The 3'-terminal nucleosides of the high molecular weight RNA of avian myeloblastosis virus

Covalent linkage between ribonucleic Acid primer and deoxyribonucleic Acid product of the avian myeloblastosis virus deoxyribonucleic Acid polymerase

Initiation of deoxyribonucleic acid (DNA) synthesis by the avian myeloblastosis virus DNA polymerase was previously suggested to involve a ribonucleic acid (RNA) primer, the initial product being a DNA molecule joined by a phosphodiester bond to the RNA primer. The existence and nature of such an RNA-DNA joint was investigated by assaying for transfer of a (32)P atom from an alpha-(32)P-deoxyribonucleotide to a 2'(3')-ribonucleotide after alkaline hydrolysis of the polymerase product. Such a transfer was observed, but only from alpha-(32)P-deoxyadenosine triphosphate and only to 2'(3')-adenosine monophosphate. This same transfer was observed in both the endogenous DNA polymerase reaction of purified virions and the reconstructed reaction of purified DNA polymerase plus purified 60 to 70S viral RNA. These results indicate a high level of specificity for the initiation process and support the idea of a low-molecular-weight initiator RNA as part of the 60 to 70S RNA complex.

From protein synthesis to genetic insertion

In 1946, (14)C-cyanide made its appearance as an offshoot of the Atomic Energy Program. Our colleague Robert Loftfield built it into (14)C-alanine by the Strecker synthesis, and a lusty program directed toward uncovering the unknown mechanism of protein synthesis grew out of this beginning. The necessity for an undiscovered series of steps and enzymes was soon evident. A cell free system was developed, and a succession of components necessary for this new pathway tumbled out. ATP dependence, amino acid activation, the ribosome as the site of polypeptide formation, discovery of tRNA as the translation molecule linking the gene and protein sequence, and GTP as the essential energy ingredient in peptide chain extension all appeared from our laboratory within the next decade. A little later the AP(4)N family, whose functions remain imperfectly defined, of intracellular molecules was discovered. Isolation of specific species of RNA became a high priority, and we sequenced a small segment of the 3' end of the Rous sarcoma virus, just inside the poly(A) tail, at the same time the Gilbert group at Harvard was sequencing the 5' end. The sequence identity and polarity of the two ends suggested a circular intermediate in replication and predicted correctly that a synthetic antisense oligonucleotide targeted against this sequence might be a specific inhibitor of replication. More recently, we have evolved a technique that appears to achieve a trinucleotide insertion into tissue culture cells bearing a specific Delta508 mRNA triplet deletion, resulting in phenotypic reversion in the tissue culture.

Analysis of avian myeloblastosis viral RNA and in vitro synthesis of proviral DNA

Two virus-specific RNA species of 7.5 and 7.0 kilobases have been identified in avian myeloblastosis virus (AMV) by denaturing gel electrophoresis and blot hybridization analysis, and they were found to be in a 10:1 ratio. The individual RNAs direccted the cell-free synthesis of the 76,000-dalton "gag" protein and the 180,000-dalton "gal-pol" protein, thereby demonstrating 5' sequence homology of approximately 4.9 kilobases between the two species. Synthesis of these two precursor proteins by the AMV genome indicates structural differences between AMV and other avian acute leukemia viruses. The two viral RNAs were transcribed into complete cDNA copies with AMV DNA polymerase. Linear proviruses were found to be 90--100% resistant to S1 nuclease. Analysis of single-stranded transcripts demonstrated two distinct species of 2.6 and 2.3 x 10(6) daltons, and analysis of duplexes formed from the single-stranded transcripts demonstrated species of 5.2 and 4.0 x 10(6) daltons.

