Structure of the poly(G) polymerase component of the bacteriophage f2 replicase

Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2

We have analyzed the molecular mechanism that makes translation of the MS2 replicase cistron dependent on the translation of the upstream coat cistron. Deletion mapping on cloned cDNA of the phage shows that the ribosomal binding site of the replicase cistron is masked by a long distance basepairing to an internal coat cistron region. Removal of the internal coat cistron region leads to uncoupled replicase synthesis. Our results confirm the model as originally proposed by Min Jou et al. (1). Activation of the replicase start is sensitive to the frequency of upstream translation, but never reaches the level of uncoupled replicase synthesis.

Template specificity of Qbeta and SP phage RNA replicases as studied by replication of small variant RNAs

Template specificity of two RNA-dependent RNA polymerases (Qbeta and SP RNA replicases) was examined using "variant RNAs" as template. Three variant RNAs, one (8S) generated by Qbeta replicase and two (6S and 5.2S) generated by SP replicase, were isolated from the reaction mixtures incubated in the absence of exogenous template RNA. All these RNAs were found to be active as template for both Qbeta and SP replicases, though homologous RNA exhibited activities about three times higher than heterologous RNA with either enzyme, in agreement with the results obtained in phage RNA-dependent reactions. In these reactions, faithful replication of variant RNA was observed, and the amount of RNA synthesized was in a many-fold excess over the template RNA added. We also found that the heterologous RNA-dependent reactions were suppressed by increasing the concentration of salts or decreasing the concentration of substrates. Under such conditions, replication of heterologous variant RNA was almost completely suppressed, while the amount of homologous variant RNA synthesized was only reduced to 50% of that synthesized under the standard conditions. Thus the template specificity of the two RNA replicases seems to be expressed more strictly in these replication systems.

Specific binding of messenger RNA and methionyl-tRNAfMet by the same initiation factor for eukaryotic protein synthesis

Affinity chromatography on columns containing globin mRNA, R17 phage mRNA, or double-stranded RNA linked to cellose is used to demonstrate unequivocally that the eukaryotic initiation factor (eIF-2) that forms a ternary complex with Met-tRNAf and GTP also binds tightly to these RNA species. Affinity chromatography of reticulocyte ribosomal wash yields over 100-fold purification of Met-tRNAf-binding factor. This factor is eluted as one of the most tightly bound proteins, and is active in protein synthesis even after passage over a column of double-stranded RNA-cellulose. eIF-2 binds mRNA and double-stranded RNA in distinctly different modes, protecting essentially all sequences in double stranded RNA, but very few in mRNA, against digestion with ribonuclease. Apparently, eIF-2 recognized the A conformation of double-stranded RNA, but not its sequence. By contrast, globin, Mengo virus, R17 and vesicular stomatitis virus mRNA are shown to possess a high-affinity binding site for eIF-2 that is absent in negative-strand RNA of vesicular stomatitis virus, an RNA that cannot serve as messenger. The results support the concept that eIF-2, the initiation factor that binds Met-tRNAf, recognizes an internal sequence in mRNA essential for protein synthesis.

Affinity adsorbents consisting of nucleic acids immobilized via bisoxirane activated polysaccharides

An easy and efficient procedure for the immobilization of polynucleotide ligands to bisoxirane activated insoluble polysaccharides has been elaborated and is described in this paper. The resulting materials have been applied to the chromatography of DNA polymerase I, and RNA polymerase from E.coli. Because of their extraordinary stability to temperature, formamide, and alkaline conditions they seem to be particularly useful adsorbents for nucleic acid hybridization.

