Biochemical studies on adenovirus multiplication, XIX. Resolution of late viral RNA species in the nucleus and cytoplasm

Differences in sequence content of nuclear and cytoplasmic polyribosomal RNA from adenovirus-infected cells

RNA molecules from nuclear and cytoplasmic polyribosomes of adenovirus-infected HeLa cells were compared by hybridization to analyse the sequence content. Nuclear polyribosomes were released by exposure of intact detergent-washed nuclei to poly(U) and purified. Cytoplasmic polyribosomes were also purified from the same cells. To show that nuclear polyribosomes contain ribosomes linked by mRNA, polyribosomes were labelled with methionine and uridine in the presence of actinomycin D in adenovirus-infected cells. Purified nuclear polyribosomes were treated with EDTA under conditions which dissociate polyribosomes into ribosomes and subunits with a simultaneous release of mRNA, and sedimented. The treatment dissociated these polyribosomes, releasing the mRNA from them. Radiolabelled total RNA from each polyribosome population was fractionated in sucrose gradients into several pools or hybridized to intact adenovirus DNA to select virus-specific RNA. Sucrose-gradient-fractionated pool-3 RNA (about 28S) and virus-specific RNA were then hybridized to fragments of adenovirus DNA cleaved by restriction endonucleases SmaI, HindIII and EcoRI by the Southern-blot technique and by filter hybridization. The results showed that nuclear RNA contained sequences, from about 0 to 18 map units, which were essentially absent from cytoplasmic RNA. Furthermore, the amount of virus-specific RNA for a particular sequence was also different in the two populations.

Identification and purification of a protein encoded by the human adenovirus type 2 transforming region

The human adenovirus type 2 (Ad2) transforming genes are located in early regions E1a (map position 1.3 to 4.5) and E1b (map position 4.6 to 11.2). We have identified and purified to near homogeneity a major 20,000-molecular-weight (20K) protein and have shown that it is coded by E1b. Using an Ad2-transformed cell antiserum which contained antibody to E1b-coded proteins, we immunoprecipitated 53K and 19K proteins from the nucleoplasm and 53K, 19K, and 20K proteins from the cytoplasmic S-100 fraction of Ad2 productively infected and Ad2-transformed cells. The 19K protein was present in both the nucleoplasm and the cytoplasm, whereas the 20K protein was found only in the cytoplasm. The 53K and 19K proteins are known Ad2 E1b-coded proteins. The 20K protein was purified to near homogeneity in 20 to 50% yields by sequential DEAE-Sephacel chromatography and reverse-phase high-performance liquid chromatography. Purified 20K protein shares most of its methionine-labeled tryptic peptides with E1b-53K, as shown by reverse-phase high-performance liquid chromatography, and therefore is closely related to the 53K protein. The 19K protein does not appear to share tryptic peptides with either 20K or 53K protein. To provide more direct evidence that 20K protein is virus-coded, we translated E1b-specific mRNA in vitro. Both immunoprecipitation analysis and high-performance liquid chromatography purification of the translated product identified a 20K protein that has the same tryptic peptides as the 20K protein isolated from infected and from transformed cells. These findings suggest that the Ad2 20K protein is a primary translation product of an Ad2 E1b mRNA.

Groups of adenovirus type 2 mRNA's derived from a large primary transcript: probable nuclear origin and possible common 3' ends

Late in adenovirus type 2 infection, a number of mRNA's apparently arise by processing a large nuclear transcript that represents the right-hand 85% of the genome (summarized in Evans et al., Cell 12:733-739, 1977). Hybridization of labeled late mRNA to a series of DNA restriction fragments representing the right-hand 70% of the genome demonstrates at least 12 discrete mRNA's that appear to fall into five groups, each possibly containing a common 3' terminus. The processing necessary to generate these mRNA's apparently occurs in the nucleus. All the mRNA's appear to contain a sequence of approximately 100 nucleotides complementary to a fragment with coordinates 25.5-27.9. This fragment contains one of the regions found by Berget et al. (Proc. Natl. Sci. U.S.A. 74:3171-3175, 1977), Chow et al. (Cell 12:1-18, 1977), and Klessig (Cell 12:9-22, 1977) to the "spliced" onto the 5' end of late adenovirus type 2 mRNA's. Because the sequences to be spliced exist only once per large transcript, any of the mRNA-specific regions might only be preserved from a small fraction of the transcripts. Measurement of the transport efficiency of regions of the large nuclear transcript, if fact, shows that only 15 to 25% of any particular region is transported to the cytoplasm. The overall conclusion of these experiments is that the large late nuclear transcript can be processed in the nucleus to yield any one of many (approximately 12) mRNA's; the unused portions of the primary transcript then accumulate in the nucleus or are destroyed.

