic virus by the polymerase chain reaction (PCR).

A direct, simple and sensitive method was developed for the detection of cymbidium mosaic virus (CyMV), based on the polymerase chain reaction (PCR). Two oligonucleotide primers were selected from regions that are homologous to potexviruses and CyMV, and used to hybridize with purified viral RNA and particles. This resulted in the amplification of a 313 bp fragment after 30 cycles of PCR in all samples. A less prominent fragment of 227 bp was also obtained due to mispriming of the second primer. The amplified fragments were easily seen in an agarose gel when stained with ethidium bromide. As little as 1 fg of viral RNA (about 200 target copies) or 10 fg of purified virus (approximately 130 viral particles) were detectable. For CyMV infected orchid leaf tissues, 10 microliters aliquots of 1 mm3 tissue homogenate in 1 ml could be detected routinely. All reverse transcription and amplification reactions were carried out in a single tube and results can be obtained within 5 h.

Base Sequence↗

PubMed1995

Cloning and sequencing of a cDNA encoding the coat protein of a Korean isolate of cymbidium mosaic virus.

The 3'-terminal nucleotide (nt) sequence of the coat protein (CP)-encoding gene of the Korean isolate of cymbidium mosaic potexvirus (CyMV-K) has been determined. The sequence contained a full-length ORF coding for the viral CP. It comprises 663 nt and a polypeptide chain of 220 amino acids with a M(r) of 23,718. The stop codon (TGA) is followed by a 3'-untranslated region (3'-UTR) of 79 nt and a poly(A) tract. The putative polyadenylation signal, AATAAA motif, is found in the terminus of the 3'-UTR.

Amino Acid Sequence↗

PubMed2004

A conserved secondary structure in the hypervariable region at the 5' end of Bamboo mosaic virus satellite RNA is functionally interchangeable.

Satellite RNA (satRNA) associated with Bamboo mosaic virus (BaMV) is dependent on BaMV for replication and encapsidation. Molecular analyses of total RNA extracted from bamboo species collected worldwide revealed that 26 out of 61 BaMV isolates harbored satBaMV. Among them, two phylogenetically distinguishable groups, A and B, with a genetic diversity of 6.9 +/- 0.7% were identified. Greatest sequence diversity occurred in the 5' untranslated region (UTR) that contained one hypervariable region with variations of up to 20.7%. Concurrent covariations in the 5' hypervariable sequences support the existence of a conserved apical hairpin stem-loop structure, which was earlier mapped by enzymatic probings and functional analyses [Annamalai, P., Hsu, Y.H., Liu, Y.P., Tsai, C.H., Lin, N.S., 2003. Structural and mutational analyses of cis-acting sequences in the 5'-untranslated region of satellite RNA of bamboo mosaic potexvirus. Virology 311 (1), 229-239]. Furthermore, chimeric satBaMVs generated by interchanging the hypervariable region between groups A and B demonstrated the replication competence of satBaMV isolates in Nicotiana benthamiana protoplasts co-inoculated with BaMV RNA. The results suggest that an evolutionarily conserved secondary structure exists in the hypervariable region of 5' UTR of satBaMV.

Base Sequence↗

PubMed2026

A conserved COBL3-like protein promotes PDLP5-dependent callose accumulation to confer broad-spectrum plasmodesmata-mediated antiviral defense.

Plasmodesmata (PDs) play vital roles in plant growth and defense by controlling the symplastic transport of important molecules. Here we report that a conserved COBRA-like protein, COBL3, positively regulates callose accumulation and is required for PD-mediated antiviral defense (PMAD) against divergent plant RNA viruses in wheat (Triticum aestivum) and tobacco (Nicotiana benthamiana). The wheat COBL3 protein, TaCOBL3, interacts with the 17K movement protein (MP) of barley yellow dwarf virus-GAV (BYDV-GAV). TaCOBL3 is associated with the plasma membrane and co-localizes with 17K MP at PDs. Genetic analysis with overexpression and knockout lines revealed that TaCOBL3 positively regulates wheat defense against BYDV-GAV by modulating callose accumulation at PDs. Interestingly, TaCOBL3 interacts with the wheat homolog of PDLP5, a conserved key regulator of PD permeability in higher plants. Silencing TaPDLP5 attenuates the elevated BYDV-GAV defense conferred by overexpression of TaCOBL3 in wheat. Furthermore, transient expression of TaCOBL3 promotes callose accumulation and lowers PD permeability in tobacco cells, and these effects are largely compromised when tobacco PDLP5 is silenced. Notably, BYDV 17K MP weakens the interaction between TaCOBL3 and TaPDLP5 and inhibits their callose-binding activities. Finally, silencing of tobacco NbCOBL3 reduces callose content and attenuates host defense against two tobraviruses, one potexvirus, and one hordeivirus. Overall, our study reveals a previously unknown role of COBRA-like proteins in PMAD and provides insight into how a plant viral MP sabotages PMAD by perturbing the COBL3-PDLP5 interaction to facilitate virus spread through PDs. The conserved COBL3 gene may be a valuable target for engineering of broad-spectrum antiviral resistance in crop plants.

COBRA-like protein↗

PubMed2000

Detection of multiple potato viruses using an oligo(dT) as a common cDNA primer in multiplex RT-PCR.

A novel usage of multiplex reverse transcription polymerase chain reaction (m-RT-PCR) for simultaneous detection of multiple viruses is reported. By use of an oligo(dT), as a common primer, nearly full-length cDNAs can be synthesized. Furthermore, combining an oligo(dT) primer with a specific antisense primer can be used to simultaneously prime reverse transcription of both polyadenylated and non-polyadenylated RNAs. Four viral genera including five potato viruses [(carlavirus (PVS), polerovirus (PLRV), potexvirus (PVX), potyvirus (PVA and PVY))] and a viroid genus including a viroid genome (pospiviroid (PSTVd)) were used to develop various formats of m-RT-PCR. In artificially created viral RNA mixtures, all six RNA pathogens were detected successfully by uniplex- and m-RT-PCR. In naturally infected field grown tubers, m-RT-PCR detected infection of two to three viruses, which were present in the tubers.

DNA, Complementary↗

PubMed2002

Analysis of putative interactions between potyviral replication proteins and plant retinoblastoma proteins.

Sequence comparisons suggest that the RNA-dependent RNA polymerase (NIb) of potyviruses and bymoviruses, as well as the viral polymerase of potexviruses may contain a putative retinoblastoma protein (pRb) binding motif. The possibility that the potyviral NIb may function in the nucleus through interactions with plant pRb-related (RBR) proteins, and the modifications of the cell cycle was investigated by a combination of mutagenesis of the NIb and yeast two-hybrid system (YTHS). Mutation of a highly conserved glutamic acid residue in the putative pRb-binding motif of the NIb had no detectable phenotypic effect on replication of Potato virus A (PVA). Furthermore, the NIb proteins from Potato virus V and PVA failed to interact with maize or tobacco RBR proteins in yeast. Although the conservation of the motif for pRb interaction in plant RNA viruses is intriguing, these proteins from plant RNA viruses appear not to interact with plant RBR proteins.

DNA-Directed RNA Polymerases↗