An Escherichia coli mutant with a temperature-sensitive function affecting bacteriophage Qbeta RNA replication

We report the isolation of E. coli mutant capable of supporting replication of bacteriophage Qbeta at 33 degrees, but not at 40 degrees. Coliphages f2, R23, fd, and yamma formed plaques on mutant cells at both temperatures. Temperature-shift experiments showed that bacteriophage Q beta replication was blocked in the mutant within the first 20-30 min of infection. The defect did not prevent translation of the Qbeta polymerase gene or assembly of catalytically active Qbeta replicase molecules. In fact, mutant cells infected at 40 degrees hyperinduced replicase active both in vivo and in vitro. However, zone sedimentation of the in vivo RNA product showed it to consist of partially double-stranded material sedimenting at 9 S, with little or no viral 32S RNA. The 9S RNA was also found, along with a predominant peak of 32S RNA in parental cells infected at 40 degrees, but not in cells infected at 33 degrees. It thus appears that the temperature-sensitive component is required for viral RNA replication, but not for other RNA synthesis catalyzed by the replicase. Uninfected mutant cells grew normally at 40 degrees in nutrient broth, but not in glucose- or glycerol-minimal media. Revertants selected for their abillity to grow in minimal medium at 40 degrees also supported bacteriophage Qbeta replication at 40 degrees.

Requirement of chain initiation factor 3 and ribosomal protein S1 in translation of synthetic and natural messenger RNA

Amino acid incorporation directed by poly(A), poly(U) or R17 RNA has been examined in S1-depleted protein synthesizing systems. We observe that the translation of either synthetic or natural messenger RNA is strictly dependent on the presence of chain initiation factor 3 and ribosomal protein S1. With poly(A) or poly(U) both IF-3 and S1 stimulate amino acid incorporation at least 25-fold, and with R17 RNA the stimulation is approximately 15-fold. More than one copy of S1 per ribosome decreases amino acid incorporation directed by poly(U) or R17 RNA. Initiation complex formation with R17 RNA is also stimulated optimally by the addition of one copy of S1 per ribosome. The function of IF-3 and S1 in protein synthesis is considered.

Isolation and properties of the replicase of encephalomyocarditis virus

The RNA-dependent RNA polymerase (replicase) of encephalomyocarditis (EMC) virus was found to be closely associated with the smooth membranes of infected BHK-21 cells. An RNA-dependent EMC replicase was extracted from the membranes with 0.15% sodium dodecyl sulfate (SDS) and 1,1,2-trichlorotri-fluoroethane (Genetron 113) and further purified by high-salt dextran-polyethylene glycol phase separation, sievorptive chromatography, and glycerol gradient sedimentation. The enzyme does not manifest strict specificity toward EMC RNA template. It can use also Qbeta RNA, rRNA of BHK cells, or poly(C). SDS-polyacrylamide gel electrophoresis of purified EMC replicase labeled with radioactive methionine revealed that, of all the stable EMC proteins, the enzyme contains predominantly the 56,000-dalton (E) polypeptide.

Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene

Bacteriophage MS2 RNA is 3,569 nucleotides long. The nucleotide sequence has been established for the third and last gene, which codes for the replicase protein. A secondary structure model has also been proposed. Biological properties, such as ribosome binding and codon interactions can now be discussed on a molecular basis. As the sequences for the other regions of this RNA have been published already, the complete, primary chemical structure of a viral genome has now been established.

R17 bacteriophage replicase: association with the inhibition of Qbeta, fd bacteriophage and beta-galactosidase production

Superinfection of Escherichia coli with amber mutants of R17 phage which produce R17 replicase inhibits production of the RNA phage Qbeta, the DNA phage fd, and the host enzyme beta-galactosidase. Inhibition required R17 replicase production and was related to the amount of replicase produced.

Initiation specificity of the poly(cytidylic acid)-dependent Qbeta replicase activity

The initiation specificity of RNA synthesis catalysed by the poly(C)-dependent Qbeta replicase activity was investigated with various synthetic ribopolymers as template. It was found that the initiation efficiency of a series of oligo(C) with various chain lengths is proportional to the template size. Synthetic riboheteropolymers containing cytidylic acid were accepted as templates only if they contained at their 3' end a cytidylic acid sequence of more than 5 nucleotides. Such an oligocytidylate sequence served also as an initiator sequence for copying the non-cytidylic-acid-containing part of the heterotemplate. RNA synthesis always began with the incorporation of GTP, even if the 3'-terminating nucleotide of the template was not cytidylic acid.

