Sequences of the three coat protein genes of a Malaysian isolate of rice tungro spherical virus reveal a close relationship to the Philippine isolate

Coat protein genes CP1, CP2 and CP3 of an isolate (MaP1) of rice tungro spherical virus (RTSV) from Malaysia were isolated, cloned and sequenced. Comparative analysis indicated that MaP1 isolate is closely related to the Philippine isolate.

Promoter elements required for phloem-specific gene expression from the RTBV promoter in rice

Previous studies indicated that a DNA fragment comprising nucleotides (nt) -164 to +45 of the RTBV promoter is sufficient to drive phloem-specific expression of a reporter gene in transgenic rice plants. In addition, two potential cis elements, Box I (nt -3 to +5) and Box II (nt -53 to -39) were identified by DNA-protein interaction assays. In this study, the results of further in vivo studies involving mutagenesis of selected DNA sequences and analysis of expression of a reporter gene in transgenic rice plants revealed that, in addition to Box I and Box II, other elements are required for phloem-specific gene expression, among which are a direct repeat (ASL Box, nt -98 to -79) and a GATA motif (nt -143 to -135). All the these elements bind rice nuclear factors specifically, and mutations of the elements were identified that resulted in loss-of-competition in electrophoretic mobility shift assays. A DNA fragment comprising nt -164 to -32, which contains Box II, the ASL Box and the GATA motif, conferred phloem-specific reporter gene expression independent of Box I when fused to a heterologous CaMV 35S minimal promoter and introduced to transgenic rice plants. Studies that introduced point mutations suggested that in the context of the -103 to +45 promoter fragment, Box II and the ASL Box act synergistically to confer tissue-specific gene expression. Similar studies in the -164 to +45 promoter fragment indicated that the -164 to -103 region, which includes the GATA motif, contains sequences that are functionally redundant with those in the -103 to -32 region, including the ASL Box and Box II. It is concluded that these regions act additively to direct phloem-specific gene expression.

Details of the arrangement of the outer capsid of rice dwarf phytoreovirus, as visualized by two-dimensional crystallography

Two-dimensional crystals were obtained from purified P8, an outer capsid protein of rice dwarf phytoreovirus. A filtered image of the two-dimensional crystal, in combination with the results of biochemical analysis, revealed the unit formation of the capsid protein, a capsomere structure, which appeared to be an approximately equilateral triangle with sides of approximately 6 nm and which was composed of a trimer of P8 protein. Details of the arrangements of the outer capsid of the virus are described.

The loss of outer capsid protein P2 results in nontransmissibility by the insect vector of rice dwarf phytoreovirus

A transmission-defective (TD) isolate of rice dwarf phytoreovirus lacked the ability to infect cells when derived from the virus-free insect vector Nephotettix cincticeps. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified virus showed that among six structural proteins, the P2 outer capsid protein (encoded by genome segment S2) was absent from the TD isolate, whereas all six proteins were present in the transmission-competent (TC) isolate. P2 was not detected on immunoblots of rice plants infected with the TD isolate. Genome segment S2 and its transcript were detected in both TD and TC isolates. Sequence analysis of the S2 segment of the TD isolate revealed the presence of a termination codon due to a point mutation in the open reading frame, which might explain the absence of P2 in the TD isolate. These results demonstrate that the P2 protein is one of the factors essential for infection by the virus of vector cells and, thus, influences transmissibility by vector insects.

Rice tungro bacilliform virus open reading frames II and III are translated from polycistronic pregenomic RNA by leaky scanning

Posttranscriptional components of the gene expression mechanism of rice tungro bacilliform virus (RTBV) were studied in transiently transfected protoplasts. RTBV translates several open reading frames from a polycistronic mRNA by leaky scanning. This mechanism is supported by the particular sequence features of the corresponding genome region and does not require a virus-encoded transactivator.

RF2a, a bZIP transcriptional activator of the phloem-specific rice tungro bacilliform virus promoter, functions in vascular development

Rice tungro bacilliform virus (RTBV) replicates only in phloem cells in infected rice plants and its promoter drives strong phloem-specific reporter gene expression in transgenic rice plants. We isolated a cDNA encoding a basic leucine zipper (bZIP) protein, RF2a, which binds to the Box II cis element that is important for expression from the promoter. RF2a, which stimulates Box II-dependent transcription in a homologous in vitro transcription system, accumulates in nuclei of phloem and certain other cell types in shoots, but is found at only very low levels in roots. Transgenic antisense plants in which RF2a accumulation was suppressed had normal roots but stunted, twisted leaves with small, disorganized vascular bundles, an enlarged sclerenchyma and large air spaces. We propose that the RTBV promoter exploits a host transcription factor that is critical for leaf tissue differentiation and vascular development for its expression.

