Synthetic oligonucleotide hybridization probes to diagnose hop stunt viroid strains and citrus exocortis viroid

Four species of synthetic oligonucleotide probes for the diagnosis of hop stunt viroid (HSV) and citrus exocortis viroid (CEV) were devised. Probe HSV-1 detected all the members of HSV group, such as HSV-hop, HSV-grapevine, HSV-cucumber, HSV-citrus and a viroid-like RNA isolated from plum trees affected by plum dapple fruit disease. Probe HSV-2 discriminated HSV-grapevine from the other members of HSV group. HSV-hop and HSV-grapevine consist of the same numbers of nucleotides, with only one nucleotide exchange. It was also shown that the two viroids were indistinguishable by their biological and physicochemical properties. However, by using probe HSV-2, HSV-hop and HSV-grapevine were apparently differentiated. Probe CEV-1 detected all the members of potato spindle tuber viroid (PSTV) group, such as PSTV, CEV and chrysanthemum stunt viroid (CSV). Probe CEV-2 discriminated CEV from the other members of PSTV group. It is thus emphasized that synthetic oligonucleotide probes are useful for the diagnosis of viroids and their related strains. It was discussed that the method can be used for the diagnosis of viruses and their related strains.

The synthesis and possible functions of virus-induced proteins in plants

Plants reacting hypersensitively to virus infection accumulate proteins that exert their activity in the cytoplasm, the cell wall or the intercellular space of the leaf. The function of a number of these proteins is described and the expression and structure of genes encoding the extracellular proteins is discussed.

Infectivity and complete nucleotide sequence of the genome of a South African isolate of maize streak virus

The complete infectious genome of a South African isolate of the geminivirus maize streak (MSV-S) has been cloned, characterized, and sequenced. Using an A. tumefaciens Ti plasmid delivery system, the cloned -2.7 kb single circular MSV component was shown to be necessary and sufficient for infection of maize. Based on sequence analysis of the infectious clone, MSV-S is highly homologous to the previously characterized Kenyan and Nigerian isolates. While the genomic organization of MSV-S has elements in common with each of these previously characterized isolates, it is identical to neither and its analysis addresses the discrepancies between them. The result is a somewhat simplified and unified picture of the viral genome, the structural organization of which is essentially identical to that of wheat dwarf virus.

Agrobacterium-mediated infectivity of cloned digitaria streak virus DNA

A monomeric clone of double-stranded DNA synthesized in vitro DNA of the geminivirus Digitaria streak (DSV) was subcloned as a tandem dimeric unit into a binary vector of Agrobacterium tumefaciens, creating a plasmid pDS2. Inoculation of digitaria sanguinalis with A. tumefaciens carrying pDS2 resulted in viral infection. The symptoms, virus particles, and DNA forms obtained were indistinguishable from those of a natural DSV infection of D. sanguinalis. Inoculations have also induced infections in Zea mays and Avena sativa. The sequence of the Agrobacterium-mediated infectious clone of DSV has been determined.

In vitro studies on the nucleocapsid-associated RNA polymerase of wheat rosette stunt virus

RNA-dependent RNA polymerase activity was detected in both virion and nucleocapsid preparations of wheat rosette stunt virus, a plant rhabdovirus. The presence of nonionic detergent such as Nonidet P40 was essential for activity in reaction mixtures containing virions. The polymerase product was proved to be single-stranded RNA. By two-step controlled dissociation of the nucleocapsids, four subviral fractions (L protein, NS-N-RNA complex, NS protein, and N-RNA complex) were prepared. None of these fractions showed RNA polymerase activity when assayed individually. In experiments combining the various fractions, RNA synthesis was observed only when the L and NS proteins and the N-RNA complex were present in reaction mixtures.

The use of filter hybridization techniques for the identification, differentiation and classification of plant viruses

In attempts to use dot-blot hybridization tests for the identification of viruses or for assigning them to a certain taxonomic group we found that hybridization signals may be given not only by the homologous virus, but also by heterologous viruses belonging to the same or different taxonomic groups. Possible reasons for this phenomenon, which was observed with uncloned as well as with cloned cDNAs, are discussed. Quantitative dot-blot hybridization tests with extracted viral RNAs proved to be very sensitive in differentiating closely related viruses which were barely distinguishable in serological tests. Estimates on the degree of homology between the RNAs of different viruses may be influenced by a number of experimental parameters, such as competition for the available cDNA between homologous and heterologous RNAs or homologous RNAs in different concentrations on the same sheet of nitrocellulose, saturation phenomena due to close packaging of highly concentrated RNA on the blot and, of course, stringency conditions during washing procedures. Taking these parameters into account we have reestimated the degree of homology between the RNAs of 5 tombusviruses. Our new data suggest that the order of sequence for the relationships among these 5 tombusviruses is similar to that proposed by Koenig and Gibbs (1986) on the basis of serological data.

