Regulation of transcription of the SV40 DNA in productively infected and in transformed cells

Methods for the determination of deoxyribonucleic Acid homologies in streptomyces

Variations of the membrane filter technique for deoxyribonucleic acid (DNA) hybridizations were studied with respect to Streptomyces species. At the temperatures required for specific hybridization of DNA with the high melting temperature (T(m)) characteristic of Streptomyces, large amounts (up to 97%) of filter-bound DNA became eluted, in all reaction mixtures studied, within 21 hr. In most solutions this leaching was increased by the presence of sheared denatured DNA. Incubation of DNA-loaded filters in a solution of 50% formamide containing 6x standard saline citrate, at 48 C for 40 hr, was judged to be the best set of conditions tested based on relatively good retention of immobilized DNA, very low hybridization with unrelated DNA of a similarly high T(m) (from Sarcina lutea), and the formation of complexes similar in thermal stability to the native DNA. The expression of results as sheared DNA bound in relation to long-chain DNA retained is recommended when a high concentration of sheared DNA relative to immobilized DNA is used.

Transcription of the viral genome in cell lines transformed by simian virus 40. I. Mapping of virus-specific nuclear RNAs

Mapping of virus-specific nuclear transcripts was carried out in three lines of rat cells transformed by SV40. Each of these cell lines contained a single copy of integrated viral DNA with identified regions adjacent to cell DNA (1). The main virus-specific nuclear transcript in all of these cell lines was shown to be complementary to the minus strand of the early region in SV40 genome. Each cell nucleus contained approximately 50 copies of these RNAs. Transcripts complementary to both strands of the late region in viral genome were also detectable in all of these cell lines. Its content varied depending on the cell line and was 20-50-fold less than that of the main virus-specific transcript. All the regions of integrated SV40 genome in isolated nuclei of transformed cells were equally sensitive to pancreatic DNase I treatment suggesting that the whole viral genome served as a template for RNA synthesis in these cell lines.

Role of the simian virus 40 gene A product in regulation of DNA synthesis in transformed cells

Cells transformed by tsA mutants of simian virus 40 (SV40) are temperature sensitive for the maintenance of the transformed phenotype. The kinetics of induction of DNA synthesis were determined for hamster cell transformants shifted to the permissive temperature after a 48-h serum arrest at the nonpermissive temperature. DNAsynthesis was initiated in the tsA transformants by 8 h after shiftdown was maximal by 12 h. The presence or absence of fetal bovine serum at the time of temperature shift had no effect on the kinetics of initiation of DNA synthesis. Analysis of TTP in tsA transformants revealed similar levels of incorporation of [3H]thymidine into TTP at both permissive and nonpermissive temperatures. Autoradiography revealed that by 12 h after a shift to the permissive temperature, approximately 50% of the cells exhibited labeled nuclei after a 60-min pulse with [3H]thymidine, indicating that a majority of the cells were actively synthesizing DNA. By 8 to 12 h after a shiftup of confluent tsA transformants to the nonpermissive temperature, the number of labeled nuclei was reduced to approximately 16%, regardless of serum concentration. These data indicate that the SV40 gene A product, either directly or indirectly, regulates cellular DNA synthesis in transformed cells.

Characterization of the 5'-terminal capped structures of late simian virus 40-specific mRNA

32P-labeled, late simian virus 40-specific RNA was isoalted from infected CV1 cells and completely degraded with RNase T2 and bacterial alkaline phosphatase. The RNase-resistant material was fractionated two dimensionally and further characterized with Penicillium nuclease and nucleotide pyrophosphatase. Two major 5' termini were identified in late simian virus 40 RNA, namely, 7-methyl Gppp 2',6-dimethyl ApUp and 7-methyl Gppp 2',6-dimethyl Ap 2'-methyl, UpUp. Both 5' termini are present in unfractionated viral RNA as well as in the separated 16S and 19S species. As both caps differ only in secondary modification, it is possible that they are derived from the same site on the DNA. The relatively higher cap II content of the 16S mRNA may be related to its slower rate of turnover.

