RNA-dependent RNA polymerases in uninfected and in alfalfa mosaic virus-infected tobacco plants

Isolation and Characterization of an RNA-Dependent RNA Polymerase from Black Beetle Virus-Infected Drosophila melanogaster Cells

Crude lysates of black beetle virus (BBV)-infected cells of Drosophila melanogaster contain an RNA-dependent RNA polymerase activity not detectable in uninfected cells. The activity (designated BBV polymerase) sedimented at 20,000 x g, indicating an association with particulate material. It was solubilized from the pellet by sonication in a magnesium-deficient buffer. Differential centrifugation resulted in a 43-fold purification with 84% recovery of polymerase activity. The effects of divalent and monovalent cations, time, temperature, and pH on the activity of the partially purified polymerase were examined. RNA synthesis was not stimulated by the addition of exogenous BBV RNA, suggesting that an enzyme-template complex existed. Analysis of the RNA products of the RNA polymerase reaction indicated that full-length "negative" strand BBV RNAs were synthesized.

Characterization of double-stranded ribonucleic acid in tobacco leaves

Double-stranded RNA was isolated from tobacco leaves and characterized in terms of base composition, density, and nuclease resistance. Although its role in the plant's physiology is not clear, evidence was adduced that it is the product of the RNA-dependent RNA polymerase previously shown to occur in this and other plants. The fact that twice as much fully than partially double-stranded RNA appears to be made favors a regulatory role for the double-stranded RNA rather than a transcriptional intermediate role.

RNA-dependent RNA polymerase of tobacco plants

Several properties of RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) active fractions obtained from tobacco plants, be they uninfected, infected with tobacco mosaic virus, or infected with tobacco necrosis virus, were compared. By the seven criteria tested, the RNA-dependent RNA polymerase from these three sources behaved the same, although its activity is greatly but variably stimulated by the two virus infections. It thus appears probable that these two viruses do not code for this enzyme, but rely for their replication on their ability to stimulate production of a host enzyme. The conclusion that cells contain RNA replicating capability represents a modification of the central dogma of molecular biology.

In Vitro Replication of Cowpea Mosaic Virus RNA III. Template Recognition by Cowpea Mosaic Virus RNA Replicase

Cowpea mosaic virus (CPMV) RNA replicase has been purified about 200-fold from CPMV-infected Vigna unguiculata leaves. Optimal reaction conditions for replicase activity have been established that allow RNA synthesis to proceed for at least 15 h. Using a polymerase assay under conditions optimal for CPMV RNA-directed RNA synthesis, all natural RNA species tested appeared to be able to direct the incorporation of labeled ribonucleotides, whereas synthetic homoribopolymers were either inactive or only slightly active. Using a nitrocellulose membrane filter assay to measure complex formation between the replicase preparation and various RNA species, all natural RNA species tested, except that of the comovirus radish mosaic virus, appeared to be unable to compete with (32)P-labeled CPMV RNA in binding to replicase. We propose that CPMV replicase is actually template specific but does not display this property in a polymerase assay, since labile complexes between heterologous templates and replicase become stabilized by the formation of phosphodiester bonds. From homoribopolymer competition binding experiments we conclude that the polyadenylic acid on the CPMV genome might be a part of the replicase binding site.

Use of dodecyl-beta-D-maltoside in the purification and stabilization of RNA polymerase from brome mosaic virus-infected barley

The activity and specificity of RNA-dependent RNA polymerase (replicase) isolated from brome mosaic virus-infected barley was enhanced by extraction with the nonionic detergent dodecyl-beta-d-maltoside. The enzyme was stable for at least 8 weeks when stored at -70 degrees . A further 100-fold purification was obtained by centrifugation through sucrose in the presence of detergent. The polymerase activity was associated with the pellet fraction; the template dependence and specificity were similar to those of the enzyme before sucrose purification. SDS-PAGE analysis revealed a 110-kd protein in the purified pellet fraction from infected leaves that was absent from a similar fraction from healthy leaves. The protein had an identical electrophoretic mobility to that of protein la, the product of brome mosaic virus RNA 1 translation in vitro, and the profile of its tryptic polypeptides was very similar to that of protein 1a. These results support data obtained by inoculation of protoplasts with separated BMV RNA components (Kiberstis, et al. (1981), Virology 112, 804-808) that are consistent with the notion that RNA 1 codes for the viral replicase, or a subunit thereof.

RNA-directed RNA polymerases from healthy and from virus-infected cucumber

Much work has been done on the isolation, purification, and characterization of the RNA-directed RNA polymerase (EC 2.7.7.48) of cucumber mosaic virus (CMV)-infected cucumbers. Uninfected plants were reported to have no such enzyme, but we recently detected low levels of the activity in cucumber. Since tobacco and cowpea contain such an enzyme that is variably increased in amount by various virus (as well as viroid) infections, we assumed that this would also be the case upon CMV infection of cucumber. However, further purification and characterization of the RNA-directed RNA polymerases from healthy and from infected cucumber suggests that these are different enzymes. The presumed CMV replicase was obtained pure and consists of a major polypeptide of Mr 100,000 and minor components of Mr 110,000 and about 10,000. The Km is 5 microM ([3H]GTP) when tobacco mosaic virus RNA is used as template.