Effect of beet necrotic yellow vein virus RNA composition on transmission by Polymyxa betae

Beet necrotic yellow vein virus (BNYVV) is naturally transmitted by the soil-borne fungus Polymyxa betae and usually remains confined to the roots of infected sugarbeets. In naturally infected sugarbeets the virion RNA always consists of four components which are uniform in size in different isolates but when BNYVV is propagated by mechanical inoculation to leaves of Chenopodium quinoa the two smallest RNA components, RNA-3 and -4, may undergo deletion or disappear from the isolate, suggesting that they are only essential for the natural mode of infection. To test this hypothesis, several C. quinoa isolates of BNYVV with different RNA-3 and -4 contents have been retransmitted to sugarbeet root via P. betae. The results show that the two isolates containing no detectable full-length RNA-3 and -4 are poorly transmitted and that cases of successful infection are associated with the reappearance of full-length RNA-3 and -4.

Nucleotide sequence of segment S10 of the rice dwarf virus genome

DNA complementary to the tenth largest (S10) of the 12 genome segments of rice dwarf virus (RDV) was cloned and its sequence was determined. This genome segment is 1319 nucleotides in length and has a single long open reading frame extending for 1059 nucleotides from the first AUG triplet (residues 27 to 29). The predicted translation product comprises 352 amino acids and has a mol. wt. of 39094. RDV transcripts synthesized in vitro have the same polarity as the plus strand of the genome. Terminal sequences were (+) 5' GGUA---UGAU 3' and (-) 3' CCAU---ACUA 5' which are similar to those of wound tumour virus RNA.

Molecular cloning and characterization of the gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A

The gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A was cloned and expressed in E. coli plasmid pUC8. Plasmid (pNC-1A.14.8) encoded M.CviBIII methylates adenine in TCGA sequences both in vivo in E. coli and in vitro. Transposon Tn5 mutagenesis localized the M.CviBIII functional domain to a 1.5 kbp region of pNC-1A.14.8 and also indicated that a virus promoter directs transcription of the gene in E. coli. The 2.1 kbp insert containing the M.CviBIII gene was sequenced and a single open reading frame of 1131 bp was identified within the domain determined by Tn5 mutagenesis. When the M.CviBIII gene was fused in-frame with the 19 amino-terminal codons of lacZ a 45 kD polypeptide was identified in maxicells as predicted by the DNA sequence. The M.CviBIII gene was not essential for virus replication since a virus M.CviBIII deletion mutant also replicated in Chlorella.

The cleavage site of the RsaI isoschizomer, CviII, is G decreases TAC

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Length, mass, and denaturation of double-stranded RNA molecules compared with DNA

The contour lengths of linear, double-stranded (ds) RNAs from mycovirus PcV and Pseudomonas bacteriophage phi 6 have been measured with samples prepared for the electron microscope from 0.05 to 0.5 M NH4Cl solutions. A linear dependence of contour length on the logarithm of ionic strength was found and compared with that of dsDNA (pBR322, linearized and open-circular forms). Conditions for molecular weight determinations of any natural dsRNA by electron microscopy have been established, and the method has been calibrated with phi 6 dsRNA of known nucleotide sequence. The results imply that dsRNA in 0.20 M NH4Cl solution has a rise per basepair of 0.271 nm, which is shorter than that in the A-conformation (4%) and in the A'-conformation (10%). The thermal behavior of dsRNA in terms of melting temperature and exhibition of fine structure of melting curves was found to be generally similar to that of dsDNA, as expected from the literature. Folding of dsRNA in ethanolic solution was similar to that of dsDNA. However, in contrast to dsDNA, coiled coils could not be induced by ethanol, which is consistent with dsRNA being stiffer than dsDNA. Concerning dsDNA, the results show that a contraction in rise per basepair by 0.1 nm is coupled with an increase in the winding angle between basepairs by 0.47 degrees, as qualitatively predicted by polyelectrolyte theory.

Segment-specific inverted repeats found adjacent to conserved terminal sequences in wound tumor virus genome and defective interfering RNAs

Defective interfering (DI) RNAs are often associated with transmission-defective isolates of wound tumor virus (WTV), a plant virus member of the Reoviridae. We report here the cloning and characterization of WTV genome segment S5 [2613 base pairs (bp)] and three related DI RNAs (587-776 bp). Each DI RNA was generated by a simple internal deletion event that resulted in no sequence rearrangement at the deletion boundaries. Remarkably, although several DI RNAs have been in continuous passage for more than 20 years, their nucleotide sequences are identical to that of corresponding portions of segment S5 present in infrequently passaged, standard, transmission-competent virus. The positions of the deletion breakpoints indicate that the minimal sequence information required for replication and packaging of segment S5 resides within 319 bp from the 5' end of the (+)-strand and 205 bp from the 3' end of the (+)-strand. The terminal portions of segment S5 were found to contain a 9-bp inverted repeat immediately adjacent to the conserved terminal 5'-hexanucleotide and 3'-tetranucleotide sequences shared by all 12 WTV genome segments. The presence of a 6- to 9-nucleotide segment-specific inverted repeat immediately adjacent to the conserved terminal sequences was found to be a feature common to all WTV genome segments. These results reveal several basic principles that govern the replication and packaging of a segmented double-stranded RNA genome.