Characterization of early simian virus 40 transcriptional complexes: late transcription in the absence of detectable DNA replication

Isolation of early viral transcriptional complexes and incorporation in vitro of radiolabeled precursors into nascent RNA has permitted an analysis of early simian virus 40 (SV40) transcription. Under conditions such that viral DNA replication was undetectable, both early and late SV40 RNA were synthesized. This finding provides evidence that viral DNA replication is not an absolute requirement for late transcription and supports earlier observations that late viral RNA is synthesized in SV40-infected nonpermissive mouse cells. The majority of the early viral transcriptional activity can be solubilized, indicating that a substantial portion of this RNA is transcribed from free rather than integrated templates. Sedimentation analysis of the transcriptional complexes resulted in the detection of two separate peaks of activity, suggesting the possibility of two distinct types of early SV40 templates.

[Molecular biology of tumor viruses]

All classes of vertebrates harbor tumor viruses that are capable of inducing either tumors or leukemias. After infection, their genomes become integral parts of the host cell's genetic material (DNA). Many biological functions such as the capacity to code for the synthesis of new proteins and, in particular, the oncogenic property (oncogen) have already been assigned to specific regions (on physical maps) of their DNA.

Characterization of a soluble simian-virus-40 transcription complex

We have previously described the isolation, from nuclei of monkey cells infected with Simian virus 40 (SV40), of a nucleoprotein complex which is able to achieve viral transcription. This complex contains SV40 DNA and RNA polymerase II molecules which have initiated transcription during the viral development. We show here, by molecular hybridization experiments, that most of the templates active in SV40 transcription can be dissociated from host DNA. In conditions where supercoiled SV40 DNA form I sediments at 21 S, the transcription complex has a sedimentation coefficient of about 25 S. Inhibition of viral DNA synthesis by cytosine arabinonucleoside or chloroquine does not affect the activity of the transcription complex, which suggests that replicating molecules are not required for viral RNA synthesis and that SV40 DNA form I could serve as template for late SV40 transcription. A large fraction of the RNA synthesized in vitro remains associated with the SV40 DNA template in cesium sulfate density gradient. The RNA chains produced by the complex are heterogeneous in size, most of them being as large or larger than the viral genome.

The control of SV40 transcription during a lytic infection: late RNA synthesis in the presence of inhibitors of DNA replication

The transition from early to late transcription of SV40 DNA in productively infected BSC-1 cells was analyzed using both inhibitors of DNA replication, and early (Group A) temperature sensitive (ts) mutants of SV40. Late virus specific cytoplasmic RNA sedimenting at 16S in neutral sucrose gradients and complementary to the plus (L) DNA strand of SV40 was detected in cultures infected in the presence of three inhibitors of DNA replication (Ara-C, FdU, and chloroquine), even though the inhibition of viral DNA replication appeared to be essentially complete. After infection with the early SV40 mutant tsA58, no DNA replication was detected at the restrictive temperature (41 degrees C) and no significant late RNA complementary to the plus (L) strand was found, in either the cytoplasm or nuclei of infected cells. These data support the concept that expression of late viral functions requires the initiation of viral DNA synthesis or a functional gene A protein, or both.

Simian virus 40 DNA replication, transcription, and antigen induction during infection with two adenovirus 2-SV40 hybrids that contain the entire SV40 genome

The Ad2++hey hybrid virus population produces simian virus 40 (SV40) efficiently during lytic infection, whereas Ad2++ley does not, although both hybrids contain a complete SV40 genome. In this report, we demonstrate the synthesis of nonhydrid SV40 DNA in Ad2++HEY-infected Vero cells, but only early SV40 RNA is transcribed efficiently in Ad2++LEY-infected cells. Ad2++HEY induces SV40 U, T, and V antigens during lytic infection of African green monkey kidney cells, whereas Ad2++LEY induces only SV40 U and T antigens. These variations in the behavior of Ad2++HEY and Ad2++LEY regarding expression of SV40 functions probably reflect differences in the rate of SV40 excision from the hybrid genomes.

