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PubMed2001

Characterization of the AdoMet-dependent guanylyltransferase activity that is associated with the N terminus of bamboo mosaic virus replicase.

Bamboo mosaic virus (BaMV), a member of the potexvirus group, infects primarily members of the Bambusoideae. Open reading frame 1 (ORF1) of BaMV encodes a 155-kDa polypeptide that has long been postulated to be a replicase involved in the replication and formation of the cap structure at the 5' end of the viral genome. To identify and characterize the enzymatic activities associated with the N-terminal domain of the BaMV ORF1 protein, the intact replicase and two C-terminally truncated proteins were expressed in Saccharomyces cerevisiae. All three versions of BaMV ORF1 proteins could be radiolabeled by [alpha-(32)P]GTP, which is a characteristic of guanylyltransferase activity. The presence of S-adenosylmethionine (AdoMet) was essential for this enzymatic activity. Thin-layer chromatography analysis suggests that the radiolabeled moiety linked to the N-terminal domain of the BaMV ORF1 protein is m(7)GMP. The N-terminal domain also exhibited methyltransferase activity that catalyzes the transfer of the [(3)H]methyl group from AdoMet to GTP or guanylylimidodiphosphate. Therefore, during cap structure formation in BaMV, methylation of GTP may occur prior to transguanylation as for alphaviruses and brome mosaic virus. This study establishes the association of RNA capping activity with the N-terminal domain of the replicase of potexviruses and further supports the idea that the reaction sequence of RNA capping is conserved throughout the alphavirus-like superfamily of RNA viruses.

Amino Acid Sequence↗

PubMed2005

Molecular characterization of banana virus X (BVX), a novel member of the Flexiviridae family.

A novel virus was identified in banana (Musa spp). Analysis of the last 2917 nucleotides of its positive strand genomic RNA showed five open reading frames corresponding, from 5' to 3', to a truncated ORF coding for a replication-associated protein, three ORFs coding for a movement-associated triple gene block (TGB) and a capsid protein (CP) gene. This genome organization is similar to that of some members of the Flexiviridae family such as potexviruses and foveaviruses. This virus was named Banana virus X (BVX). Comparative sequence analysis showed that BVX is only distantly related to other members of the Flexiviridae family, in which it appears to define a new genus. BVX produces defective RNAs derived from its genomic RNA by non-homologous recombination. Three distinct pairs of donor/acceptor recombination sites involving short direct nucleotide repeats were characterized, accounting for deletions of 1268, 1358 and 1503 nucleotides. Contrary to the situation encountered for Potexviruses, these recombination sites are located within the TGB1 and CP genes and result in a truncated TGB1 protein.

Capsid Proteins↗

PubMed1998

Foveavirus, a new plant virus genus.

Foveavirus is a novel genus of plant viruses with helically constructed filamentous particles ca. 800 nm long, typified by apple stem pitting virus (ASPV). Virions do not contain lipids or carbohydrates, have a positive sense, single-stranded, polyadenylated RNA genome 8.4 to 9.3 kb in size, and a single type of coat protein with a size of 28 to 44 kDa. The genome of definitive viral species is made up of five ORFs encoding respectively, the replication-related proteins (ORF 1), the putative movement proteins (ORF 2 to 4, constituting the triple block gene), and the coat protein (ORF 5). Virions accumulate in the cytoplasm, where replication is likely to occur with a strategy comparable to that of potexviruses, based on direct expression of the 5'-proximal ORF, and expression of downstream ORFs through subgenomic RNAs. No vector is known. Virus transmission is by grafting, and dispersal is through infected propagating material. The genome structure and organization (i.e., number and order of genes) closely resembles that of the genera Potexvirus, Carlavirus and Allexvirus, but ORF 1 and the coat protein cistron (ASPV only) are significantly larger.

Open Reading Frames↗

PubMed1989

Partial nucleotide sequence of potato virus M RNA shows similarities to protexviruses in gene arrangement and the encoded amino acid sequences.

The nucleotide sequence of the 3'-proximal 2630 nucleotides of potato virus M (PVM) genomic RNA was determined. The sequenced region contained five long open reading frames (ORFs). The ORF nearest to the 3'-terminal pol(A) tail corresponds to a polypeptide of Mr 10,848. This ORF is preceded by one which encodes a protein of Mr 33,906 (34K) which has an amino acid sequence that is very similar in its carboxyterminal part to that of the coat proteins of some potexviruses. Three other ORFs encoding polypeptides of Mr 24,615, 11,983 and 6739 are present in the region 5' to the 34K protein gene. There is extensive similarity between these proteins and the corresponding proteins encoded by the conserved triple gene block in the RNA of potexviruses.

Amino Acid Sequence↗

PubMed1989

Nucleotide sequence of the 3'-terminal region of clover yellow mosaic virus RNA.