[Difference in the mechanism of self-assembly in vitro in tobacco mosaic virus and potato virus X]

The effects of 254 nm UV-irradiation of tobacco mosaic virus (TMV) and potato virus X (PVX) RNA preparations on the RNA ability to self-assembly in vitro with the viral coat proteins were studied. It was found that while TMV RNA ability to assemble with the homologous protein is rapidly inactivated by the UV-irradiation, PVX RNA ability to be encapsidated by the PVX coat protein is quite resistant to the irradiation. More than that, the irradiation of TMV RNA with the dose strongly inhibiting its assembly with the homologous protein, did not result in any significant inhibition of this RNA ability to be coated with the PVX protein. The results testify to the profound differences in the mechanisms of RNA-protein interactions in the processes of self-assembly in vitro of tobamoviruses and potexviruses.

A defective interfering RNA that contains a mosaic of a plant virus genome

A symptom-modulating RNA associated with tomato bushy stunt virus (TBSV) was investigated with respect to physical and biological properties. Linear RNA of approximately 396 nucleotides was packaged in viral coat protein and was dependent on TBSV for replication. Coinoculation of the small RNA with TBSV resulted in the attenuation of TBSV-induced symptoms and depression of virus synthesis in whole plants. Nucleotide sequence analysis revealed that the symptom-modulating RNA was derived from 5', 3', and internal segments of the TBSV genome. The identification of this symptom-modulating RNA as a co-linear deletion mutant of the helper virus genome establishes it as the first definitive defective interfering RNA (DI RNA) to be identified in association with a plant virus.

Effect of Mg2+ ions on the in vitro translation of red clover mottle virus M RNA

Red clover mottle virus middle-component RNA was translated in rabbit reticulocyte lysate into two primary polypeptides with molecular weights of 95,000 and 105,000. The relative ratio of the two polypeptides synthesized was affected by Mg2+ concentration.

The nucleotide sequence of a geminivirus from Digitaria sanguinalis

The encapsidated single-stranded circular DNA of a geminivirus isolated from Digitaria sanguinalis has been sequenced. The data obtained are consistent with there being one DNA circle of 2701 nucleotides. Comparison of the nucleotide sequence with those of maize streak virus (MSV) and wheat dwarf virus showed 64 and 47% DNA homology, respectively. The sequence has four potential coding regions for proteins of greater than 10 kDa, two in the viral (+) sense and two in the complementary (-) sense. Each of these potential coding regions has a highly homologous counterpart among the seven open reading frames previously described for MSV. Virion DNA contained, in addition to the circular single-stranded DNA, a population of small DNA molecules similar to those associated with MSV particles. A comparison with MSV DNA of the region complementary to these small DNA molecules revealed conserved sequences, which may have a role in defining the limits of these primer-like molecules.

Structure of the M2 protein gene of sonchus yellow net virus

The nucleotide sequence of the gene immediately following the nucleocapsid protein gene of sonchus yellow net virus (SYNV), a plant rhabdovirus, is presented. Serological reactions of SYNV proteins with antibodies elicited by a fusion protein constructed from the sequenced gene indicate that this gene encodes an SYNV structural protein designated M2. The 5' end of the M2 protein mRNA appears to correspond to position 1700 relative to the 3' end of SYNV RNA, because an extension product that maps to this position was synthesized by reverse transcription of polyadenylated [poly(A)+] RNA from infected tobacco that had been primed with an SYNV-specific oligodeoxyribonucleotide. The 3' end of the gene encoding the M2 protein is defined by a recombinant DNA plasmid derived from poly(A)+ RNA from SYNV-infected plants. This plasmid contains an insert with a 3'-terminal region corresponding to a uridylate-rich sequence present at positions 2832 to 2836 on SYNV genomic (g) RNA. These data thus suggest that the M2 protein mRNA is 1132 nucleotides (NT) long, excluding the poly(A) tail, and consists of a 50-NT untranslated 5' region, a 1035-NT open reading frame (ORF), and a 47-NT untranslated 3'region. The ORF is capable of encoding a 345-amino acid protein with a calculated molecular weight of 38,332. A small region of the M2 protein appears to have some similarity to the phosphoproteins of other rhabdoviruses. An identical 14-NT region occurs at the two sequenced gene junctions on SYNV gRNA and shares homology with regions separating the genes of some animal rhabdoviruses.