Viral DNA in transformed cells. III. The amounts of different regions of the SV40 genome present in a line of transformed mouse cells

(32)P-Labeled SV40 DNA was treated sequentially with restricting endonucleases EcoRI and Hpa I, and the resulting four fragments of DNA were separated by gel electrophoresis. The kinetics of renaturation of each of the fragments and of complete SV40 DNA were measured in the presence of DNA extracted from the SVT2 line of SV40-transformed mouse cells. It was found that these cells contain about six copies of a segment of DNA which includes the early region of the SV40 genome, and about one copy of the late viral sequences. To map the region of the viral genome which is transcribed in SVT2 cells, separated strands of each of the four fragments were prepared and hybridized to total transformed cell RNA. Part of the E strands of the two DNA fragments (A and C) which span the early region of the SV40 genome were found to enter the hybrid.

Simian virus 40 transcription in productively infected and transformed cells

Several independent cell lines transformed by simian virus 40 carry a species of viral RNA of 900,000 to 1,000,000 daltons. A viral RNA species of similar size is found early in the lytic cycle. Late in the viral lytic cycle, two prominent viral RNA species of about 600,000 and 900,000 daltons are seen. The larger late species shares nucleotide sequences with, and is less stable than, the smaller. These RNA species are located in the cytoplasm of the infected cell. The regions of the viral genome coding for these RNA species are mapped by hybridization of lytic RNA species to fragments of the genome produced by cleavage with Haemophilus aegyptius endonuclease.

Viral DNA-RNA hybrids in cells infected with simian virus: the simian virus 40 transcriptional intermediates

Brief labeling of cells infected with simian virus 40 with tritiated uridine resulted in the incorporation of part of the label into material that was soluble in 1 M NaCl and sensitive to KOH, with a buoyant density close to that of DNA. The properties of this material suggest that it represents single-stranded nascent molecules of messenger RNA of simian virus 40 hydrogen-bonded over a small portion of their length to viral DNA templates. The name "simian virus 40 transcriptional intermediate molecules" is suggested for these naturally occurring DNA.RNA hybrid molecules. The DNA in the hybrid seems to be in the form of replicative intermediate molecules.

Studies of nondefective adenovirus 2-simian virus 40 hybrid viruses. IX. Template topography in the early region of simian virus 40

The DNAs of the five nondefective adenovirus 2 (Ad2)-simian virus 40 (SV40) hybrid viruses contain overlapping segments of the early region of wild-type SV40 DNA. The complementary DNA strands of these five viruses have been separated with synthetic polyribonucleotides in isopycnic cesium chloride gradients. The relative amounts of early and late SV40 template in the DNA of each virus were determined by RNA-DNA hybridization with late lytic SV40 RNA, which contains sequences complementary to both templates. From the distribution of early and late templates in the five overlapping SV40 segments, we conclude that either the entire early region of SV40 is symmetrically transcribed in vivo, or, more probably, that the early SV40 templates are not contiguous.

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.

Control of simian virus 40 gene expression in adenovirus-simian virus 40 hybrid viruses. Synthesis of hybrid adenovirus 2-simian virus 40 RNA molecules in cells infected with a nondefective adenovirus 2-simian virus 40 hybrid virus