Partial purification and characterization of rat-liver messenger RNA coding for phosphoenolpyruvate carboxykinase (GTP)

The mRNA coding for the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) was partially purified from the liver of cyclic-AMP-treated rats by a procedure involving multiple oligo(dT)-cellulose chromatographies and sucrose gradient fractionations. The purification was monitored by translational assay using a wheat germ extract. Relative to RNA bound once to oligo(dT)-cellulose, the final material was enriched 20-fold in template activity for phosphoenolpyruvate carboxykinase synthesis. With this RNA preparation, cell-free enzyme synthesis amounted to 5% of total mRNA-directed protein synthesis. The apparent sedimentation coefficient of phosphoenolpyruvate carboxykinase mRNA in sucrose gradients was between 20 and 22 S, corresponding to an average molecular weight of 0.93 X 10(6). By formamide/polyacrylamide gel electrophoresis the molecular weight of the enzyme mRNA was estimated at between 0.91 X 10(6) and 1.12 X 10(6). From these estimates, it was concluded that considerable non-coding sequence(s) are present in the mRNA. Approximately 20% of the enzyme mRNA in rat liver failed to bind to oligo(dT)-cellulose, presumably because of the absence of a poly(A) segment. The translation of phosphoenolpyruvate carboxykinase mRNA by the wheat germ extract was inhibited in the presence of 7-methylguanosine 5'-phosphate. The enzyme mRNA appears therefore to have a 'cap' at the 5' end.

RNA associated with murine intracisternal type A particles codes for the main particle protein

Intracisternal type A particles were isolated from MOPC-104E myeloma grown subcutaneously and from N 4 neuroblastoma cells in culture. Polyadenylated RNA was prepared from the particles and tested in a cell-free translation system derived from rabbit reticulocytes. RNA from the two sources directed the synthesis of multiple polypeptides with similar distributions of electrophoretic mobilities in sodium dodecyl sulfate-containing polyacrylamide gels, including one conponent of the same size as the major A-particle structural protein (73,000 daltons). Analysis of the RNAs by electrophoresis in methyl mercury-containing agarose gels revealed a 35S component common to A-particles from both cell types. This was a major component of the N4 preparations, whereas a 28S species predominated in the case of MOPC-104E. These two RNAs (35S from N4 cells and 28S from MOPC-104E), when isolated on isokinetic sucrose gradients, each directed the synthesis of a 73,000-molecular-weight polypeptide that comigrated on gels with authentic A-particle structural protein. Idnetity of the cell-free product was confirmed by two-dimensional analysis of the [35S]methionine-labeled tryptic peptides. The N4 RNA preparations also contained a major32S component which did not code effectively for the A-particle structural protein.

Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide

A tridecamer oligodeoxynucleotide, d(A-A-T-G-G-T-A-A-A-A-T-G-G), which is complementary to reiterated 3'- and 5'-terminal nucleotides of Rous sarcoma virus 35S RNA, is an efficient inhibitor of the translation of proteins specified by the viral RNA in the wheat embryo cell-free system. The inhibition specificity for oncornavirus RNA is greater than for rabbit reticulocyte mRNA or brome mosaic virus RNA. Other oligodeoxynucleotides of similar size have little or no specific effect on the RNA-directed translation. The tridecamer acts as a primer for the avian myeloblastosis virus DNA polymerase when Rous sarcoma virus heated 70S RNA is used as a template, offering evidence that it can hybridize to the RNA. The possible use of such an oligodeoxynucleotide hybridization competitor to inhibit Rous sarcoma virus replication is described in the preceding paper [Zamecnik, P. C. & Stephenson, M. L. (1978) Proc. Natl. Acad. Sci. USA. 75, 280--284].

Cell-free synthesis of the precursor polypeptide for avian myeloblastosis virus DNA polymerase

High molecular weight RNA (35S) isolated from avian myeloblastosis virus directs the cell-free synthesis of two prominent polypeptides of 180,000 and 76,000 molecular weight. The latter polypeptide has previously been identified as the precursor to the group-specific antigens of the virus ("gag" proteins) [Vogt, V. M., Eisenman, R. & Diggelmann, H. (1975) J. Mol. Biol. 96, 471-493]. Two-dimensional tryptic peptide analyses of the [35S]methionine-labeled peptides demonstrate that the 180,000-dalton product is a polyprotein that can account for all the peptides of the avian myeloblastosis virus DNA polymerase (DNA nucleotidyltransferase, EC 2.7.7.7) and those of the gag viral proteins. This is direct confirmation of the genomic order of the viral structural genes, placing the polymerase gene adjacent to the 5'-proximal gag gene of the virus. Furthermore, our findings suggest that the primary polymerase gene product is the beta subunit of the enzyme. These results are discussed in relation to the proposed structural gene map for the avian retraviruses and suggest a model for the in vivo processing of the viral polymerase.