The proteins encoded by rice grassy stunt virus RNA5 and RNA6 are only distantly related to the corresponding proteins of other members of the genus Tenuivirus

The genome of rice grassy stunt virus (RGSV) consists of six RNA segments. The nucleotide (nt) sequences of the two smallest segments, RNAs 5 and 6, were determined and found to comprise 2704 and 2584 nt, respectively. The 5'- and 3'-terminal sequences of both RNAs were identical over a length of 21 nt and could potentially form a panhandle-like structure due to intramolecular complementarity. Each RNA segment contained a virus (v) sense open reading frame (ORF) in the 5'-proximate region, and a virus complementary (vc) ORF in the 3'-proximate region, indicating an ambisense coding strategy. The protein encoded by the ORF on the vc strand of RNA5 was identified as the viral nucleocapsid protein (M(r) 35927). The ORF on the v strand of RNA6 encoded a protein of M(r) 20581 which represented the major nonstructural protein, previously shown to be produced in RGSV-infected rice tissues. The predicted proteins encoded by RGSV RNAs 5 and 6 were only distantly similar in sequence to the four proteins encoded by RNAs 3 and 4 of other viruses belonging to the genus Tenuivirus. These low sequence similarities, together with the apparently distinct number of genome segments, set RGSV apart from the other tenuiviruses and indicate that it should be placed in a taxonomically separate genus.

Plant ribosome shunting in vitro

It has been proposed that cauliflower mosaic virus 35S RNA with its 600 nt long leader uses an unusual translation process (the translational shunt). A wheat germ in vitro translation assay was used to improve the study of this mechanism. Deletions, the introduction of stable stem-loop structures, and the inhibitory effect of antisense oligonucleotides on gene expression were used to determine the roles of various parts of the leader. It was found that the 5'- and 3'-ends of the leader are absolutely required for translation whereas the middle part is apparently dispensable. These results confirm the data already reported from transient expression experiments with protoplasts. However, the in vitro data suggest in contrast to protoplast experiments that only two relatively short regions at both ends, approximately 100 nt each, are required. The in vitro system provides tools for further studying the shunt model at the molecular level and for examining the involvement of proteins in this mechanism. Shunting was also found to occur with the rice tungro bacilliform virus leader. As wheat is neither a host plant of cauliflower mosaic virus nor rice tungro bacilliform virus, the shunt seems to be host independent, a finding that deviates from earlier studies in protoplasts.

Molecular cloning, sequencing, functional analysis and expression in E. coli of major core protein gene (S3) of rice dwarf virus Chinese isolate

The complete nucleotide sequence of major core protein gene (segment S3) of rice dwarf virus (RDV) Chinese isolate was determined after cDNA cloning from the viral genomic RNA. Sequence analysis showed that the cloned fragment is 3195 bp in length and contains a single open reading frame (ORF), encoding the major core protein (P3) which M(r) of 114 K. The nucleotide and deduced amino acid sequences of S3 of this isolate share significant homology (94.1% and 97%, respectively) with those of S3 of the Japanese isolate. At the amino acid level, P3 of RDV Chinese isolate shares significant homology with P3 of rice gall dwarf virus (RGDV), significant regional homology with the rotavirus penetration, and homology with spheroidin of amsacta entomopoxvirus (SPH), which is the major protein of the occlusion body, with clp-like ATP-dependent protease binding subunit and with ATP-dependent protease ATP-binding subunit. Amino acid sequence analysis also showed that P3 contains RNA-dependent RNA polymerase (RDRP) motif-like elements such as DXXXD, SGXXXXXXN, GDD and ENXXXY. These results may suggest that P3 is a multifunctional protein which plays very important roles in the virus structure formation, virus replication and penetration processes. The full length cDNA sequence of RDV S3 and a partial one which covers nt 1004-3195 were cloned into bacterial expression vector pTrcHisB for expression. The full length cDNA sequence failed to be expressed in E. coli, but the partial sequence was successfully expressed there as confirmed by the Western blot analysis. Further analysis of RDV P3 is under way.