The effect of interferon on simian virus 40 (SV40) and adenovirus 2 (Ad2) T antigen synthesis has been examined in cells infected with SV40, with Ad2, and with a nondefective Ad2-SV40 hybrid virus, Ad2(+)ND(4). The induction of SV40 T antigen by SV40 was highly sensitive to interferon, whereas the induction of Ad2 T-antigen by Ad2 was resistant. This difference in interferon sensitivity was also noted in cells simultaneously infected with both viruses. However, the induction of SV40 T antigen by Ad2(+)ND(4), which contains covalently linked SV40 and Ad2 DNAs, was as resistant to interferon as the induction of Ad2 T antigen. This change in the interferon sensitivity of SV40 T antigen synthesis suggests that the expression of at least this portion of the SV40 genetic information in Ad2(+)ND(4) is under Ad2 genetic control. When RNA extracted from Ad2(+)ND(4)-infected cells was examined by means of sequential hybridization with Ad2 DNA, elution, and rehybridization with SV40 DNA, 27% of the SV40-specific RNA was found to be linked to Ad2 RNA. No such linkage was detected in control mixtures of Ad2 and SV40 RNAs. The presence of Ad2 and SV40 nucleotide sequences in the same RNA molecule implies that, in Ad2(+)ND(4) infection, transcription is initiated in the DNA of one virus (Ad2 or SV40) and continues without interruption across the point of junction into the DNA of the other virus. Furthermore, the interferon resistance of Ad2(+)ND(4)-induced SV40 T antigen synthesis suggests that transcription of the genetic information for SV40 T antigen is initiated in a region of Ad2 DNA.

In vitro transcription of the viral-specific sequences present in the chromatin of cells transformed by simian virus 40

Separated strands of simian virus 40 (SV40) DNA fragments were used in hybridization experiments to study the RNA transcribed by Escherichia coli RNA polymerase from the chromatin of cells transformed by SV40. The template activity of chromatin of the transformed cell line 11A8 (mouse-embryo cells) examined is about 17% that of purified DNA, suggesting that most of the chromatin DNA is repressed by chromosomal proteins. The SV40-specific RNA present in the RNA transcribed in vitro from 11A8 chromatin hybridizes specifically with the minus strand of SV40 DNA. Little or no reaction occurs with the plus strand of viral DNA. The SV40-specific RNA transcribed in vitro from chromatin of transformed cells shares sequences with the RNA produced during the early phase of SV40 lytic infection, and is similar to that present in the 11A8 cell line in vivo. Although the influence of chromosomal proteins on this pattern of transcription was not definitely determined, preliminary evidence indicates that an asymmetric pattern of transcription may also occur when 11A8 DNA is transcribed by E. coli RNA polymerase.

Studies of nondefective Adenovirus 2-Simian virus 40 hybrid viruses. 8. Association of Simian virus 40 transplantation antigen with a specific region of the early viral genome

Two of the five nondefective adenovirus 2 (Ad2)-simian virus 40 (SV40) hybrids induce SV40 transplantation resistance in immunized hamsters. These two hybrids, Ad2(+)ND(2) and Ad2(+)ND(4), contain 32 and 43% of the SV40 genome, respectively. The pattern of induction of SV40 transplantation antigen (TSTA) by the various hybrids differentiates TSTA from both SV40 U and T antigens. Since the SV40 RNA induced by both these hybrids is early SV40 RNA, these findings confirm that TSTA is an early SV40 function. By combining available data on SV40 antigen induction by these hybrids with electron microscopy heteroduplex mapping studies, the DNA segment responsible for the induction of SV40 TSTA can be inferred to lie in the region between 0.17 and 0.43 SV40 units from the site on the SV40 chromosome cleaved by E. coli R(1) restriction endonuclease.

Use of nondefective adenovirus-simian virus 40 hybrids for mapping the simian virus 40 genome

A series of viable recombinants between adenovirus 2 (Ad2) and simian virus 40 (SV40) (nondefective Ad2-SV40 hybrids) have been isolated. The members of this series (designated Ad2(+)ND(1) through Ad2(+)ND(5)) differ from one another in the early SV40-specific antigens and the SV40-specific RNA species which they induce in infected cells. They also contain different amounts of SV40 DNA as shown by RNA-DNA hybridization techniques. We have examined the structure of the DNA molecules from these hybrids, using electron microscope heteroduplex mapping techniques. Each hybrid was found to contain a single segment of SV40 DNA of characteristic size covalently inserted at a unique location in the adenovirus 2 DNA molecule. The SV40 segments of the various hybrids formed an overlapping series with a common end point. When the results of the electron microscopic study were combined with data on antigen induction, it was found that a self-consistent map could be constructed which related specific regions of the SV40 genome to the induction of specific antigens. The order of these early SV40 antigen inducing regions in the SV40 DNA segments contained in the nondefective hybrids is: U antigen, tumor specific transplantation antigen, and T antigen with the U antigen region being nearest the common end point.