Rous sarcoma virus genome is terminally redundant: the 3' sequence

A sequence of 20 nucleotide residues immediately adjacent to the 3'-terminal poly(A) in Rous sarcoma virus (Prague strain, subgroup C) 35S RNA has been determined by extension of a riboguanylic acid-terminated oligothymidylic acid primer hybridized at the 5' end of the 3'-terminal poly(A) with purified reverse transcriptase (RNA-directed DNA polymerase; deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC 2.7.7.7) from avian myeloblastosis virus. The sequence is 5'GCCAUUUUACCAUUCACCACpoly(A)3'. This same nucleotide sequence, excluding the poly(A) segment, has also been found at the 5' terminus of Rous sarcoma virus RNA (W. A. Haseltine, A. Maxam, and W. Gilbert, this issue pp. 989-993), and therefore the RNA genome of this virus is terminally redundant. Possible mechanisms for endogenous in vitro copying of the complete RNA genome by reverse transcriptase which involve terminally repeated nucleotide sequences are discussed.

Lysine tRNA's associated with avian myeloblastosis virus 70S RNA

The lysine tRNA released from the 70S RNA of avian myeloblastosis virus was separated by reversed-phase chromatography. All of the AAG-coding lysine tRNA's were present in the 70S-associated fraction; however, the AAA-coding lysine tRNA could not be detected. Chromatography of the lysine tRNA released at various temperatures did not show any preferential release of one AAG-coding species over another.

Analysis of oncornavirus RNA subunits by electron microscopy

Subunits of oncornavirus (avian myeloblastosis virus) RNA were isolated from purified 60--70S viral RNA by heat dissociation. Molecules sedimenting at 35 S, assumed to be the major component of the viral genome, were visualized in the electron microscope and their lengths were statistically analyzed. The results indicate a rather heterogeneous population of molecules with five distinct, reproducible size groups, an observation that excludes the assumption of random degradation of the genome. In addition, molecules of 28 and 18S RNA, always present in oncornavirus RNA preparations, were examined with the same methods. Some of these molecules possess secondary-structure regions similar to those characteristic for ribosomal RNA.

Properties of Visna Virus Particles Harvested at Short Time Intervals: RNA Content, Infectivity, and Ultrastructure

The major RNA component of Visna virus harvested at short intervals of time (5 min) is not the 60 to 70 S RNA but a molecule of higher electrophoretic mobility. This RNA has been isolated and characterized. Its sedimentation coefficient is identical to that of 30 to 40 S RNA subunits obtained by heat denaturation of the 60 to 70 S RNA. In 1.8% acrylamide gels without agarose the electrophoretic mobility of 30 to 40 S RNA subunits present in rapidly harvested virus is slightly lower than that of the subunits obtained by denaturation of the 60 to 70 S RNA; after heat denaturation the mobilities are identical. These free RNA subunits present in early virus particles assemble into a 60 to 70 S RNA complex as shown by following the RNA content of early virus incubated at 37 C for various lengths of time. The rate of this maturation process is slow. There is no difference between the infectivity of immature and mature virus particles. Both particles have a dense core when examined in sections of virus pellets.

Affinity chromatography of viral DNA polymerases on pyran-sepharose

Pyran covalently linked to cyanogen bromide-activated Sepharose has been shown to be an effective affinity matrix for several viral DNA polymerases. Differential salt elution of viral compared with cellular polymerases, as well as substrate elution, suggests the affinity nature for the matrix. Unlike some other affinity systems described, pyran-Sepharose is totally resistant to nuclease digestion and is stable at 4 degrees for several months. DNA polymerases isolated from several viruses by detergent treatment were recovered in good yield. Analysis of iodinated proteins by sodium dodecyl sulfate-gel electrophoresis revealed that the DNA polymerase of avian myeloblastosis virus found in crude preparations of the virus could be purified nearly to homogeneity by a single passage through the column. These results suggest that pyran-Sepharose is an effective affinity column that is potentially adaptable as part of a general purification procedure for viral DNA polymerases.