Transcriptional complexity of vaccinia virus in vivo and in vitro

The transcriptional complexity of vaccinia virus both in vivo and in vitro has been measured by using DNA:RNA hybridization with RNA in excess. In vivo, "early" or prereplicative RNA was found to saturate at 25% or one-half of the viral genome. "Late" or postreplicative RNA from infected HeLa cells saturated at 52% or essentially the entire genome. This well-regulated transcriptional pattern of the virus in vivo was not maintained in vitro. In a number of experiments a range of saturation values from 40 to 50% was obtained for in vitro synthesized RNA. The complexity of polyadenylated and non-polyadenylated RNA, as well as total purified 8 to 12S RNA released from the virus, was indistinguishable from purified high-molecular-weight virion-associated RNA with a sedimentation value of greater than 20S and equivalent to total in vitro synthesized RNA. No additional hybrid formation was observed in experiments in which total in vitro RNA and late in vivo RNA from infected HeLa cells were combined, suggesting that the virus does not transcribe in vitro DNA sequences that are not also transcribed during productive infection. Approximately 15% complementary RNA was detected when radiolabeled total in vitro RNA was allowed to reanneal with late in vivo RNA, while as much as 8% of the in vitro synthesized RNA was found to be complementary.

Species identification and genome mapping of cytoplasmic adenovirus type 2 RNAs synthesized late in infection

Adenovirus type 2 cytoplasmic RNAs synthesized late in productive infection were resolved by electrophoresis on formamide gels. Regions of the adenovirus 2 genome specifying RNAs of distinct size were determined by hybridization to specific DNA fragments generated by cleavage with endo R.EcoRI and endo R.SmaI. From these studies 13 distinct viral RNA species were identified. A 26S to 28S size class and a 21S to 23S size class were each found to consist of four distinct RNA species. Three RNA species were identified in a 16S to 18S size class, and a fourth size class, 11S to 13S, was resolved into two components. The SmaI-D region (0.38 to 0.51 on the unit genome) and the EcoRI-F, D region (0.70 to 0.83) of the genome were found to code for multiple transcripts. Three RNAs (28S, 22S, and 18S) are specified by SmaI-D, and four components, 28S, 22S, 18S, and 16S, are encoded by EcoRI-F,D. The RNA represented by each set of multiple transcripts exceeds the coding capacity of the respective region, and the species within each set of RNAs appear to contain common sequences. The relationship between the cytoplasmic RNA species synthesized at late times and early cytoplasmic RNAs was determined by hybridization-inhibition experiments. The multiple transcripts encoded by the EcoRI-D fragment were found to contain sequences that are present in early cytoplasmic RNA. These studies enabled preparation of a map which accounts for transcription of approximately 67% of the r strand of the adenovirus 2 genome.

Fidelity of adenovirus RNA transcription in isolated HeLa cell nuclei

An in vitro nuclear system from adenovirus type 2-infected cells was developed to study transcription of viral RNA. Nuclei isolated from adenovirus-infected HeLa cells late in the infectious cycle synthesized in vitro only RNA from the r-strand of adenovirus DNA. Around 15% of the virus-specific RNA in isolated nuclei was polyadenylated. Short pulse labeling of nascent RNA followbd by hybrization of size-fractionated RNA to specific restriction endonuclease fragments of the genome suggested that the origin(s) for transcription is located on the r-strand in the left 30% of the adenovirus 2 genome at late times in the infectious cycle. Pulse-chase experiments were used to estimate the elongation rate of adenovirus high-molecular-weight RNA in isolated nuclei. An elongation of a least six nucleotides per second was observed in vitro. Viral RNA synthesis in the vitro nuclei showed several similarities to the in vivo system late in the infectious cycle.

Genome expression and mRNA maturation at late stages of productive adenovirus type 2 infection

RNA from adenovirus 2-infected KB cells was annealed in liquid with RNA in vast excess to viral heavy (l) and light (r) 32P-labeled DNA strands. Hybridization kinetics were analyzed by computer to estimate the number of viral RNA abundance classes, their relative concentrations, and the fraction of each DNA strand from which they originated. Early whole cell RNA extracted 5 h postinfection annealed rapidly to 10 to 15% of l and r strands and then slowly to final values of 60 and 40% of l and r strands. By 9 h postinfection the expression of late genes was apparent and whole cell RNA annealed to 20 and 75% of l and r strands. Whole cell RNA extracted between 12 and 36 h postinfection annealed to 7 to 15% and 75 to 90% of l and r strands. Late nuclear RNA hybridized to 10 and 90% of l and r strands, and late polyribosomal RNA hybridized to 20 and 75% of l and r strands. Based upon kinetic analyses, we estimate that mRNA synthesized exclusively during late stages arises from about 6 to 8% and 45 to 49% of l and r strands. This assumes that the early class I mRNA (in low concentration late) originates from 8 to 10% and 6 to 10% of l and r strands and that early class II mRNA (in high concentration late) is derived from 2% and 8 to 13% of l and r strands. Mixing experiments indicated that early mRNA is a subset of RNA extracted from polyribosomes late after infection and that late nuclear RNA contains sequences complementary to early l strand class I nRNA. RNA-RNA hybrids were isolated from late mRNA containing sequences from 60% of l and r strands, but it is not known when these were synthesized, and therefore whether complementary RNA transcripts are synthesized late after infection, as they are known to be synthesized early. These results demonstrate that portions of the genome are transcribed into RNA sequences that remain confined to the nucleus and are not exported to polyribosomes as mRNA.