Mapping of simian virus 40 early functions on the viral chromosome

The simian virus 40 (SV40) DNA segment in the nondefective adenovirus 2-SV40 hybrid, Ad2(+)ND(4), is colinear with the segment between 0.11 and 0.59 SV40 fractional length from the site at which the R(1) restriction endonuclease cleaves SV40 DNA. This specifies the region of the SV40 DNA molecule which induces the early SV40 antigens: U antigen, tumor specific transplantation antigen, and T antigen. A variant of Ad2(+)ND(4), called Ad2(+)ND(4del), was found which has a deletion of the DNA segment between 0.50 and 0.57 SV40 fractional length from the R(1) endonuclease cleavage point.

Relationship of replication and transcription of Simian Virus 40 DNA

RNA produced by the Simian Virus 40 (SV40) mutant tsA30 during lytic infection of kidney cells of African green monkeys was examined by RNA-DNA competition-hybridization. This mutant is temperature-sensitive in a function (gene A) that regulates synthesis of viral DNA. No detectable difference between mutant RNA synthesized at the permissive temperature (33 degrees ) and wild-type viral RNA was found. During continuous infection with the mutant at the restrictive temperature (41 degrees ) only early viral RNA was produced. When mutant DNA and late RNA synthesis were initiated at the permissive temperature, a shift to the restrictive temperature rapidly terminated synthesis of viral DNA but not that of late viral RNA. The data indicate that the function of gene A is required before synthesis of late viral RNA and that after initiation, the production of late RNA continues without further expression of gene A or concomittant viral DNA synthesis.

Variants of simian virus 40-transformed 3T3 cells that are resistant to concanavalin A

By treating populations of simian virus 40 (SV40)-transformed 3T3 cells with concanavalin A, variants have been isolated which are resistant to the killing action of the lectin. The variants (i) resemble 3T3 cells morphologically and in some of their growth characteristics; (ii) are not agglutinated by high concentrations of concanavalin A or wheat germ agglutinin, but can be rendered agglutinable by treatment with low concentrations of trypsin; (iii) bind the same number of concanavalin A molecules as 3T3 or SV3T3 cells; (iv) cannot be transformed by SV40 and are resistant to focus formation after infection with murine sarcoma virus; (v) contain SV40-specific T antigen and RNA and; (vi) yield wild-type SV40 virus after heterokaryon formation with BS-C-1 cells.

Studies of nondefective adenovirus 2-simian virus 40 hybrid viruses. VII. Characterization of the simian virus 40 RNA species induced by five nondefective hybrid viruses

Five nondefective adenovirus 2 (Ad2)-simian virus 40 (SV40) hybrid viruses have been isolated and found to contain segments of SV40 DNA covalently linked to Ad2 DNA. The quantity of SV40 DNA present is a stable characteristic of each hybrid virus, and varies from less than 5% (in Ad2(+)ND(3)) to more than 30% (in Ad2(+)ND(4)) of the SV40 genome. We have characterized the SV40 portions of these hybrids by relating the SV40-specific RNA sequences transcribed in cells infected with each hybrid virus to those transcribed in cells infected with each of the other hybrid viruses and with SV40 itself. RNA-DNA hybridization-competition experiments indicate that the number of unique SV40 RNA sequences transcribed in infected cells is proportional to the size of the SV40 DNA segment contained within each hybrid and, in the case of the three hybrids which induce detectable SV40-specific antigens, to the number of SV40 antigens induced. Furthermore, the SV40-specific RNA sequences transcribed from any one of the hybrids are completely represented in the RNA transcribed from all other hybrids with longer SV40 segments. Thus, the SV40 DNA regions in the five hybrid viruses appear to contain some nucleotide sequences in common. The SV40-specific RNA transcribed from Ad2(+)ND(4), the hybrid containing the largest SV40 segment, is qualitatively similar to the SV40-specific RNA transcribed early (i.e., prior to viral DNA replication) in SV40 lytic infection. Thus, it appears that no significant amount of late SV40 DNA is transcribed during infection by any of the five nondefective Ad2-SV40 hybrid viruses.