Characterization of the in vitro activity of the RNA-dependent RNA polymerase associated with the ribonucleoproteins of rice hoja blanca tenuivirus

An RNA-dependent RNA polymerase (RdRp) activity associated with the ribonucleoproteins of rice hoja blanca tenuivirus (RHBV) was detected and analyzed. Conditions for in vitro RNA synthesis and for coupled RNA synthesis-translation of RHBV were established. In both cases, synthesis of the viral and viral complementary genomic and subgenomic RNA3 and RNA4 were observed, demonstrating that both transcription and replication occurred. Though coupling of RNA synthesis to translation allowed efficient translation of the newly synthesized subgenomic RNAs, studies of the effect of various inhibitors of protein synthesis revealed that RNA synthesis was independent of translation. Primer extension experiments demonstrated that in the presence of capped exogenous RNAs, a stretch of 10 to 16 nonviral nucleotides was added to the 5' end of a population of newly synthesized viral complementary RNA4. It appears that in addition to RdRp activity, RHBV-associated protein(s) also possessed cap-snatching capacity.

Plant regeneration of indica rice (Oryza sativa) cultivars from mature embryo-derived calli

Plant regeneration from seven-week-old callus cultures derived from mature embryos of several indica rice cultivars was achieved with frequencies of morphogenic calli from 10 to 47%. Three media were tested both for callogenesis and plant regeneration. For 3 of the 7 genotypes examined, the best combination of media for plant regeneration was Murashige & Skoog basal medium: MSC (callogenesis) and MSR (regeneration). The rates of callogenesis were not related to the capacity for plant regeneration. Two genotypes CR-1113 and CR-5272 produced the highest number of regenerated green plants. The results of this study suggest that genetic differences could be directly linked to the ability to regenerate in these plant cultivars.

Characterization of rice yellow mottle virus isolates in Sudano-Sahelian areas

The use of a panel of polyclonal antisera and monoclonal antibodies (MAbs) raised against West African isolates of rice yellow mottle virus (RYMV) in ELISA resulted in separation of 73 RYMV isolates into three distinct serogroups. Using a set of differential rice varieties, the serogroups could be correlated to two RYMV pathotypes. A relationship was found between serological properties of the RYMV isolates and their probable ecological origin. It was concluded that RYMV isolates originating in closely related agroecological zones displayed variability in coat protein and pathogenicity. This should be taken into account in developing tolerant or resistant rice varieties.

Genome segment 5 of rice ragged stunt virus encodes a virion protein

The complete nucleotide sequence of the genome segment 5 (S5) of a Thai isolate of rice ragged stunt virus (RRSV) was determined. The 2682 nucleotide sequence contains a single long open reading frame capable of encoding a polypeptide with a molecular mass of approximately 91 kDa. Polypeptides encoded by various truncated cDNAs of S5 were expressed using the pGEX fusion protein vector and the highest level of fusion protein was obtained from a construct encoding a hydrophilic region of S5 protein. Antibodies raised against this fusion protein recognized a minor polypeptide, with a molecular mass of approximately 91 kDa, that was present in purified preparations of RRSV particles, infected insect vectors and infected rice plants. This indicates that RRSV S5 encodes a minor structural protein. Comparing the RRSV S5 sequence with sequences of other reoviruses did not reveal any significant sequence similarities.

Efficient transcription from the rice tungro bacilliform virus promoter requires elements downstream of the transcription start site

Elements downstream of the transcription start site enhance the activity of the rice tungro bacilliform virus (RTBV) promoter in protoplasts derived from cultured rice cells. This enhancer region was located to the first 90 nucleotides of the RTBV leader sequence. Within this region, at least two components which act together to enhance expression from the RTBV promoter could be identified. One is a position- and orientation-independent DNA element within a CT-rich region, and the other is a position-dependent element. Either element was found to be capable of acting independently on a heterologous promoter. The enhancer activity of the DNA element correlates with specific binding of nuclear proteins. Nuclear proteins also recognize an RNA transcript covering the first 90 nucleotides of the RTBV leader.

P2 protein encoded by genome segment S2 of rice dwarf phytoreovirus is essential for virus infection

Loss of infectivity to insect vector cell monolayers of rice dwarf phytoreovirus (RDV) after CCl4 treatment was associated with the removal of one of the viral proteins from the virus particles. This protein, encoded by genome segment S2 and thus named P2 protein, was located at the outer capsid of the virus particle. When RDV was treated with CCl4 for various times, the reduction in the amount of P2 protein and the loss of viral infectivity to vector cell monolayers were proportional to treatment time. RDV purified using CCl4 treatment thus lacking P2 protein, lost the ability to infect vector insects through feeding and consequently failed to be transmitted to plants. These results suggest that P2 protein is essential for RDV infection of the insect cells and may be related to transmission of the virus by the vector insect.