The synthetase gene of the RNA phages R17, MS2 and f2 has a single UAG terminator codon

Translation of the RNA from the wild-type bacteriophages R17, MS2, and f2 in bacterial cell-free extracts containing an amber suppressor yields 30-40% of the synthetase with an approximate molecular weight of 63 500, slightly larger than the major synthetase product (63 000 daltons). The occurrence of the 63 500 dalton in vitro product is dependent on the presence of an amber suppressor, and we predict that it is due to read-through of a UAG termination codon at the end of the synthetase gene. Previous results of Capecchi and Klein (Nature, 226, 1029-1033, 1070) showed that antibodies to both release factors RF1 and RF2 are required to block release of synthetase, suggesting that synthetase is released at a UAA codon. If the interpretations of both experiments are correct, the termination and release may not be synonomous and may be spatially separated. In addition there is the unexplained fact that 7% of the synthetase made in vitro in both su+ and su- extracts with either R17, MS2 or f2 as template has an apparent molecular weight of 66 000.

Discriminative effect of rifampin of RNA replication of various RNA bacteriophages

Rifampin interferes exclusively with RNA replication in vivo of the group I phages MS2, f2, and R17, whereas QbetaRNA replication is unaffected by the drug. In addition, rifampin has a discriminative effect of group I phage RNA replication. In the experimental system employed by us the antibiotic differentially interferes with the synthesis of minus RNA strands in f2, whereas it has almost no effect on the synthesis of progeny plus strands. In MS2, the drug differentially arrests the synthesis of progeny plus strands and almost fails to affect the synthesis of minus RNA strands. In R17 both steps of its RNA replication are affected by rifampin, although each step is only partially (approximately 50%) inhibited. The relation of the present results to the possible role of bacterial proteins and tertiary structure of phage RNA in the process of template recognition is discussed.

Growth of ribonucleic acid bacteriophage f2 in a conditional putrescine auxotroph of Escherichia coli: evidence for a polyamine role in translation

The ribonucleic acid (RNA) bacteriophage, f2, grows poorly in a conditional putrescine auxotroph during polyamine starvation. The addition of putrescine simultaneously with f2 enhances phage growth, shortens the latent period, and increases the burst size. The stimulation of f2 growth is reflected in higher rates of phage RNA and protein syntheses as measured by radioactive labeling of infected cells in the presence of rifampin. Putrescine does not affect f2 adsorption or the penetration of its RNA. Rather, in vitro assays demonstrate that in putrescine-supplemented cells more molecules of f2 replicase are made per incoming parental RNA than in polyamine-starved cultures. The ability of polyamines to stimulate the translation of a preformed messenger suggests a physiological role for these organic cations in normal protein synthesis.

An RNA that multiplies indefinitely with DNA-dependent RNA polymerase: selection from a random copolymer

We have selected from a mixture of random polynucleotides an RNA that is able to replicate in the presence of the DNA-dependent RNA polymerase of Escherichia coli, provided the medium contains Mn(2+) and ITP, in addition to ATP, CTP, and UTP. The RNA consists of a chain of about 125 (+/-25) nucleotides and appears to have a defined, nonrepetitive sequence.

Bacteriophage Q replicase contains the protein biosynthesis elongation factors EF Tu and EF Ts

The enzyme, Qbeta replicase, responsible for the replication of the RNA of Escherichia coli pahge Qbeta, is composed of four nonidentical subunits, three of which, I, III, and IV, are coded for by the bacterial genome, while subunit II is phage-specific. SUBUNIT IV IS SHOWN TO BE IDENTICAL TO THE PROTEIN SYNTHESIS ELONGATION FACTOR EF TS BY THE FOLLOWING CRITERIA: coelectrophoresis on polyacrylamide gels in sodium dodecyl sulfate and in urea buffers, identity of the first seven amino acids at the amino-terminus, precipitation of sub-unit IV by anti-EF T-factor serum, and stimulation of EF Tu-GDP exchange by subunit IV. Subunit III is shown to be identical to the protein synthesis elongation factor EF Tu by the following criteria: coelectrophoresis on sodium dodecyl sulfate gels, precipitation of EF Tu by anti-Qbeta replicase serum, binding of guanine nucleotides, and binding of phenylalanyl-tRNA. In addition, Qbeta replicase activity can be reconstituted from subunits I and II with EF Tu and EF Ts.