The nucleotide sequence of the 3'-terminal region of clover yellow mosaic virus RNA determined from cDNA clones contains one major open reading frame (ORF) encoding a protein with an Mr of 28,093 (28.1 K). A smaller ORF, in frame with the major one, is also present and encodes a 23.5K protein which is similar in size to the capsid protein of the virus and has several sequence similarities with the coat proteins of four other potexviruses. The smaller ORF is probably used for the expression of the coat protein because the capsid subgenomic mRNA probably does not include the AUG of the 28.1K protein. Comparison of the amino acid sequences of the coat proteins of five potexviruses revealed a large number of identical and conservative replacements of amino acid residues.

Amino Acid Sequence↗

PubMed1989

Nucleotide sequence of papaya mosaic virus RNA.

The RNA genome of papaya mosaic virus is 6656 nucleotides long [excluding the poly(A) tail] with six open reading frames (ORFs) more than 200 nucleotides long. The four nearest the 5' end each overlap with adjacent ORFs and could code for proteins with Mr 176307, 26248, 11949 and 7224 (ORFs 1 to 4). The fifth ORF produces the capsid protein of Mr 23043 and the sixth ORF, located completely within ORF1, could code for a protein with Mr 14113. The translation products of ORFs 1 to 3 show strong similarity with those of other potexviruses but the ORF 4 protein has only limited similarity with the other potexvirus ORF 4 proteins of 7K to 11K.

Amino Acid Sequence↗

PubMed1991

The entire nucleotide sequence of foxtail mosaic virus RNA.

The nucleotide sequence of the RNA genome of foxtail mosaic virus (FMV), a member of the potexvirus family, is 6151 nucleotides long, exclusive of a poly(A) tail. The RNA contains five principal open reading frames (ORFs), designated from the 5' terminus as encoding proteins with Mr values of 152.3K (ORF1), 26.4K (ORF2) which overlaps an 11.3K (ORF3) product, 5.8K (ORF4) which overlaps a 28.8K readthrough protein (ORF5A) which leads into the coat protein cistron of 23.7K (ORF5). The sizes and composition of the proteins encoded by the ORFs are generally similar to those found in other potexviruses; the least similar is the coat protein which nonetheless retains apparently critical consensus regions. The 5' terminus of the previously reported 0.9 kb subgenomic (sg) RNA was determined by S1 nuclease mapping and shown to begin with the sequence GAAGA, 43 nucleotides upstream from the first nucleotide of the coat protein initiation codon. The positions of the 5' end of this sgRNA and of that deduced from the nucleotide sequence for a 1.9 kb sgRNA are entirely consistent with the previously published sizes of these sgRNAs.

Amino Acid Sequence↗

PubMed1993

Nucleotide sequence of the 7 K gene of Helenium virus S.

The sequence of 380 nucleotides upstream of the start codon of the open reading frame (ORF) of the coat protein of the carlavirus Helenium virus (HelVS) was determined from cloned cDNA. This portion of the viral RNA contained one complete ORF encoding a protein of 7 K which had homology with similar sized proteins from other members of the carla- and potexvirus groups. Sequence data was also obtained beyond the start codon of the 7 K ORF into what was presumed to be the 12 K protein gene of the previously identified triple gene block of carla- and potexviruses. Significant sequence similarity of 46.3% and 41.6% was evident at the amino acid level with the equivalent regions of the 12 K proteins of potato virus S, Andean strain (PVSA) and potato virus M (PVM), respectively, with 25.4% similarity detected with the equivalent region of potato virus X (PVX).

Amino Acid Sequence↗

PubMed1997

Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation.

The putative subgenomic RNA (sgRNA) promoter regions upstream of the potato virus X (PVX) triple block and coat protein (CP) genes contain sequences common to other potexviruses. The importance of these sequences to PVX sgRNA accumulation was determined by inoculation of Nicotiana tabacum NT1 cell suspension protoplasts with transcripts derived from wild-type and modified PVX cDNA clones. Analyses of RNA accumulation by S1 nuclease digestion and primer extension indicated that a conserved octanucleotide sequence element and the spacing between this element and the start-site for sgRNA synthesis are critical for accumulation of the two major sgRNA species. The impact of mutations on CP sgRNA levels was also reflected in the accumulation of CP. In contrast, genomic minus- and plus-strand RNA accumulation were not significantly affected by mutations in these regions. Studies involving inoculation of tobacco plants with the modified transcripts suggested that the conserved octanucleotide element functions in sgRNA accumulation and some other aspect of the infection process.

Base Sequence↗

PubMed1998

Coat protein interactions involved in tobacco mosaic tobamovirus cross-protection.