The complete nucleotide sequence of tobacco rattle virus RNA-1

The complete nucleotide sequence of tobacco rattle virus (TRV) strain SYM RNA-1 was determined from a series of overlapping cDNA clones. cDNA prepared by primer extension was used to determine the exact 5' terminus. The RNA sequence was 6791 nucleotides in length and contained four open reading frames (ORFs). The ORF nearest the 5' terminus coded for a polypeptide of predicted mol. wt. 134,000 (134K) and terminated at an opal (UGA) stop codon. Readthrough of this stop codon would result in the production of a protein of 194K. The gene for a 29K polypeptide started one base beyond the 194K stop codon and, in turn, was followed by the gene for a 16K protein at the 3' end of RNA-1. Amino acid comparisons of the 194K protein with the putative replicase of tobacco mosaic virus showed three regions of strong homology, suggesting that the 134K and 194K proteins were similarly involved in virus replication. The 5' terminal sequences of both genome RNA species of TRV strains ORY, N5 and PRN together with that of SYM RNA-2 were also determined. Alignments of these sequences showed that there was a 22 base repeated sequence close to the 5' terminus in all these RNA species. It was also shown that the 5' terminus of RNA-1 was homologous with the same region in RNA-2.

Nucleotide sequence and secondary structure of apple scar skin viroid

The complete nucleotide sequence of apple scar skin viroid(ASSV) has been established, and a probable secondary structure is proposed. A single-stranded circular ASSV RNA consists of 330 nucleotides and can assume the rodlike conformation with extensive base-pairing characteristic of all the known viroids. ASSV shows low sequence homologies with other viroids and lacks the central conserved region. These indicate that ASSV should be allocated to a separate viroid group. However, homologous sequences with potato spindle tuber viroid(PSTV) in ASSV occur in limited and scattered regions of both viroids. These homologous regions fall within the particular domains in the viroid domain model which has been previously proposed by Keese and Symons(Proc. Natl. Acad. Sci. USA. 82, 4582-4586, 1985).

A nucleotide sequence rearrangement distinguishes two isolates of satellite tobacco ringspot virus RNA

Several strains of tobacco ringspot virus (TobRV) support the replication and encapsidation of satellite tobacco ringspot virus RNA (STobRV RNA). We have compared the nucleotide sequences of four STobRV RNAs, each initially associated with a different isolate of TobRV. A STobRV RNA from a geranium isolate of TobRV and STobRV RNA from the previously analyzed budblight isolate (J.M. Buzayan, W.L. Gerlach, G. Bruening, P. Keese, and A.R. Gould, 1986, Virology 151, 186-199) differed by a single nucleotide residue substitution. STobRV RNAs from TobRV isolates 62L and NC-87 have the same 360-residue nucleotide sequence. This sequence differs from that of the 359-nucleotide residue budblight STobRV RNA principally at locations 100 through 140. The differences between the two sequences in this region are consistent with a rearrangement of blocks of nucleotide residues. The two sequences can be folded with similar patterns of base pairing. All four STobRV RNAs share a sequence of eighty 5'-terminal and of twenty 3'-terminal residues, including the 5' hydroxyl group and 2':3'-cyclic phosphodiester group.

Identification of two messenger RNA cap binding proteins in wheat germ. Evidence that the 28-kDa subunit of eIF-4B and the 26-kDa subunit of eIF-4F are antigenically distinct polypeptides

Previous work has shown that eukaryotic initiation factor (eIF)-4B from wheat germ is a complex containing two subunits, 80 and 28 kDa, and eIF-4F from wheat germ is a complex containing two subunits, 220 and 26 kDa (Lax, S., Fritz, W., Browning, K., and Ravel, J. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 330-333). Here we show that both the 28-kDa subunit of eIF-4B and the 26-kDa subunit of eIF-4F cross-link to the 5' terminus of capped and oxidized satellite tobacco necrosis virus RNA in the absence of ATP and that the cross-linking of both polypeptides is inhibited by m7GDP. Several lines of evidence indicate that the 28-kDa and the 26-kDa cap binding proteins of eIF-4B and eIF-4F are antigenically distinct polypeptides. Rabbit polyclonal antibodies raised to intact eIF-4B or to the isolated 28-kDa subunit of eIF-4B react strongly with the 28-kDa subunit of eIF-4B on immunoblots, but show only a very weak reaction with the 26-kDa subunit of eIF-4F under the same conditions. In addition, a mouse monoclonal antibody was obtained that reacts strongly with the 26-kDa subunit of eIF-4F but does not react with the 28-kDa subunit of eIF-4B. Evidence is presented also which indicates that the higher molecular weight subunits of eIF-4B and eIF-4F are antigenically distinct. Rabbit polyclonal antibodies raised to intact eIF-4B or the isolated 80-kDa subunit inhibit eIF-4B-dependent polypeptide synthesis but do not inhibit eIF-4F-dependent polypeptide synthesis. Rabbit polyclonal antibodies raised to eIF-4F inhibit eIF-4F-dependent polypeptide synthesis but do not inhibit eIF-4B-dependent polypeptide synthesis.