The M(r) 43K major capsid protein of rice ragged stunt oryzavirus is a post-translationally processed product of a M(r) 67,348 polypeptide encoded by genome segment 8

The nucleotide sequence of DNA complementary to rice ragged stunt oryzavirus (RRSV) genome segment 8 (S8) of an isolate from Thailand was determined. RRSVS8 is 1914 bp in size and contains a single large open reading frame (ORF) spanning nucleotides 23 to 1810 which is capable of encoding a protein of M(r) 67,348. The N-terminal amino acid sequence of a approximately 43K virion polypeptide matched to that inferred for an internal region of the S8 coding sequence. These data suggest that the 43K protein is encoded by S8 and is derived by a proteolytic cleavage. Predicted polypeptide sizes from this possible cleavage of S8 protein are 26K and 42K. Polyclonal antibodies raised against a maltose binding protein (MBP)-S8 fusion polypeptide (expressed in Escherichia coli) recognised four RRSV particle associated polypeptides of M(r) 67K, 46K, 43K and 26K and all except the 26K polypeptide were also highly immunoreactive to polyclonal antibodies raised against purified RRSV particles. Cleavage of the MBP-S8 fusion polypeptide with protease Factor X produced the expected 40K MBP and two polypeptides of apparent M(r) 46K and 26K. Antibodies to purified RRSV particles reacted strongly with the intact fusion protein and the 46K cleavage product but weakly to the 26K product. Furthermore, in vitro transcription and translation of the S8 coding region revealed a post-translational self cleavage of the 67K polypeptide to 46K and 26K products. These data indicate that S8 encodes a structural polypeptide, the majority of which is auto-catalytically cleaved to 26K and 46K proteins. The data also suggest that the 26K protein is the self cleaving protease and that the 46K product is further processed or undergoes stable conformational changes to a approximately 43K major capsid protein.

Immunological characterization of rice tungro spherical virus coat proteins and differentiation of isolates from the Philippines and India

Rice tungro spherical virus (RTSV) has an RNA genome of more than 12 kb with various features which classify it as a plant picornavirus. The capsid comprises three coat protein (CP) species, CP1, CP2 and CP3, with predicted molecular masses of 22.5, 22.0 and 33 kDa, respectively, which are cleaved from a polyprotein. In order to obtain information on the properties of these proteins, each was expressed in E. coli, purified as a fusion to the maltose-binding protein and used for raising a polyclonal antiserum. CP1, CP2 and CP3 with the expected molecular masses were detected specifically in virus preparations. CP3 is probably the major antigenic determinant on the surface of RTSV particles, as was shown by ELISA, Western blotting and immunogold electron microscopy using antisera obtained against whole virus particles and to each CP separately. In some cases, especially in crude extracts, CP3 antiserum detected several other proteins (40-42 kDa), which could be products of CP3 post-translational modification. No serological differences were detected between the three CPs from isolates from the Philippines, Thailand, Malaysia and India. The CP3-related 40-42 kDa proteins of the Indian RTSV isolate have a slightly higher electrophoretic mobility (42-44 kDa) and a different response to cellulolytic enzyme preparations, which allows them to be differentiated from south-east Asian isolates.

Effect of protectants in L-drying on the conformation and infectivity of rice dwarf phytoreovirus

Purified rice dwarf phytoreovirus preparations, after rehydration following drying without freezing (L-drying) and sucrose density gradient centrifugation, sedimented to the same position as untreated controls. Upon storage at 65 degrees C, virion conformation in L-dried preparations supplemented with 1% sucrose was maintained better than without additives. Moreover, during storage for 6 years at -70 degrees C, infectivity of L-dried preparations from crude extracts of infected rice plants containing 5% sucrose was higher than controls based on the number of count of infected foci on cell monolayers and transmission to rice seedlings by leafhopper of the vector Nephotettix cincticeps, which had been injected with such extracts.