Adenovirus transcription. IV. Synthesis of viral-specific RNA in human cells infected with temperature-sensitive mutants of adenovirus 5

Cytoplasmic RNA sequences produced in HeLa cells infected with the adeno-virus 5 temperature-sensitive mutants ts1, ts2, ts9, ts17, ts18, ts19, ts20, ts22, ts49, ts36, and ts125 were characterized by hybridization to DNA probes generated by strand separation of restriction endonuclease fragments of adenovirus 5 DNA. Two ""early'' mutants defective in DNA synthesis, ts125 and ts36, fail to make wild-type levels of all previously reported classes of late RNA at the nonpermissive temperature. At 40.5 degrees C, both ts125 and ts36 synthesize a wild-type complement of early cytoplasmic RNA 16 h after infection. Under these conditions, no ""late'' cytoplasmic RNA sequences were observed. Similarly, nuclear RNA present in these cells resembled early cytoplasmic RNA rather than late nuclear RNA. All the late adenovirus 5 temperature-sensitive mutants synthesized normal wild-type levels of late cytoplasmic RNA at the nonpermissive temperature, except ts2, which appears to overproduce certain cytoplasmic species.

Characterization of adenovirus type 2 transcriptional complexes isolated from infected HeLa cell nuclei

HeLa cell nuclei, isolated 17 h after infection with human adenovirus type 2 (Ad2), were treated with 200 mM ammonium sulfate. The extract (S200 fraction) contained 50 to 70% of the nonintegrated Ad2 DNA, which was in the form of nucleoprotein complexes. These complexes contained native, intact Ad2 DNA (with the exception of replicative intermediates) and could be partially purified and resolved by velocity gradient centrifugation. Using high-salt (200 mM ammonium sulfate) incubation conditions, more than 95% of the nuclear RNA polymerase activity belonged to class B. About 45% of the class B enzyme molecules bound to DNA in the nuclei (those "engaged" in RNA synthesis) were released from the nuclei in the form of Ad2 transcriptional complexes by treatment with 200 mM ammonium sulfate. At least 90% of the RNA synthesized in high salt in the nuclei or in the S200 fraction was Ad2 specific, and essentially all of this RNA was complementary to the l strand of Ad2 DNA. These findings are compatible with what is known about Ad2-specific RNA synthesis in vivo. The analysis of the RNA synthesized from partially purified transcriptional complexes supports the contention that its transcription is almost entirely asymmetric, and that the asymmetry observed in vivo is not a consequence of the rapid degradation of h-strand transcripts. The RNA synthesized in vitro in the absence of detectable RNase activity sedimented with a maximum size of 35 to 40S. Less than 5% of the nuclear or the S200 fraction RNA polymerase activity was class C when assayed under non-reinitiating conditions. Although much of the RNA synthesized by the class C enzyme was Ad2 specific, 5.5S virus-associated RNA was not the predominant product. The isolation of Ad2 DNA transcriptional complexes provides an attractive system for further characterizing the Ad2 DNA template used for transcription and for studying the regulation of the expression of the Ad2 genome during the productive infection cycle.

The methylation of adenovirus-specific nuclear and cytoplasmic RNA

Each poly(A) containing cytoplasmic AD-2 MRNA contains at its 5' terminus the general structure m7 GpppN1 pN2p or m7 GpppN1mpN2mpNp as well as an average of 4 m6A and 0.5-1 m5C residues per molecule. Almost all of the N1m residues are adenine derivatives including Am, m6Am and probably m26,6Am. The N2m is mostly Cm but small amounts of the other three methylated bases are also present. All the methylated constitutents of mRNA are distant from the 3' terminal poly(A). The amount of m6A appears to be greater in larger mRNA than in smaller mRNA. Nuclear Ad-2 specific RNA also contains caps, m6A, and m5C with about twice as much m6A relative to caps as cytoplasmic mRNA. The similarity of Ad-2 nuclear and mRNA to HeLa hnRNA and mRNA suggests that adenovirus mRNA production is a good model for eukaryotic mRNA production.