The evolution of multicompartmental genomes in viruses

The genetic information of many viruses is divided between separately encapsidated nucleic acid molecules. A simple evolutionary model is constructed to explain this phenomenon. All multicompartmental viruses infect plants, and most are RNA viruses. The former fact may be due to the high transmission multiplicities enjoyed by plant viruses. The latter may be due to the low replication fidelity of RNA, although another explanation is also offered. The logic of the analysis is contrasted with that of previous explanations. In particular, this paper proceeds from a "selfish DNA" viewpoint. It is not necessary to suppose that the division of the genome fills any adaptive function for the virus. The theory makes testable predictions about the parameters of multicompartmental viruses.

Double-stranded cucumovirus associated RNA 5: experimental analysis of necrogenic and non-necrogenic variants by temperature-gradient gel electrophoresis

Cucumber mosaic virus (CMV) and peanut stunt virus (PSV) each contain a fifth major RNA in the size range of 334 to 393 nucleotides. This fifth RNA is a satellite capable of modulating the expression of viral disease symptoms. It is present in infected tissue in single-stranded and double-stranded form. Nucleotide sequence variants of the double-stranded CMV-associated RNA 5 (dsCARNA 5) and PSV-associated RNA 5 (dsPARNA 5) were analysed by temperature-gradient gel electrophoresis. Gels were 5% polyacrylamide, containing 8 M urea in 8.9 mM Tris-borate buffer, with temperature differences of 25-40 degrees C establishing gradients either perpendicular or parallel to the direction of the electric field. For dsCARNA 5 two characteristic transitions were detected with increasing temperature: at temperatures between 40 degrees C and 46 degrees C a drastic retardation in electrophoretic mobility induced by partial dissociation of the duplex structure from the ends and at temperatures above 52 degrees C an abrupt increase in mobility due to complete strand dissociation. dsPARNA 5 exhibited both transitions at up to 10 degrees C higher temperatures and an additional retardation between the transitions mentioned. Seven different variants of dsCARNA 5, 4 necrogenic and 3 non-necrogenic, were analysed. Some showed only one single band, others gave rise to up to six well separated bands corresponding to six molecular species. From all experimental results a correlation between the temperature of the retardation transition and the necrogenicity of CARNA 5 was derived. The diagnostic application of the temperature-gradient gel analysis in agriculture, particularly for the use of non-necrogenic variants as biological control agents to impede CMV-infections, is discussed.

Double-stranded cucumovirus associated RNA 5: which sequence variations may be detected by optical melting and temperature-gradient gel electrophoresis?

Sequence variants of the double-stranded form of satellite RNAs of cucumber mosaic virus (dsCARNA 5) were analyzed for the possibility to experimentally detect minor nucleotide sequence changes. Denaturation maps (helix-probability versus position of the nucleotide in the sequence versus temperature) were calculated applying the Poland algorithm. Optical denaturation curves and temperature-gradient gel mobility curves were simulated using the denaturation maps and were compared with experimental results from optical melting and temperature-gradient gel electrophoresis (Tien Po et al., accompanying paper). Melting of the dsRNAs starts from both ends of the molecule in two transitions of low co-operativity, continues in the right part in a highly co-operative transition, and is finished in another highly co-operative transition including strand-separation. Whereas all parts of the molecule contribute uniformly to the optical melting curve, opening of the ends predominates in the retardation transition in gel electrophoresis. Detailed discussion of the influence of base pair changes in the sequence shows that a single base pair change may be detected by temperature-gradient gel electrophoresis, if it is located in certain favorable locations, whereas its detection in optical melting curves is possible only in very special cases. The systematic differences found in the accompanying paper between necrogenic and non-necrogenic dsCARNA 5 could be interpreted on the basis of such nucleotide sequence differences.

Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site

Virusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation. Recently, we showed that an in vitro-synthesized RNA containing 273 nucleotides of the 324-nucleotide virusoid of lucerne transient streak virus self-cleaves at a unique site. The reaction requires heating and snap cooling of the RNA and the subsequent addition of magnesium ions. Here, we test the 55-nucleotide, hammerhead-shaped, structural model proposed for the active site by preparing RNAs with both 5' and 3' terminal deletions. Results indicate that the hammerhead structure is sufficient and necessary for self-cleavage, that certain sequences prevent the formation of the hammerhead structure in the native virusoid RNA, and that an RNA molecule containing only 52 nucleotides is capable of an RNA-mediated reaction.