RNA of simian sarcoma-associated virus type 1 produced in human tumor cells

Simian sarcoma-associated virus type 1 propagated in human rhabdomyosarcoma cells exhibited characteristics typical of oncornaviruses but seemed to have several aberrant properties. It had a buoyant density of 1.14 g/cm3, had RNA-dependent DNA polymerase activity, seemed to be labile to high salt concentrations, and contained little 50 to 60S RNA but relatively large amounts of human ribosomal RNA. In addition to 50 to 60S RNA, purified virions contained smaller RNA molecules with sedimentation coefficients of 28 to 30S, 18 TO 20S, and 4 to 10S. Unlike the 50 to 60S RNA species, the smaller virion-associated RNAs lacked polyadenylic acid, and the 28 to 30S RNA had an average base composition similar to that of human ribosomal RNA. Upon heat denaturation, the native 50 to 60S RNA genome yielded polyadenylic acid-containing 28 to 30S subunits that degraded in to 18 to 20S molecules upon further heat treatment. The 50 to 60S viral RNA had a guanine plus cytosine content of 56%.

A new chemical procedure for 32P-labeling of ribonucleic acids at their 5'-ends after isolation

A new technique, which utilizes the chemical reaction between [32P]diimidazolidate of orthophosphate and the cetyltrimethylammonium salt of high-molecular-weight RNA in nonaqueous dimethyl formamide, has been developed for the 32P-labeling of RNAs after isolation. The radioactive label of high specific activity is introduced onto a phosphorylated 5'-end of the RNA and renders it suitable for 5'-terminal group analysis. When the labeling reaction was applied to the 70S RNA of avian myeloblastosis virus, a labeled 35S RNA was isolated on sucrose-dimethyl sulfoxide gradients without apparent degradation.

Characterization of the end groups of RNA of Rous sarcoma virus

The 3' terminus of the 30-35S RNA of Rous sarcoma virus is adenosine. Its amount indicates an average molecular weight for that RNA of about 3 x 10(6). The 5' terminus of 30-35S RNA of Rous sarcoma virus was not di- or triphosphorylated, whether isolated by the standard procedure or from virus collected within 3 min of its release from the cells.

Effect of chemically modified 70S RNA from avian myeloblastosis virus (AMV) upon the activity of AMV DNA polymerase

Adenine residues of 70S avian myeloblastosis virus (AMV) RNA are modified when reacted with chloroacetaldehyde. This modification introduces characteristic fluorescent epsilon-adenosine (epsilonA) probes which were used to monitor the reaction. Under suitable conditions, modified 70S(epsilonA) RNA was maintained intact and was inactive as a template for the AMV DNA polymerase. Furthermore, it inhibited the reaction catalyzed by AMV polymerase when 70S RNA was used as template-primer and had no effect on the two tested bacterial polymerases. Protection against the 70S (epsilonA) RNA inhibition was observed when 70S RNA was primed with oligo(dT) indicating preference of the polymerase for the oligo(dT) primed regions.

The homopolyadenylate and adjacent nucleotides at the 3'-terminus of 30-40s RNA subunits in the genome of murine sarcoma-leukemia virus

Adenosine is the major 3'OH-terminal nucleoside of the 60-70S RNA genome of the murine sarcoma-leukemia virus, its 30-40S RNA subunits, and the poly(A) segments derived by RNase treatment of both RNA species, as determined by periodate oxidation-[(3)H]-borohydride reduction. The binding 30-40S RNA to oligo(dT)-cellulose suggests that most viral RNA subunits contain poly(A). The molecular weight of poly(A) derived from viral RNA by digestion with RNase and purified by affinity chromatography is 64,000-68,000, as determined by gel electrophoresis. From the size of poly(A) and the poly(A) content of viral RNA (1.6%), it is estimated that there is about one poly(A) segment for each viral 30-40S RNA subunit. The results of 3'-termini labeling with [(3)H]borohydride, in vivo labeling with [(3)H]adenosine, and base composition of [(32)P]poly(A) indicate that a homopoly(A) segment is located at the 3'-end of a 30-40S RNA subunit. The homogeneous poly(A) segments isolated from RNase T1 digests of 60-70S [(32)P]RNA consist of one cytidylate, one uridylate, and about 190 adenylate residues, while those isolated from RNase A digests consist exclusively of adenylate residues. These results indicate that -G(C,U)A(190)A(OH) is the 3'-terminal nucleotide sequence of the viral 30-40S RNA subunits.