Viral RNA synthesis and levels of DNA-dependent RNA polymerases during replication of adenovirus 2

The rates of RNA synthesis in cultured human KB cells infected by adenovirus 2 were estimated by measuring the endogenous RNA polymerase activities in isolated nuclei. The fungal toxin alpha-amanitin was used to determine the relative and absolute levels of RNA polymerases I, II, and III in nuclei isolated during the course of infection. Whereas the level of endogenous RNA polymerase I activity in nuclei from infected cells remained constant relative to the level in nuclei from mock-infected cells, the endogenous RNA polymerase II and III activities each increased about 10-fold. These increases in endogenous RNA polymerase activities were accompanied by concomitant increases in the rates of synthesis in isolated nuclei of viral mRNA precursor, which was quantitated by electrophoretic analysis on polyacrylamide gels. The cellular RNA polymerase levels were measured with exogenous templates after solubilization and chromatographic resolution of the enzymes on DEAE-Sephadex, using procedures in which no losses of activity were apparent. In contrast to the endogenous RNA polymerase activities in isolated nuclei, the cellular levels of the solubilized class I, II, and III RNA polymerases remained constant throughout the course of the infection. Furthermore, no differences were detected in the chromatographic properties of the RNA polymerases obtained from infected or control mock-infected cells. These observations suggest that the increases in endogenous RNA polymerase activities in isolated nuclei are not due to variations in the cellular concentrations of the enzymes. Instead, it is likely that the increased endogenous enzyme activities result from either the large amounts of viral DNA template available as a consequence of viral replication of from replication or from functional modifications of the RNA polymerases or from a combination of these effects.

Adenovirus-2 mRNA is transcribed as part of a high-molecular-weight precursor RNA

The order of transcription and the length of nascent RNA transcripts from adenovirus-2 (Ad-2) DNA in the nucleus of infected cells has been deduced by labeling the growing RNA chains in vivo for a very brief period, separating the RNA on the basis of size, and hybridizine to the ordered EcoRI restriction endonuclease fragments derived from Ad-2 DNA. The majority of the virus-specific RNA molecules are synthesized as very high-molecular-weight units beginning at a common point at least 25-30,000 base pairs from one end of the Ad-2 DNA. These molecules can be reduced in size without further RNA synthesis. The experiments indicate the obligatory origin of Ad-2 mRNA from a high-molecular-weight precursor molecule.

Identification of early adenovirus type 2 RNA species transcribed from the left-hand end of the genome

Unique fragments of adenovirus type 2 DNA generated by cleavage with endonuclease R-Eco RI or endonuclease R-Hsu I (Hin dIII) were used to map cytoplasmic viral RNAs transcribed early in productive infection. Radioactive early viral RNA was first fractionated by polyacrylamide gel electrophoresis. Eluted viral RNAs were then tested for hybrid formation with DNA fragments. The Eco RI DNA fragment (Eco RI-A) which contains the left-hand 58% of the genome hybridized 13S and 11S RNAs. More detailed mapping of these RNAs was achieved by hybridization to the seven Hsu I fragments of Eco RI-A. The early RNA annealed only to Hsu I-G and C, two fragments which comprise the extreme left-hand 17% of the genome. Viral RNA migrating as 13S and 11S annealed to Hsu I-G, and 13S RNA annealed to Hsu I-C. A 13S RNA is transcribed from Eco RI-A late in infection (18 h). Hybridization-inhibition studies with Eco RI-A DNA, early cytoplasmic RNA, and 3H-labeled 13S late RNA demonstrated that this RNA synthesized at late times is an early RNA species which continues to be synthesized in large amounts at 18 h. This 13S RNA synthesized at 18 h hybridized to Hsu I-C but not to Hsu I-G DNA. These results establish that the 13S RNAs transcribed from Hsu I-G and C at early times must be different species.