Novel NTP binding property of rice dwarf phytoreovirus minor core protein P5

Rice dwarf phytoreovirus (RDV) mRNA synthesized from purified virion has a cap structure, m7GpppAm-, which suggests the presence of guanylyltransferase activity in the virion. We attempted to identify the enzyme involved in the cap formation by using a nucleoside triphosphate binding assay. Incubation of virion with [alpha-32P]GTP resulted in labeling of an 89-kDa protein that had not previously been identified in purified virus preparations. Interestingly this protein also covalently bound UTP and ATP, which is not a property of the known guanylytransferases. RDV particles catalyzed GTP-PPi, dGTP-PPi, ATP-PPi, and UTP-PPi exchange reactions. In SDS-polyacrylamide gel electrophoresis, the 89-kDa protein comigrated with the S5-coded protein, P5, which had been expressed by a baculovirus vector. Moreover, the labeled 89-kDa protein was precipitated by an antiserum against this recombinant RDV P5. Careful reinvestigation of purified virus particles by SDS-polyacrylamide gel electrophoresis and Western blotting analyses showed that they contained a small amount of P5 (<0.5% of the total protein) within the core. These results may suggest that the minor core protein of RDV, which is coded by S5, is a candidate guanylyltransferase, although the biological significance of its ATP and UTP binding activities remains largely unknown.

Position-dependent ATT initiation during plant pararetrovirus rice tungro bacilliform virus translation

The expression of the rice tungro bacilliform virus open reading frame I was studied in transiently transfected protoplasts. Expression occurs despite the presence of a long leader sequence and the absence of a proper ATG initiation codon. Translation is initiated at an ATT codon. The efficiency of initiation in rice protoplasts depends strongly on the mechanism by which ribosomes reach this codon. From the effects of scanning-inhibiting structures inserted into different leader regions, it can be deduced that this mechanism is related to the ribosome shunt described for cauliflower mosaic virus 35S RNA. The process delivers initiation-competent ribosomes to the region downstream of the leader and is so precise that only the second of two potential start codons only 12 nucleotides apart is recognized. The ATT codon that is used when it is present downstream of the leader is hardly recognized as a start codon by ribosomes that reach it by scanning.

Infection and replication of a planthopper transmitted virus-rice stripe virus in rice protoplasts

Rice stripe virus (RSV), a planthopper-transmitted virus, was inoculated into rice protoplasts, and a one-step growth curve was determined. The amount of virus in the protoplasts decreased following the inoculation, and then increased after 8 h. The replication of RSV reached its peak 20 h after inoculation. RSV replication in the inoculated protoplasts was further demonstrated by electron microscopy.

Variation in the genome of rice tungro bacilliform virus: molecular characterization of six isolates

The DNA genomes of isolates of rice tungro bacilliform virus from Bangladesh, India, Indonesia, Malaysia and Thailand were cloned and compared with that of the type isolate from the Philippines. Restriction endonuclease maps revealed differences between the isolates and cross-hybridization showed that they fell into two groups, those from the Indian subcontinent and those from south-east Asian countries. The genomes of isolates from the Indian subcontinent contained a deletion of 64 bp when compared with those from south-east Asia. The implications of this variation are discussed.

Detection of rice tungro bacilliform virus in field and glasshouse samples from India using the polymerase chain reaction

Rice tungro bacilliform virus (RTBV) together with rice tungro spherical virus (RTSV) is the causal agent for the rice tungro disease. A rapid technique was developed to detect RTBV DNA in the crude extract of freshly collected leaf samples by polymerase chain reaction (PCR). This technique can detect the viral DNA in 1000-fold diluted leaf extract. Detection has been possible in samples stored upto 5 days after the collection. This technique may have wide application for the field diagnosis of RTBV infection.

Genomic rearrangement in genome segment 12 of rice dwarf phytoreovirus

The genome segment 12 (S12) of rice dwarf phytoreovirus (RDV) isolated from the Philippines (RDV-P) and of a variant (RDV-S-6) of RDV severe strain (RDV-S) migrated abnormally slower during polyacrylamide gel electrophoresis than that of the isolate maintained at Hokkaido University (RDV-H). Nucleotide sequence analysis revealed that rearrangement had occurred in these segments, affecting the open reading frame. A polypeptide encoded by S12 (Pns12) of RDV-P had a duplication of 28 amino acids while 1/3 of the carboxyl terminus of Pns12 was deleted in RDV-S-6 by premature termination due to a frameshift. RDV-S is always present in plants infected with the RDV-S-6 variant, suggesting that Pns12 of RDV-S-6 is defective. On the other hand, Pns12 of RDV-P was expressed and appeared to be functional in infected cells in spite of the duplication, as demonstrated by immunoblot analyses using antibody raised against Pns12 expressed in Escherichia coli.