The capsid polypeptides of the 190S virus of Helminthosporium victoriae

SDS-PAGE of the 190S virus of Helminthosporium victoriae, using a discontinuous buffer system, revealed two major capsid polypeptides of mol. wt. 88K and 83K (p88 and p83) and a minor polypeptide, p78. Peptide mapping by both limited proteolysis and selective chemical cleavage showed p83 and p78 to be closely related to p88. The origin of p83/p78 could not be explained by proteolysis of p88 during virus preparation and storage. In rabbit reticulocyte lysates, denatured dsRNA directed the synthesis of a single major translation product which was identical to capsid polypeptide p88 on the basis of coelectrophoresis, immunoprecipitation and peptide mapping. No translation products comparable in size to p83 or p78 were detected in vitro. These data indicated that the capsid of the 190S virus is encoded by a single gene and verified the classification of the virus as a member of the family Totiviridae. Radioiodination of intact virus under conditions considered optimum for surface-specific iodination showed p88 to be more readily available for labelling than p83 or p78. Furthermore, when Western blots of capsid polypeptides were reacted with an antiserum to glutaraldehyde-stabilized virus (190S-G), p88 was more reactive to 190S-G antibodies than was p83/p78. These results suggest p88 is external to p83/p78 in the capsid.

Genome similarities between plant and animal RNA viruses

Gene sequence comparisons and protein comparisons provide more and more evidence that evolutionary links exist between plant and animal RNA viruses, irrespective of whether they have an isometric or rod-shaped particle, or of whether they have a divided or non-divided genome. Although a phylogeny based on these molecular data cannot yet be constructed the results obtained so far shed a new light on the origin and evolution of RNA viruses and are important in terms of their taxonomy.

Nonradioactive, photobiotin-labelled DNA probes for the routine diagnosis of barley yellow dwarf virus

Photobiotin was used to prepare biotinylated, nonradioactive nucleic acid probes for the detection of the RNA of barley yellow dwarf virus (BYDV) in plant extracts. A 1.7-kb cDNA of the PAV isolate of BYDV in the plasmid pUC8 vector was biotinylated and then used intact or as sonicated double-stranded DNA fragments. Simple methods were developed for the preparation of partially purified nucleic acid extracts of cereals and their spotting, after formaldehyde treatment, onto nitrocellulose membranes. After hybridization, biotin-labelled DNA bound to BYDV RNA on the nitrocellulose was detected with an avidin-alkaline phosphatase conjugate. BYDV RNA was readily detected with a sensitivity similar to that found with the same probe labelled with 32P by nick translation. Healthy plant extracts gave colourless spots.

Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites

Virusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation. Virusoid replication appears to involve longer-than-unit-length plus and minus RNAs, indicating that unit-length plus RNA is generated by specific cleavage reactions. Here, we synthesize plus and minus partial-length RNAs of the 324-nucleotide virusoid from lucerne transient streak virus in vitro. Both RNAs self-cleave at a unique site in the presence of magnesium ions to give 5' hydroxyl and 2',3' cyclic phosphodiester termini. Conformations other than the native structures are necessary for cleavage. Similar secondary structures with considerable sequence homology are proposed for the active sites of these and other plant pathogenic RNAs. Our results are consistent with certain rolling-circle replication models.

tRNA-like properties of tobacco rattle virus RNA

The 3' terminal forty nucleotides of tobraviral RNAs readily fold into a tertiary structure, resembling that of tymo- and tobamoviral RNAs. The latter RNAs possess a tRNA-like structure at their 3' end that is recognized by a number of tRNA-specific enzymes (Rietveld et al. (1984), EMBO J. 3, 2613-2619). Characteristic for their aminoacyl acceptor arm is the presence of a so-called pseudoknot which we now also find in a corresponding position at the 3' terminus of TRV RNA2 (PSG strain). The nucleotide sequences of all tobraviral RNAs analysed so far indicate that they all possess a similar 3' terminal structure. A domain resembling the anticodon arm of canonical tRNA is not readily recognizable. TRV RNA2 can be adenylated with CTP, ATP; tRNA nucleotidyl transferase and ATP. It is unable, however, to accept any of the twenty common amino acids when incubated with ATP and aminoacyl-tRNA synthetases from wheat germ or yeast. We conclude that TRV RNA contains a tRNA-like structure, which, in contrast to the tymo- and tobamoviral tRNA-like structures, cannot be aminoacylated. It is unlikely therefore, that aminoacylation of plant viral RNAs with a tRNA-like structure is a prerequisite for viral RNA replication.