Analysis of early adenovirus 2 RNA using Eco R-R1 viral DNA fragments

Adenovirus 2 RNA synthesized early in productive infection was analyzed by RNA-DNA hybridization. Hybridization experiments were performed with adenovirus 2 DNA and wit, the six adenovirus 2 DNA fragments generated 0y digestion with the restriction endonuclease Eco R.R1. Duplex formation between RNA and -32P-labeled viral DNA was assayed by S(1) nuclease digestion. RNA from the cytoplasm annealed 12 percent of the total viral DNA and the following percentage of each of the R.R1 fragments: 6 percent of R1-A, 24 percent of R1-B, 0 percent of R1-F, 40 percent of R1-D, 13 percent of R1-E, and 22 percent of R1-C. The early cytoplasmic RNA is composed of two sequence classes: class I, present in greatly reduced quantities at late times in infection (18 h), and class II, which remains at high concentrations at 18 h. In hybridization-inhibition experiments, hybridization of class II RNA is inhibited by late cytoplasmic RNA, whereas hybridization of class I RNA is not blocked by late cytoplasmic RNA (J. J. Lucas and H. S. Ginsberg, 1971; E.A. Craig and H. J. Raskas, 1971). To determine the location of class I and II sequences on the genome, membrane bound DNA fragments were used in hybridization-inhibition experiments. These studies demonstrated that the early cytoplasmic transcripts of R1-D belong to class II, whereas R1-C transcripts are class I sequences. The cytoplasmic RNAs transcribed from fragments A and B contain both class I and class II sequences. Analysis of cytoplasmic RNA fractionated by size demonstrated that the class I sequences include a 19 S RNA transcribed from R1-B and class II sequences include a 20S RNA derived from R1-D. Nuclear RNA purified from cultures early in infection was annealed with -32P-labeled R1 fragments. With all six fragments the nuclear RNA annealed as much or more of the DNA than did cytoplasmic RNA. Eco R1-F annealed at least 25 percent with early nuclear RNA, whereas no sequences homologous to R1-F were detected in early cytoplasmic RNA. When cultures were labeled from 2 to 6 h after infection, at least 5 percent of the -3H-labeled early nuclear viral RNA annealed to Eco R1-F. Some of these nuclear transcripts from R1-F appear to be covalently linked to sequences transcribed from a contiguous region of the genome (Eco R1-B). 8.4 percent of the RNA selected by hybridization of R1-F reannealed to R1-B, whereas no more than 1.5 percent reannealed to R1 fragments A, D, E, or C.

Sequence relationships between adenovirus 2 early RNA and viral RNA size classes synthesized at 18 hours after infection

Synthesis of cytoplasmic viral RNA was studied during infection of cultured human (KB) cells with adenovirus 2. At 6 h, before viral DNA synthesis began 5% of the poly(A)-containing RNA hybridized to viral DNA; by 12 h and at later times more than 80% was virus specified. At 18 h after infection, four major size classes of cytoplasmic viral RNA were identified among the poly(A)-containing molecules. These size classes migrated as 27S, 24S, 19S, and 12 to 15S in polyacrylamide gels. The three larger size classes could also be identified in denaturing formamide gels. Hybridization of the 27S, 24S, and 19S viral RNAs was not inhibited by RNA harvested from cells at early times in infection. Therefore, these three major RNAs must code for late viral proteins. Hybridization of the 12 to 15S RNA was partially inhibited by RNA from cultures harvested at early times, suggesting that in this size class some of the RNA labeled at 18 h codes for early viral proteins.

Localization of adenovirus 2 messenger RNA's to segments of the viral genome defined by endonuclease R-R1

Adenovirus 2 mRNAs synthesized in productive infection were assigned to specific regions of the genome by hybridization to unique fragments of viral DNA. Radioactive viral RNA synthesized early or late in infection was first fractionated by polyacrylamide gel electrophoresis. Eluted RNAs were then tested for complementary hybrid formation with each of the six fragments of adenovirus 2 DNA generated by cleavage with endonuclease R.R1. Early RNA species migrating as 13S, 19S, and 20S RNAs were identified as transcription products of fragments A, B, and D, respectively. In addition to the 13S RNA transcribed from A fragment DNA, 13S RNA also hybridized to the D and E fragment DNAs; 11S RNA annealed to both A and B fragments. The RNA that hybridized to fragment C DNA was heterogeneous in size. Viral RNA synthesized late in infection included 27S, 24S, 19S, and 11S size classes, all of which annealed to A fragment DNA. Additional RNA migrating as 24S hybridized to E and C fragment DNA, and 23S RNA annealed to F fragment DNA. The results of the hybridizations of size fractionated RNAs with viral DNA fragments enabled formation of a partial map of viral mRNAs with respect to the adenovirus 2 genome. Some of the viral RNAs may represent transcripts which overlap R1 cleavage sites, because in at least three instances hybridization revealed viral RNAs which have the same electrophoretic mobility and anneal to fragments that are contiguous on the genome.

