Cucumber mosaic virus-associated RNA 5. VI. Characterization and denaturation-renaturation behavior of the double-stranded form

Cucumber mosaic virus-associated RNA 5, VIII. Identification and partial characterization of a CARNA 5 incapable of inducing tomato necrosis

A new satellite-like replicating RNA found in association with cucumber mosaic virus type 1 (CMV-1), one of the earliest CMV isolates described (Doolittle, 1920), was identified and partially characterized. CMV-1-associated RNA 5, or (1)CARNA 5, was isolated from CMV-1 propagated in tomato, where it failed to induce lethal necrosis. In this way it was distinguished from CARNA 5 with the tomato necrosis-causing ability, which was redesignated (n)CARNA 5. Although (1)CARNA 5 and (n)CARNA 5 could be separated by 7.5% polyacrylamide gel electrophoresis under certain conditions, the molecules are probably identical in size, or nearly so. (1)CARNA 5 and (n)CARNA 5 have only limited nucleotide sequence homology. This is also evident from the different multitransitional absorbance-temperature profiles that can be obtained during the thermal denaturation of their respective double-stranded forms. In mixed infections in tomato, the replication of (1)CARNA 5 was also supported by CMV strains WT or S, while (n)CARNA 5 was supported by CMV-1. The biologically different (1)CARNA 5 and (n)CARNA 5 can be considered sequence variants among a group of small satellite-like RNA molecules dependent upon CMV for their replication.

A simple method for detection of viral satellite RNAs in small plant tissue samples

A procedure is described that allows extraction and can estimate the total amount of single-stranded and double-stranded viral satellite RNAs and viral RNA present in a minimal amount of infected plant tissue, and is capable of distinguishing different cucumber mosaic viral and nepoviral satellites by polyacrylamide gel electrophoresis under semi-denaturing or fully-denaturing conditions.

Low molecular weight RNA of Drosophila cells which is induced by heat shock--II. Structural properties

Heat shock-induced small cytoplasmic RNA (HSI scRNA) from Drosophila culture cell was larger in size after dimethylchloroacetal treatment than in 7 M urea. Judging from its thermal denaturation profile and the nuclease S1 digestion experiment it was supposed that HSI scRNA is double-stranded. Nucleotide sequence analysis of the scRNA also suggested that it is double-stranded RNA with the blunt-ends.

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.

Isolation and partial characterization of a monoclonal antibody specific for a naturally occurring double-stranded RNA

A monoclonal antibody (Mab) against the double-stranded form of the cucumber mosaic virus-associated RNA 5, the sequence variant that induces the tomato necrosis disease (ds(n)CARNA 5), has been obtained. Specificity studies using a radioimmunoassay showed that the purified Mab recognizes neither DNA nor ssRNA of different sources including ss(n)CARNA 5, poly(I).poly(C), nor dsRNA of two other sequence variants of CARNA 5. Therefore, the Mab seems to recognize a conformational variation only present in the double helical structure of ds(n)CARNA 5.

The stiffness of dsRNA: hydrodynamic studies on fluorescence-labelled RNA segments of bovine rotavirus

The sedimentation coefficients of dsRNA segments of bovine rotavirus were determined in the analytical ultracentrifuge. The eleven segments were separated by preparative gel electrophoresis, and isolated by elution from gel pieces. The RNA was labelled by the intercalating fluorescent dye ethidium bromide at a ratio bound dye per base pair between 0.003 to 0.018. The analytical ultracentrifuge was equipped with a fluorescence recording optics. Sedimentation coefficients could be determined with amounts of RNA as little as 8 ng. All sedimentation coefficients were extrapolated to zero-concentration, zero-dye binding, and zero-impurities from the preparative gel electrophoresis. The hydrodynamic model of flexible cylinders was applied for the interpretation of the sedimentation coefficients. All dsRNA segments of rotavirus (663-3409 base pairs) and the dsRNA5 of cucumber mosaic virus (335 base pairs) fit the model of a "worm-like" or flexible cylinder with a persistence length of 1125 A and a hydrated diameter of 30 A. The results are compared with data from the literature on the persistence lengths of the B- and Z-forms of dsDNA and of viroids.

Stiffness of viroids and viroid-like RNA in solution

The sedimentation coefficients of the potato spindle tuber viroid, four viroid-like RNAs from cadang-cadang-disease, circular RNA from velvet tobacco mottle virus, circular RNA from Solanum nodiflorum mottle virus and double stranded RNA5 from cucumber mosaic virus were measured in the analytical ultracentrifuge. The numbers of nucleotides of the RNA species varied between 246 and 670. The hydrodynamic models of rigid rods and flexible cylinders were applied for the interpretation of the sedimentation coefficients. Double-stranded RNA5 from cucumber mosaic virus with 335 basepairs fits the model of a rigid rod with an hydrated diameter of 29 A. Potato spindle tuber viroid and the four viroid-like RNA species of cadang-cadang-disease form a homologous series of flexible cylinders with a Kuhn's statistical length lambda-1 of 600 A. The circular RNA from the two viruses mentioned above are more flexibel than the viroids and viroid-like RNAs. The hydrodynamic interpretation is in accordance with thermodynamic data and secondary structure models. In two of the RNAs from cadang-cadang, cruciform structures would also be possible on the basis of the nucleotide sequence. The hydrodynamic data, however, favour clearly the extended structure over the cruciform.