To investigate the molecular role of the tobacco mosaic tobamovirus (TMV) coat protein (CP) in conferring cross-protection, a potato X potexvirus (PVX) vector (S. Chapman, Plant J. 2, 549-557, 1992) was used to systemically express a set of TMV mutant CPs in Nicotiana benthamiana prior to challenge inoculation with TMV. PVX-expressed wild-type TMV CP delayed TMV accumulation for up to 2 weeks compared to unprotected plants or plants preinfected with the unmodified PVX vector. Similar delays in TMV accumulation were obtained using TMV CPs that were deficient in virion formation but competent to assemble into helical aggregates. In contrast, TMV CPs that were incapable of helical aggregation or unable to bind viral RNA did not delay the accumulation of TMV. Furthermore, TMV CPs with enhanced intersubunit interactions that favor helical aggregation produced significantly greater delays in the accumulation of challenge TMV than obtained from the wild-type CP. Thus the capabilities of TMV CP to interact with viral RNA and self-associate in a helical fashion appear to be essential to its ability to confer protection. Taken together, these findings support a model for CP-mediated resistance in which the protecting CP recoats the challenge virus RNA as it disassembles.

Capsid Proteins↗

PubMed1999

Evidence for two nonoverlapping functional domains in the potato virus X 25K movement protein.

To study subdomain organization of the potato virus X (PVX) movement protein (MP) encoded by the first gene in the triple gene block (TGB), we mutated the 25-kDa TGBp1 protein. The N-terminal deletion of the helicase motifs I, IA, and II resulted in loss of the ATPase activity and RNA binding. A frameshift mutation truncating the C-terminal motifs V and VI gave rise to increase of the TGBp1 ATPase activity and had little effect on RNA binding in vitro. Fusions of the green fluorescent protein with 25-kDa MP and its derivative lacking motifs V-VI exhibited similar fluorescence patterns in epidermal cells of Nicotiana benthamiana leaves. Cell-to-cell movement of the 25K-deficient PVX genome was not complemented by the TGBp1 of Plantago asiatica mosaic potexvirus (PlAMV) but was efficiently complemented by a chimeric TGBp1 consisting of the N-terminal part of PlAMV protein (motifs I-IV) and the PVX-specific C-terminal part (motifs V-VI). These results suggest that NTP hydrolysis, RNA binding, and targeting to the specific cellular compartment(s) are associated with the N-terminal domain of the TGBp1 including the helicase motifs I-IV and that the C-terminal domain is involved in specific interactions with other virus proteins.

Adenosine Triphosphatases↗

PubMed2000

The movement protein-triggered in situ conversion of potato virus X virion RNA from a nontranslatable into a translatable form.

Plant virus-encoded movement protein(s) (MP), and for many viruses the coat protein (CP), is required to mediate viral spread between plant cells via plasmodesmata (PD). Most probably, the genomic RNA of potexviruses moves through PD as assembled virions and/or as ribonucleoprotein complexes containing the CP and 25-kDa MP. Here we report that encapsidated potato virus X (PVX) virion RNA, which is nontranslatable in a cell-free protein synthesizing system, can be converted into a fully translatable form after interaction of intact PVX particles with the PVX 25-kDa MP. The 25-kDa MP molecules bind selectively to only one extremity of the viral particle (that presumably contains the 5' end of the genomic RNA). The process of complex formation is ATP-independent; i.e., the ATPase activity of the 25-kDa MP is not involved in the binding of the MP to PVX virion.

Plant Viral Movement Proteins↗

PubMed2001

Trans-complementation of long-distance movement of White clover mosaic virus triple gene block (TGB) mutants: phloem-associated movement of TGBp1.

The triple gene block proteins (TGBp1-3) and coat protein (CP) of potexviruses are required for cell-to-cell movement. Both cell-to-cell and long-distance movement of White clover mosaic virus in which individual, combinations, or all movement functions were mutated could be rescued by transgenic Nicotiana benthamiana expressing complementary viral products. To address the importance of TGB functions in vascular transport, we used an experimental system based on grafted plants and trans-complementation, to define co-translocated viral products and the minimal requirements for viral exit from the plant vasculature. Evidence is presented that TGBp1 is co-translocated with viral RNA and CP and that, once viral RNA is loaded into the phloem translocation stream, it can exit in sink tissues and replicate in the absence of TGBp2-3. These results are discussed in the context of the recent finding that TGBp1 can mediate the suppression of signaling involved in systemic gene silencing.

Capsid↗

PubMed2002

RNA helicase activity of the plant virus movement proteins encoded by the first gene of the triple gene block.