Synthesis of viral-specific RNA in cells infected with the parvovirus, Kilham rat virus

We have studied the viral-specific RNA synthesized after infection of a permissive cell line with Kilham rat virus (KRV). The RNA was shown to be virus specific by analysis of its nucleotide base ratios and by hybridization with KRV and cellular DNA. Viral RNA is synthesized as early as 2 h after infection. This viral RNA synthesis occurs before viral progeny DNA synthesis which is initiated at 7 to 8 h after infection. The predominant viral RNA synthesized before and after viral progeny DNA synthesis has a sedimentation coefficient of approximately 18S in dimethylsulfoxide-sucrose gradients and a calculated molecular weight of 6.5 x 10(5) to 7.5 x 10(5). KRV contains a molecule of single-stranded DNA with a molecular weight of approximately 1.6 x 10(6). If the viral-specific 18S RNA is a homogenous species, it would account for 40 to 50% of the viral genome. A small amount of 26S viral RNA with a molecular weight of 1.6 x 10(6) to 1.7 x 10(6) can also be detected. If this 26S RNA is a single viral-specific entity, it could represent a transcription of the entire KRV genome.

Translation in vitro of total nuclear RNA from HeLa cell nuclei infected with adenovirus 2

Total heterogeneous nuclear RNA from HeLa cells infected with adenovirus for 18-20 hr stimulates amino acid incorporation into protein in a cell-free system from Ehrlich ascites tumors. This stimulation of protein synthesis by the nuclear RNA requires intact nuclei. The role of nuclei in this system is unknown, but evidence is presented that the nuclei are involved in the conversion of high-molecular-weight RNA to low-molecular-weight species. Some of the newly synthesized polypeptides appear to resemble the virion polypeptides.

Cell-free synthesis of adenovirus 2 proteins programmed by fractionated messenger RNA: a comparison of polypeptide products and messenger RNA lengths

Cytoplasmic RNA extracted from human tissue culture cells infected with adenovirus type 2 was used to program protein synthesis in a cell-free system derived from mammalian cells. Analysis of the protein product by polyacrylamide gel electrophoresis revealed ten adenovirus-specific polypeptides. Five of these were further identified by analysis of tryptic peptides. Translation of RNA fractionated by sedimentation through sucrose gradients containing formamide demonstrated seven size classes of RNA, each of which programmed the synthesis of only one or two virus-specific polypeptides. Six of the virus-specific polypeptides were translated from RNAs much larger than expected for the size of the polypeptide.

Relationship of mRNA from productively infected cells to the complementary strands of adenovirus type 2 DNA

The complementary strands of adenovirus type 2 (Ad2) DNA were separated by buoyant density gradient centrifugation with poly (U, G). The complementary strand DNA was shown to remain intact through the course of strand separation. The l-strand of Ad2 DNA, appearing in the less dense complex with poly (U, G) in neutral CsCl density gradients, was shown to have a buoyant density in alkaline (pH 12.5) CsCl density gradients which is 2 to 3 mg per ml greater than that of its complement (h-strand). Renaturation of purified complementary strand DNA was observed only in mixtures of h- and l-strand DNA, and then with the second-order reaction rate expected for Ad2 DNA. Hybridization of the complementary strands of Ad2 DNA with cytoplasmic mRNA isolated from infected HeLa cells was performed in liquid phase and analyzed by hydroxylapatite chromatography. Before viral DNA synthesis (6 h after infection), 13 to 18% of the h-strand and 30 to 35% of the l-strand were represented in viral mRNA. Late (18 h) after infection the mRNA represented 20 to 25% and 63 to 68% of the h- and l-strands, respectively. Most, if not all sequences present in viral mRNA before viral DNA synthesis were also present in the cytoplasm late in infection.

Processing of adenovirus 2-induced proteins

Analysis of (35)S-methionine-labeled extracts of adenovirus 2-infected KB cells revealed 22 virus-induced polypeptide components. Most proteins of the virion were easily detected in extracts of whole cells labeled for short periods between 15 and 30 h after infection; however, several virion components were conspicuously absent. Radioactivity appeared in two of these virion components during a chase in nonradioactive medium, and this appearance was paralleled by a decrease in the radioactivity associated with two nonvirion adenovirus-induced proteins, results which imply precursor-product relationships for these components. Comparison of one of the chasable adenovirus-induced components (designated P-VII; mass of 20,000 daltons) and the major core protein (VII; mass of 18,500 daltons) of the virion showed that they have four common methionine-containing tryptic peptides; P-VII has an additional methionine residue which is not found in the major core protein. We propose that at least two of the adenovirus 2 virion components are derived by the cleavage of higher molecular weight precursor polypeptides.