Structure and assembly of turnip crinkle virus. IV. Analysis of the coat protein gene and implications of the subunit primary structure

The structure of the turnip crinkle virus (TCV) coat protein and coat protein gene has been examined by cDNA cloning, nucleotide sequencing and high-resolution mRNA mapping. We have cloned a 1450-nucleotide cDNA fragment, representing the 3' end of the TCV genome, using genomic RNA polyadenylated in vitro as the reverse transcriptional template. Nucleic acid sequence analysis reveals the presence of a 1053 nucleotide open reading frame capable of encoding a protein of 38,131 Mr, identified as the coat protein subunit. The 1446 base subgenomic mRNA for the coat protein, mapped using high-resolution primer extension techniques, contains a 137 nucleotide leader sequence upstream from the initiation codon. We have characterized a second subgenomic RNA of approximately 1700 bases, roughly 250 nucleotides longer than the 1446 base species in the 5' direction. No TCV-related RNAs are polyadenylated in vivo. The derived amino acid sequence of the TCV coat protein has been built into the 3.2 A resolution electron density map of TCV reported in paper I of this series. We describe here some of the important features of the structure. Alignment of the three-dimensional structures of tomato bushy stunt virus and southern bean mosaic virus shows significant sequence relationships in the arms and S domains, although the conserved residues do not appear to have any special role in stabilizing the beta-barrel fold or in mediating subunit interactions. The sequences of TCV and carnation mottle virus can be aligned. Comparisons among the four are discussed in terms of the organization of the S domain.

[Primary structure of the potato virus X genome: the region preceding the capsid protein cistron]

DNA copies of the potato virus X (PVX) RNA corresponding to 2300 nucleotides at the 3'-end have been cloned. The cloned cDNA copies containing the nucleotides 445-1280 from the 3'-end have been sequenced. The 5'-terminal region of the PVX coat protein gene corresponds to residues 445-786 from the 3'-end. The amino acid sequences of two more open reading frames (ORF) have been deduced from the nucleotide sequence. The potential translation products of these ORF's would correspond to the nonstructural viral proteins. We have located the ORF1 within the region of residues 799-1009 preceding the coat protein cistron. The tentative protein is composed of 70 amino acids and has an aminoterminal segment which is markedly hydrophobic. ORF2 in the PVX sequence ends with UAG at nucleotides 942-944 and extends to the 5'-terminus for additional 340 nucleotides. The distant sequence homology exists between a carboxyterminal portion of PVX ORF2 and that of the nonstructural "30 K-proteins" of the plant tobamoviruses.

Structure and replication of geminivirus genomes

The geminiviruses are a group of plant viruses containing single-stranded (ss) DNA in particles comprising two quasi-icosahedral units. Some are transmitted by whiteflies, others by leafhoppers. Comparisons were made of the genome organization and expression of cassava latent virus (CLV) and maize streak virus (MSV) and beet curly top virus (BCTV), each with distinct host range and insect vector species characteristics. From these studies, several indications as to the replication mechanism(s) are suggested.

Synthesis in vitro of infectious RNA copies of the virulent satellite of turnip crinkle virus

RNA copies, synthesized in vitro, of the virulent satellite (RNA C) of turnip crinkle virus (TCV) infect plants when coinoculated with helper virus RNA. RNA C is a small linear RNA of about 355 bases which intensifies TCV symptoms in infected plants. Full-length cDNA copies of the satellite were inserted in an expression vector (for RNA synthesis in vitro) in such a way that RNA synthesized in vitro had the same 5'-end as the native satellite. Plus-strand RNA copies of the satellite in near-monomer and multimer form infected plants, while minus-strand RNA copies and DNA copies of the satellite RNA did not do so under the conditions tested. When plants were inoculated with RNAs synthesized in vitro from two independently cloned satellite cDNAs with base sequence and length differences, the products of infection corresponded in sequence to the different cRNAs used in the inocula. Satellite RNAs synthesized in vitro from either cDNA produced the same symptoms as the native satellite RNA.

Geminivirus genomes

The geminiviruses are unusual plant viruses containing circular single-stranded DNA. The sequences and organization of several of their genomes are described, and recent experiments towards understanding their replication, gene expression and gene functions are discussed.