Analysis of simian virus 40 DNA with the restriction enzyme of Haemophilus aegyptius, endonuclease Z

Limited digestion of simian virus 40 (SV40) DNA from both small- and large- plaque strains with the restriction endonuclease Z from Haemophilus aegyptius yielded 10 specific fragments. The number of nucleotide pairs for each fragment, determined by co-electrophoresis with phiX174 RF fragments produced by endonuclease Z, ranges from 2,050 to 80. The difference in the pattern between the large- and small-plaque strains is the disappearance of one fragment containing approximately 255 nucleotide pairs and the appearance of a new fragment with 145 nucleotide pairs. This finding can be explained either by deletions or insertions totaling 110 nucleotide pairs. Complementary RNA synthesized in vitro from the adeno-SV40 hybrid virus, strain ND-1, hybridized preferentially to four of the fragments of SV40 DNA.

Aspects of the encapsidation of simian virus 40 deoxyribonucleic acid

Growing subcloned CV1-cells were infected with simian virus 40, and the time course of virus formation was determined. When infected cells were fractionated into cytoplasmic and nuclear fractions, most of the progeny virus particles were recovered in the cytoplasmic extract and not in the nuclei. This result was independent of the technique used for the preparation of nuclei and of the time after infection at which the extracts were prepared. Leakage of the virions from the nucleus occurred during the course of cell fractionation, suggesting that the nuclear membrane of the infected cells is damaged. Virions were found to accumulate in a nonlinear fashion, at the time when the number of viral deoxyribonucleic acid (DNA) molecules increases linearly with time after infection. This suggests that the size of the intracellular pool of capsid proteins increases constantly during the late phase of virus replication. Progeny viral DNA to become encapsidated is withdrawn at random from the pool of replicated DNA molecules.

Patterns of simian virus 40 deoxyribonucleic acid transcription. II. In transformed cells

The pattern of simian virus 40 (SV40) deoxyribonucleic acid transcription has been examined in 11 SV40-transformed cell lines. In all cases, substantial regions of the minus strand (35-75%) appeared to be transcribed. In the lines tested, these regions included the "early" gene sequences. The SV40-specific ribonucleic acid from at least two of the transformed cell lines represented significantly greater portions of the minus strand than are represented in "early" lytic ribonucleic acid. Small regions of the plus strand appeared to be transcribed in only two of the transformed cell lines.

Replication of simian virus 40 deoxyribonucleic acid: analysis of the one-step growth cycle

The time course of replication of simian virus 40 deoxyribonucleic acid (DNA) was investigated in growing monolayer cultures of subcloned CV1 cells. At multiplicities of infection of 30 to 60 plaque-forming units (PFU)/cell, first progeny DNA molecules (component 1) were detected by 10 hr after infection. During the following 10 to 12 hr, accumulation of virus DNA proceeded at ever increasing rates, albeit in a non-exponential fashion. The rate of synthesis then remained constant, until approximately the 40th hour postinfection, when DNA replication stopped. Under these conditions, the duration of the virus growth cycle was approximately 50 hr. The time needed for the synthesis of one DNA molecule was found to be approximately 15 min. At multiplicities of infection of 1 or less than 1 PFU/cell, the onset of the linear phase of DNA accumulation was delayed, but the final rate of DNA synthesis was the same, independent of the input multiplicity. This was taken as a proof that templates for the synthesis of viral DNA multiply in the cell during the early phase of replication. However, the probability for every replicated DNA molecule to become in turn replicative decreased constantly during that phase. This could be accounted for by assuming a limited number of replication sites in the infected cell.