Transcription and transport of virus-specific ribonucleic acids in African green monkey kidney cells abortively infected with type 2 adenovirus

The techniques of deoxyribonucleic acid-ribonucleic acid (DNA-RNA) hybridization and immunological precipitation were used to compare the synthesis of adenovirus-specific macromolecules in African green monkey kidney (AGMK) cells infected with adenovirus, an abortive infection, and coinfected with both adenovirus and simian virus 40 (SV40), which renders the cells permissive for adenovirus replication. When viral protein synthesis was proceeding at its maximum rate, the incorporation of (14)C-amino acids into adenovirus structural proteins was about 90 times greater in the doubly infected cells than in cells infected only with adenovirus. However, the rates of synthesis of virus-specific ribonucleic acid appeared to be comparable in the two infections at all times measured. A time-dependent increase in the rate of RNA synthesis observed late in the abortive infection was dependent upon the prior replication of viral DNA. Moreover, all virus-specific RNA species that are normally made late in a productive adenovirus infection (i.e., the true late and class II early RNA species) were also detected in the abortive infection. Adenovirus-specific RNA was detected by molecular hybridization in both the cytoplasm and nuclei of abortively infected cells. Comparable amounts of viral RNA were found in the cytoplasmic fractions of AGMK cells infected either with adenovirus or with both adenovirus and SV40. The results of hybridization-inhibition experiments clearly showed that there was a class of virus-specific RNA molecules, representing about 30% of the total, in the nucleus that was not transported to the cytoplasm. This class of RNA was also identified in similar amounts in productively infected human KB cells. The difference in the abilities of cytoplasmic and nuclear RNA to inhibit the hybridization of virus-specific RNA from whole cells was shown not to be due to a difference in the molecular size of the RNA species from the two cell fractions or to the specific loss of a cytoplasmic species during RNA extraction procedures.

Procedure for the preparation of milligram quantities of adenovirus messenger ribonucleic acid

Late after adenovirus 2 infection (18 hr), nearly all newly synthesized polysomal messenger ribonucleic acid (mRNA) is viral specified. Large amounts of adenovirus mRNA have been purified by utilizing membrane filtration at high ionic strength. With this procedure, molecules that contain polyadenylic acid [poly (A)] tracts are bound selectively, and ribosomal RNA can be separated from the viral mRNA which contains poly(A). Polysomal RNA synthesized 18 hr after infection was labeled in the presence of 0.02 mug of actinomycin D per ml and extracted at pH 9.0. This RNA annealed 40% to 3 mug of adenovirus 2 deoxyribonucleic acid; the RNA selected by membrane filtration bound 80% under the same conditions. The RNA eluted from membrane filters was 80 to 90% greater than 18S and contained species migrating as 31, 27, and 24S. Binding of polysomal RNA to individual membrane filters was linear, using as much as 300 mug of RNA per membrane. A 1.1-mg amount of viral RNA was prepared from 17.7 mg of polysomal RNA that had been purified by extraction at pH 9.0.

Processing of adenovirus RNA before release from isolated nuclei

Nuclei isolated from cultured human cells (KB) infected with adenovirus type-2 were used to study events occurring during the adenosine triphosphate-dependent release of viral RNA. When cells were labeled with [(3)H]uridine for 50 min beginning 18 hr after infection, most nuclear viral messenger RNA was in the form of high molecular weight precursors with sedimentation coefficients greater than 28 S. When nuclei were incubated in the presence of ATP and an ATP-generating system, labeled RNA the size of viral mRNA (10-29 S) was released. Cleavage of viral RNA precursor molecules of high molecular weight occurred during incubation of nuclei. The change in size of viral RNA did not require exogenous ATP and occurred before release of RNA from nuclei. This RNA cleavage seems comparable to processing of mRNA in vivo, for discrete viral species were produced. Cleavage was completed after 10 min of incubation but was not the rate-limiting step in the release reaction, which required about 20 min for completion.

Isolation and characterization of adenovirus messenger ribonucleic acid in productive infection

Messenger ribonucleic acid (mRNA) from cells productively infected with adenovirus type 2 was isolated by affinity chromatography on polyuridylic acid [poly (U)] bound to Sepharose. At least 90% of the polyadenylic acid [poly (A)]-containing polysomal mRNA was retained by the poly (U) Sepharose and thus separated from more than 95% of the ribosomal RNA and transfer RNA. In these experiments, 65% of the early (3 to 5 hr postinfection) and 85% of the late (14 to 16 hr postinfection) virus-specific RNA was retained by the poly (U) Sepharose. Early in the infection 18%, and late in the infection more than 95%, of the poly (A)-containing fraction, eluted from the poly (U) Sepharose with 90% formamide, was adenovirus-specific, as shown by exhaustive hybridization. Different patterns, containing several distinct species of viral mRNA, were detected early and late in the infectious cycle. No distinct viral mRNA lacking poly (A) was discovered.

