Mechanism of viral replication. I. Structure of replication complexes of R17 bacteriophage

TYMV RNA replication in vivo: replicative intermediate is mainly single stranded

We have used an in vitro labeled, membrane-bound ds[3H]RNA (C. Mouches, C. Bove, and J. M. Bove, 1974, Virology 58, 409-423) to develop a technique by which dsRNA can be detected on glycol methacrylate-embedded ultrathin sections by its resistance to RNase digestion at high but not at low ionic strength. The RNase-resistant ds[3H]RNA is detected on the sections by high-resolution autoradiography. The technique requires that prior to RNase digestion the ultrathin sections be first submitted to a Pronase step. This is accomplished by floating the sections on Pronase (1 mg/ml) for 15 min at 30 degrees , washing the sections three times, and digesting with RNase at high ionic strength for 90 min at 30 degrees . When the washing steps and the RNase hydrolysis are carried out at low ionic strength, dsRNA is completely hydrolyzed. We have applied the Pronase-RNase technique to investigate whether TYMV-specific dsRNA exists in situ after in vivo labeling of the RNAs. [3H]Uridine was fed for 1, 3, and 6 hr through the petiole of healthy or TYMV-infected leaves in the presence or absence of actinomycin D. For a given treatment aliquots of the same leaves were used for three parallel experiments: (1) Araldite embedding for autoradiography; (2) glycol methacrylate embedding for enzyme digestion and autoradiography; and (3) RNA extraction and analysis by polyacrylamide gel electrophoresis. These experiments have shown that after a [3H]uridine absorption by TYMV-infected leaves for 1 hr, in the presence of actinomycin D:dsRNA was the main labeled RNA species seen on the gels; Araldite-embedded sections were labeled specifically at the chloroplast periphery, while glycol methacrylate-embedded sections, submitted to the Pronase-RNase technique to detect dsRNA, were found to contain no dsRNA. Thus replicative intermediate RNA in TYMV-infected cells is essentially single stranded in vivo, and dsRNA is an artifact generated during the RNA extraction procedure.

Functional circularity of legitimate Qbeta replicase templates

Qbeta replicase (RNA-directed RNA polymerase of bacteriophage Qbeta) exponentially amplifies certain RNAs in vitro. Previous studies have shown that Qbeta replicase can initiate and elongate on a variety of RNAs; however, only a minute fraction of them are recognized as 'legitimate' templates. Guanosine 5'-triphosphate (GTP)-dependent initiation on a legitimate template generates a stable replicative complex capable of elongation in the presence of aurintricarboxylic acid, a powerful inhibitor of RNA-protein interactions. On the contrary, initiation on an illegitimate template is GTP independent and does not result in the aurintricarboxylic-acid-resistant replicative complex. This article demonstrates that the 3' and 5' termini of a legitimate template cooperate during and after the initiation step. Breach of the cooperation by dividing the template into fragments or by introducing point mutations at the 5' terminus reduces the rate and the yield of initiation, increases the GTP requirement, decreases the overall rate of template copying, and destabilizes the postinitiation replicative complex. These results revive the old idea of a functional circularity of legitimate Qbeta replicase templates and complement the increasing body of evidence that functional circularity may be a common property of RNA templates directing the synthesis of either RNA or protein molecules.

Presence of double stranded regions of viral RNA in infected cells

Ribonuclease treatment of rhinovirus-infected human embryo lung cells after cell disruption reveals that double stranded RNA is present in the preparation before nucleic acids are extracted with phenol. This shows that the hydrogen bonding between complementary molecules of viral RNA which occurs in infected cells is not a result of the extraction of RNA with phenol.

DNA electron microscopy

In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).

Adsorption of DNA molecules to different support films

Protein-free adsorption of the DNA of the Escherichia coli bacteriophage T7 to carbon, collodion, aluminium-beryllium and aluminium films was studied. It was found that the appearance of DNA strands depended greatly upon the kind of support film used. Direct adsorption of DNA to aluminium-beryllium or aluminium films yielded specimens with 'thin and long' and 'thick and short' regions along the strand. Well extended, uncoiled and unaggregated DNA molecules were obtained only when DNA was adsorbed to carbon, collodion or mica in the presence of intercalating dyes such as ethidium bromide. Adsorption properties of the different films are well correlated with their surface charge. Aluminium-beryllium films carry a strong positive surface charge, aluminium films a weak positive charge and carbon films a weak negative charge. It is suggested that for the preparation of specimens by spontaneous adsorption of well extended and unaggregated strands it is necessary that the DNA molecule is stiffened by a ligand such as an intercalating dye, and that the charge on the surface of the support film is opposite to the charge of the macromolecule.

Intermediates in the biosynthesis of double-stranded ribonucleic acids of bacteriophage phi 6

Pseudomonas phaseolicola infected with bacteriophage phi 6 synthesized all three viral double-stranded RNA segments, three single-stranded RNAs, and three replicative intermediate-like RNAs in the presence of rifampin. The single-stranded RNA intermediates sedimented and electrophoresed along with melted viral double-stranded RNA, annealed with melted viral double-stranded RNA, and were transient in nature. The relative amounts of the single-stranded RNA intermediates varied during the infection cycle and were altered in the presence of chloramphenicol. The replicative intermediate-like RNAs sedimented faster than double-stranded RNA, failed to enter 2.5% polyacrylamide gels, eluted with double-stranded RNA from a CF-11 cellulose column, were precipitated with single-stranded RNA in 2 M LiC1, and yielded three genome-size pieces of double-stranded RNA upon digestion with RNase. These results are consistent with the hypothesis that complementary strands of the phi 6 double-stranded RNAs are synthesized asynchronously during the infection cycle.

The mechanism of viral replication. Structure of replication complexes of encephalomyocarditis virus

The structure of the purified replicative intermediate of encephalomyocarditis virus was determined by electron microscopy. Approximately 80% of the replicative intermediate complexes were characterized by a filament of double-stranded RNA of widely variable length, which had a "bush" of single-stranded RNA at one end. In many examples one or more additional single-stranded bushes were appended internally to the double-stranded RNA filament. These results support the view that before deproteinization, replicative intermediate contains little if any double-stranded RNA.