Diversity of citrus tristeza virus isolates indicated by dsRNA analysis

One major dsRNA of molecular weight (MW) 13.3 X 10(6) and two others (MW 1.9 X 10(6) and 0.8 X 10(6] were routinely detected by polyacrylamide gel electrophoresis in extracts from sweet orange (Citrus sinensis) or citron (Citrus medica) infected with each of 66 isolates of citrus tristeza virus (CTV). Several additional dsRNA were also commonly detected, usually as weakly stained bands in reproducible positions in gels, but some were very prominent, e.g., a dsRNA of MW 1.7 X 10(6) associated with a seedling yellows isolate (sy-1). No dsRNA was detected in equivalent extracts from noninoculated sweet orange and citron. End-labeled [32P] probes were made from purified full-length viral RNA or polyacrylamide gel-purified full-length dsRNA of a nonseedling yellows (nsy-1) and a seedling yellows (sy-1) isolate of CTV. Each of the four probes was able to hybridize to all major and most minor dsRNAs of both isolates in composite polyacrylamide/agrarose gels, including the 1.7 X 10(6) dsRNA specific to the seedling yellows isolate, and could readily detect CTV nucleic acid sequences in extracts from bark of infected sweet orange plants spotted onto nitrocellulose membranes. One dsRNA (MW 0.5 X 10(6] was very prominent in some isolates and much less so, or undetectable, in other isolates and 66 isolates have been screened for the presence of this dsRNA. There was a strong correlation between inability to detect the 0.5 X 10(6) dsRNA and the designation of an isolate as neither a seedling yellows type nor a stem pitting isolate of grapefruit; these properties were typical for isolates of CTV from southern California.

Lack of homology among potexvirus RNAs

Representative cDNAs prepared against each of five different potexvirus RNAs were annealed to these and other viral RNAs to assess the extent to which these viruses might be related. In all cases, the cDNA hybridized to completion with its homologous RNA but failed to cross-hybridize significantly to any other viral RNA. Partial hybridization was detected when the cDNA of one virus was annealed to the RNA of a distinct strain of the same virus. We conclude that despite their morphological similarities, members of the potexvirus group have diverged substantially in nucleotide sequence.

Structure of viroid replicative intermediates: physico-chemical studies on SP6 transcripts of cloned oligomeric potato spindle tuber viroid

The structure and structural transitions of transcripts of cloned oligomeric viroid were studied in physico-chemical experiments and stability calculations. Transcripts of (+) and (-) polarity, from unit up to sixfold length, were synthesized from DNA clones of the potato spindle tuber viroid (PSTV) with the SP6 transcription system. Their structural properties were investigated by optical denaturation curves, high performance liquid chromatography (HPLC), electron microscopy, sedimentation-diffusion equilibrium and velocity sedimentation. Secondary structures of the RNAs and theoretical denaturation curves were calculated using an energy optimization program. The secondary structure of lowest free energy for unit length and oligomeric transcripts is a rod-like structure similar to that of the mature circular viroids. When this structure is used as a model for calculations, there is a large degree of agreement between the theoretical and the experimental denaturation curves. At high temperatures, however, (+) strand transcripts exhibited a transition which was more stable than expected from the calculations or than was known from curves of mature viroids. This transition arises from a rearrangement of the central conserved region of viroids to a helical region of 28 stable base pairs either intermolecularly leading to bimolecular complexes, or intramolecularly giving rise to a branched secondary structure. The rearrangement could be detected by electron microscopy, HPLC, and analytical ultracentrifugation. The helical region serves to divide up the oligomeric (+) strand into structural units which may be recognized by cleavage and ligation enzymes which process the oligomeric intermediates to circular mature viroids.

Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA

The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) polarity, cleaves autolytically at a specific ApG bond. Purified autolysis products spontaneously join in a non-enzymic reaction. We report characteristics of this RNA ligation reaction: the terminal groups that react, the type of bond in the newly formed junction and the nucleotide sequence of the joined RNA. The nucleotide sequence of the ligated RNA shows that joining of the reacting RNAs restored an ApG bond. The junction ApG has a 3'-to-5' phosphodiester bond. Thus the net ligation reaction of STobRV (-)RNA is the precise reversal of autolysis. We discuss this new type of RNA ligation reaction and its implications for the formation of multimeric STobRV RNAs during replication.

ATPase activities of wheat germ initiation factors 4A, 4B, and 4F

Eukaryotic initiation factors (eIF)-4A, -4B, and -4F isolated from wheat germ were tested for their ability to catalyze ATP hydrolysis in the absence and presence of RNA. We find that eIF-4B or eIF-4F alone exhibit ATPase activity in the presence of poly(U), satellite tobacco necrosis virus (STNV) RNA, or globin mRNA but not in the absence of RNA. eIF-4A alone exhibits ATPase activity in the absence of RNA, but this activity is not stimulated by the addition of RNA. eIF-4A does, however, enhance RNA-dependent ATP hydrolysis in the presence of either eIF-4B or eIF-4F. The RNA-dependent ATPase activities of eIF-4B and eIF-4F are additive, not synergistic. At saturating concentrations of eIF-4F, little or no stimulation of ATP hydrolysis is obtained upon the addition of eIF-4B and at saturating concentrations of eIF-4B little or no stimulation is obtained upon the addition of eIF-4F. This observation is in agreement with our previous finding (Lax, S., Fritz, W., Browning, K., and Ravel, J. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 330-333) that initiation of polypeptide synthesis is obtained in vitro with either eIF-4F or eIF-4B.