Comparative studies on ribonucleic acid dependent RNA polymerases in cucumber mosaic virus infected cucumber and tobacco and uninfected tobacco plants

RNA-dependent RNA polymerases have been isolated in almost pure form from cucumber mosaic virus (CMV) infected cucumber cotyledons and from tobacco leaves and were compared with the less pure enzyme from uninfected tobacco. The purified polymerase from cucumber shows on sodium dodecyl sulfate gels two peptide chains of about 100 and 112 kdaltons. The enzyme from tobacco shows a close doublet of about 125 kdaltons, which is also present in the less pure preparation from healthy tobacco. While both the cucumber and tobacco enzymes can use many polynucleotides and RNAs as templates, considerable quantitative differences exist, poly(C) being by far the most effective template for the cucumber enzyme but of low activity with the tobacco enzyme and poly(UG) being highly active with the latter but not the former. Poly(A) and poly(G) are inactive. Different viral RNAs, including CMV RNA, show smaller differences. The sedimentation rates of the enzyme from both sources are the same as that of gamma-globulin. A uridine 5'-triphosphate (UTP) terminal transferase also present in both plants sediments much more slowly and can be completely removed from the RNA polymerases. However, slight nucleolytic activity remains associated with the purified polymerases and appears to be proportional to the polymerase activity. The conclusion derived from these data is that the RNA-dependent RNA polymerases of different plants differ and are not detectably affected by virus infection in qualitative terms while being produced in greatly increased amounts upon some virus infections. Similar conclusions were previously reached with less purified enzyme preparations from tobacco as compared to cowpea, infected with different viruses, if any.

Heterogeneous chromatographic behaviour or soluble RNA replicase from healthy and virus-infected tobacco leaves: an improvement of the purification methodology

During purification of soluble RNA replicase from healthy and alfalfa mosaic virus-infected tobacco leaves, crude extracts were chromatographed on DEAE-Sephadex A-25, and three RNA-dependent RNA polymerase activities were obtained; one of these was previously characterized as a true RNA replicase, the remaining two were not studied (Chifflot et al., 1980, Virology 100, 91). We now demonstrate that all of these activities correspond to the same RNA replicase, complexed or not to cellular or viral RNA. Upon chromatography on DEAE-Sephadex A-25, the free replicase did not bind to the gel at low ionic strength, whereas the RNA-replicase complexes were bound to the gel through the medium of RNA. Increasing the ionic strength allowed the dissociation of the complexes and elution of the replicase only. From this observation, a new and rapid purification procedure combining all these activities and yielding large amounts of replicase was developed; the first main step of purification was chromatography on Blue-Sepharose CL6B under conditions conductive to the dissociation of RNA-replicase complexes, and thus maximal adsorption of the replicase. The enzyme was then eluted by increasing the ionic strength and was further purified on coupled DEAE-Sephadex A-25 and phosphocellulose columns. The DEA-Sephadex A-25 was used to bind the remaining RNA, while the replicase passed through, and bound to the cationic ion exchanger. The final replicase preparations which were obtained were very stable and had a purification factor of 1100-1400. The recovery averaged 70% and specific activities were much higher than those already described for similar enzymes from healthy or virus-infected tobacco leaves.

Viroids: structure and function

Viroids are nucleic acid species of relatively low molecular weight and unique structure that cause several important diseases of cultivated plants. Similar nucleic acid species may be responsible for certain diseases of animals and humans. Viroids are the smallest known agents of infectious disease. Unlike viral nucleic acids, viroids are not encapsidated. Despite their small size, viroids replicate autonomously in cells of susceptible plant species. Known viroids are single-stranded, covalently closed circular, as well as linear, RNA molecules with extensive regions of intramolecular complementarity; they exist in their native state as highly base-paired rods.

Coat protein binds to the 3'-terminal part of RNA 4 of alfalfa mosaic virus

All four RNAs of alfalfa mosaic virus contain a limited number of sites with a high affinity for coat protein [Van Boxsel, J. A. M. (1976), Ph.D. Thesis, University of Leiden]. In order to localize these sites in the viral RNAs, RNA 4 Tthe subgenomic messenger for coat protein) was subjected to a very mild digestion with ribonucleast T1. The ten major fragments, apparently resulting from five preferential hits, were separated and tested for messenger activity in a wheat germ cell-free system, as well as for the capacity to withdraw coat protein from intact particles. Fragments which stimulated amino acid incorporation were assumed to contain the 5 terminus. Strong evidence was obtained for the location of sites with a high affinity for coat protein near the 3' terminus. The smallest fragment which has the 3'-terminal cytosine comprises only 10% of the length of intact RNA 4 but still possesses these sites. Evidence is presented that the complete coat protein cistron is in the complementing 90% fragment. Possibly, the high-affinity sites are entirely located in the 3'-terminal extracistronic part of RNA 4. They will have the same position in RNA 3 and, possibly, also in the other parts of the genome of alfalfa mosaic virus. The need of this genome for coat protein in order to become infectious may therefore find its explanation in the fact that a conformational change at the 3' ends of the genome parts brought about by the coat protein is required for recognition by the viral replicase.