Cell-to-cell and long-distance transport of some plant viruses requires coordinated action of three movement proteins encoded by triple gene block (TGB). The largest of TGB proteins, TGBp1, is a member of the superfamily I of DNA/RNA helicases and possesses a set of conserved helicase sequence motifs necessary for virus movement. A recombinant His-tagged form of TGBp1 of two hordeiviruses and potato virus X, a potexvirus, produced in Escherichia coli had unwinding activity on a partially duplexed RNA, but not DNA substrate. The helicase activity of these proteins was dependent on Mg2+ and ATP. The isolated C-terminal half of the PSLV TGBp1 retaining all helicase motifs was also able to unwind RNA duplex.

Adenosine Triphosphatases↗

PubMed2002

Complete sequence of the Pepino mosaic virus RNA genome.

We have determined the complete nucleotide sequence (Accession No. AF484251) of the Pepino mosaic virus (PepMV) RNA genome. PepMV is the etiological agent of a new disease which affects tomato crops in Europe and North America. The PepMV genome consists of one single stranded positive sense RNA 6410 nt long that contains five open reading frames (ORFs). ORF 1 is the putative RNA dependent RNA polymerase (RdRp), as it has the characteristic methyltransferase, NTP-binding and polymerase motifs. ORF 2 to 4 form the PepMV triple gene block. ORF 5 codes for the capsid protein. Two short untranslated regions flank the coding regions and there is a poly(A) tail at the 3'end of the genomic RNA. Thus, the genome organization of PepMV is that of a typical member of the genus Potexvirus. The nucleotide sequence obtained shares an overall 99% identity with the genomic RNA of a PepMV isolate from UK which has been partially sequenced. Protein coded by ORF4 is the least conserved between both isolates (95% amino acid identity), whereas proteins coded by ORF3 and ORF5 are identical.

Base Sequence↗

PubMed2002

Nucleotide sequence, genome organisation and phylogenetic analysis of Indian citrus ringspot virus. Brief report.

The sequence of the single-stranded RNA genome of Indian citrus ringspot virus (ICRSV) consists of 7560 nucleotides. It contains six open reading frames (ORFs) which encode putative proteins of 187.3, 25, 12, 6.4, 34 and 23 kDa respectively. ORF1 encodes a polypeptide that contains all the elements of a replicase; ORFs 2, 3 and 4 compose a triple-gene block; ORF5 encodes the capsid protein; the function of ORF6 is unknown. Phylogenetic analysis of the complete genome and each ORF separately, and database searches indicate that ICRSV, though showing some similarities to potexviruses, is significantly different, as in the presence of ORF6, the genome and CP sizes, and particle morphology. These differences favour its inclusion in a new virus genus.

Base Sequence↗

PubMed2002

Molecular studies of the synergistic interactions between plum pox virus HC-Pro protein and potato virus X.

Helper component proteinase (HC-Pro) is a multifunctional viral protein involved in vection and movement of potyvirus; suppression of host post-transcriptional gene silencing reaction; and synergism of potyvirus with other viruses, notably potexvirus. When the HC-Pro of plum pox potyvirus (PPV) was transiently expressed in N. benthamiana and N. clevelandii plants via potato virus X (PVX) vector, a highly synergistic response of leaf necrosis or plant death, was observed in PVXHC-infected plants. However, when mutations were introduced into the highly conserved "PTK" and "KITC" motifs of HC-Pro, known for their involvement in protein/protein interaction during aphid-mediated transmission of potyvirus, the resulting change of amino acid residue from lysine (K) to glutamic acid (E) in the "KITC" motif had no obvious influence.

Amino Acid Substitution↗

PubMed2000

The open reading frame 5A of foxtail mosaic virus is expressed in vivo and is dispensable for systemic infection.

Infectious transcripts were successfully derived from full-length cDNA clones of foxtail mosaic potexvirus (FoMV). Full-length clones were constructed by RT-PCR whereby 5' and 3' genomic segments of 2.7 and 3.4 kb, respectively, were ligated into Bluescript II KS. The in vitro RNA transcripts were infectious to moncotyledonous (barley) and dicotyledonous (Chenopodium amaranticolor) plant species. Individual mutation studies on clones of each of the five major ORFs confirmed predicted gene function for the polymerase, TGB (triple gene block), and coat protein (CP) genes. Protoplast studies on expression of a unique open reading frame, ORF 5A, which initiates 143 nts upstream of the CP before it "reads through" the CP, revealed that the 5A protein was produced in vivo. Mutation analysis of the 5A ORF indicated, however, that it was not required for either replication or for productive infection of plants. However, the nucleic acid sequences encoding the extended CP segment were shown to be important for CP expression. Additional mutations in 5A had no effect on FoMV replication in protoplasts but rendered the virus noninfectious to plants. A correlation with diminished CP production from both mutant clones implies that synthesis of subgenomic CP mRNA was compromised, and this limited systemic infection.

3' Untranslated Regions↗