Adenovirus-associated virus multiplication. 8. Analysis of in vivo transcription induced by complete or partial helper viruses

We have analyzed ribonucleic acid (RNA) synthesized in KB cells co-infected with adenovirus-associated virus (AAV) type 2 and either adenovirus type 2 (Ad2) or herpes simplex virus type 1 (HSV-1). With either type of helper virus, synthesis of AAV RNA was readily detected by deoxyribonucleic acid (DNA)-RNA hybridization. As is the case for AAV RNA synthesized with helper Ad2, the AAV RNA synthesized with HSV-1 as helper annealed only to the thymidine-rich (minus) AAV DNA strand. In addition, AAV RNA synthesized with either type of helper (i) contained similar nucleotide sequences as determined by hybridization inhibition tests and (ii) had a mean molecular weight of approximately 7.5 x 10(5) based on sedimentation in dimethylsulfoxide-sucrose gradients. These experiments suggest that the restricted helper function of HSV-1 is not due to abnormal transcription of the AAV genome. Since the mean molecular weight of AAV RNA is equivalent to 40 to 50% of the AAV genome, as few as two or three AAV RNA species may be transcribed in vivo. In contrast to adenovirus RNA, cleavage of AAV RNA after transcription was not observed.

Adenovirus messenger RNA in mammalian cells: failure of polyribosome association in the absence of nuclear cleavage

The nuclear synthesis of adenovirus-specific RNA late in the infectious cycle in the presence of toyocamycin (an adenosine analogue) has been investigated. There is reduced synthesis of viral RNA with an accumulation of virus-specific RNA in the molecular weight range of at least 4 to 8 x 10(6). No new viral RNA associates with cytoplasmic polyribosomes. In addition, hybridization competition experiments indicate a 70% competition between these large nuclear transcripts and polyribosome-associated viral RNA that was synthesized in the absence of inhibitor. These data are consistent with the following interpretations: complete nuclear processing of viral RNA is necessary for polyribosome association, and precursor viral message(s) contain sequences that are lost normally during post-transcriptional processing.

Polyadenylic acid sequences in the virion RNA of poliovirus and Eastern Equine Encephalitis virus

Poliovirus virion RNA contains a single covalently bound sequence of polyadenylic acid which is approximately 49 nucleotides long. A single, slightly longer polyadenylic acid sequence is contained in Eastern Equine Encephalitis virus RNA. Since these viruses are otherwise dissimilar these sequences may play a common role in viral replication, possibly in translation of the viral RNA.

State of adenovirus 2 deoxyribonucleic acid in the nucleus and its mode of transcription: studies with isolated viral deoxyribonucleic acid-protein complexes and isolated nuclei

Newly replicated adenovirus 2 deoxyribonucleic acid (DNA) can be isolated from the nucleus of HeLa cells by a gentle lysis procedure as a fairly homogeneous complex with a sedimentation of 73S. The viral DNA complex can be prepared completely free from host cell DNA. The viral complex is slightly active in ribonucleic acid (RNA) synthesis in vitro. Treatment of the complex with Pronase and sodium dodecyl sulfate converts the DNA to a form which sediments at 43S. Nuclei isolated from adeno-infected cells synthesize high-molecular-weight virus-specific RNA in vitro. Optimal RNA synthesis requires a divalent cation, preferentially manganese, and relatively high salt concentrations. The synthesis of virus-specific RNA by the isolated nuclei is strongly inhibited by low doses of alpha-amanitine. The latter experimental result is discussed in terms of the polymerase used to transcribe the adenovirus DNA in vivo.

Transcription of the adenovirus genome by an -amanitine-sensitive ribonucleic acid polymerase in HeLa cells

The properties of the ribonucleic acid (RNA) polymerase activity which transcribes the major portion of the adenovirus genome were studied. Nuclei were prepared from infected cells and incubated in vitro. Virus-specific RNA was determined by hybridization to adenovirus deoxyribonucleic acid (DNA). Adenovirus DNA is transcribed principally by an activity which resembles closely polymerase II of the host cell. This activity is inhibited by alpha-amanitine and stimulated by (NH(4))(2)SO(4). Its product is high-molecular-weight heterogeneous RNA. The polymerase activity measured early in infection (3 to 5 hr) resembles that found late in infection (16 to 18 hr).

Addition of polyadenylate sequences to virus-specific RNA during adenovirus replication

Adenovirus-specific nuclear and polysomal RNA, both early and late in the infectious cycle, contain a covalently linked region of polyadenylic acid 150-250 nucleotides long. A large proportion of the adenovirus-specific messenger RNA contains poly(A). As revealed by hybridization experiments, the poly(A) is not transcribed from adenovirus DNA. Furthermore, an adenosine analogue, cordycepin, blocks the synthesis of poly(A) and also inhibits the accumulation of adenovirus messenger RNA on polysomes. Addition of poly(A) to viral RNA may involve a host-controlled mechanism that regulates the processing and transport of messenger RNA.