Inhibition of RNA-dependent DNA polymerase of avian myeloblastosis virus by pyran copolymer

PYRAN COPOLYMER, A KNOWN IMMUNOSTIMULATOR, WAS FOUND TO BE A POTENT INHIBITOR OF PURIFIED DNA POLYMERASE (DEOXYNUCLEOSIDETRIPHOSPHATE: DNA deoxynucleotidyltransferase; EC 2.7.7.7) isolated from avian myeloblastosis virus. Unlike other inhibitors, pyran showed unique features of inhibition. It interacts with the polymerase at a region other than the template site. The inhibitory effect was overcome only by excess enzyme and not affected by excess template. The degree of inhibition was not template specific for the templates tested: 70S RNA from avian myeloblastosis virus, synthetic hybrid poly(rA).oligo(dT)(10), synthetic copolymer poly(dA-dT), and activated calf-thymus DNA. The observed rate of inhibition by pyran was shown to vary with the different polymerases tested. Inhibition was shown with all oncornaviral polymerases and, to a lesser extent, with mammalian polymerases. However, two of the three bacterial polymerases, by contrast, showed a marked activation.

Characterization of RNA from noninfectious virions produced by sarcoma positive-leukemia negative transformed 3T3 cells

RNA from noninfectious virions produced by two established clonal lines of sarcoma positive-leukemia negative (S+L-)-transformed 3T3 cells has been characterized. RNA from virions or nucleoids of S+L--(C243) cells consisted of three to four sizes: +/-44 S (6%), 28 S (17%), 18 S (38%), and <18 S (39%). 28S virion RNA contained some virus-specific information demonstrable by RNA.DNA hybridization with a DNA probe derived from the RNA-directed DNA polymerase product of murine sarcoma-leukemia virus, while parallel studies indicated that 28S ribosomal RNA from ribosomal subunits of transformed and nontransformed 3T3 cells did not contain virus-specific information. In contrast to the S+L-(C243) virions, RNA from virions or nucleoids of S+L-(D56) cells consisted of five sizes: 80 S (6%), 68 S (8%), 56 S (5%), 28 S (28%), and <28 S (53%). Thermal dissociation studies suggested that this S+L- genome is comprised of 28S RNA subunits. From these studies we postulate that the 28S viral RNA is most probably the monomeric genome of S+L- virions.

Amino-acid acceptor activity of the "70S-associated" 4S RNA from avian myeloblastosis virus

The "70S-associated" 4S RNA from avian myeloblastosis virus contains transfer RNA, as determined by aminoacylation. The various amino acids esterified, plus the great number of minor bases found in this "70S-associated" 4S RNA indicate that a sizeable fraction, but not all, of this RNA is transfer RNA.

Minor base composition of "70S-associated" 4S RNA from avian myeloblastosis virus

Using a chemical isotope derivative method, we have determined the minor base composition of the "70S-associated" 4S RNA isolated from avian myeloblastosis virus. The minor base composition of this "70S-associated" 4S RNA is strikingly similar to that of the corresponding "free" 4S RNA of the virion. This minor base content, plus the capacity to esterify amino acids, establishes that both of these virion 4S RNA fractions contain transfer RNA. The percentage of minor bases in virion "70S-associated" 4S RNA is, however, much lower than in "free" 4S virion RNA and in myeloblast 4S RNA. The implication is that the "70S-associated" 4S RNA fraction as isolated herein also contains RNA that is not transfer RNA. This latter RNA may represent either degradation products of high molecular weight RNA or indigenous 4S RNA of undetermined function.

Analysis of high-molecular-weight ribonucleic acid associated with intracisternal A particles

Intracisternal A particles, known primarily for their association with various tumors, have been shown to contain high-molecular-weight (HMW) ribonucleic acid (RNA) by velocity centrifugation, using linear glycerol gradients. This HMW RNA is sensitive to ribonuclease digestion and alkali treatment but is resistant to Pronase treatment. By a double-labeling experiment, HMW RNA was shown to be intrinsic to intracisternal A particles and not to have resulted from cytoplasmic polysomal RNA aggregation. By a reconstitution experiment, it was determined that the results were not due to C-type virus contamination. The synthesis of HMW RNA in intracisternal A particles is inhibited by actinomycin D and ethidium bromide. These observations emphasize that there are probably some taxonomic relationships between intracisternal A particles and oncogenic RNA viruses.