The SV40 DNA template for transcription of late mRNA in viral nucleoprotein complexes

RNA polymerases stall and/or prematurely terminate nearby both early and late promoters on polyomavirus DNA

Levels of transcription within the E and L strands of the five major PstI fragments of polyomavirus (strain AT3) were measured by pulse-labeling RNA both in infected cells and in isolated nuclei or viral transcription complexes during the late phase of infection. Quantification was assured by hybridization to single-stranded DNAs in solution followed by collection of hybrids on nitrocellulose filters and ribonuclease treatment. The level of in vivo transcription in the region of the early (E strand) promoter was two- to threefold higher than that in all other E-strand regions, suggesting that most RNA polymerases prematurely terminate transcription shortly downstream from this promoter during the late phase. In vitro transcription levels in this region were five- to tenfold higher than in the remainder of the E strand, suggesting that many RNA polymerases 'stall' shortly after initiation in vivo but can be reactivated and continue transcription in vitro upon exposure to detergents and high salt solution. Some premature termination nearby the late (L strand) promoter was also detected by the same method. Strikingly, many RNA polymerases also stalled on the L strand in the region of the early promoter, some 5 x 10(3) bases downstream from the late promoter. Treatment of cells with dichlororibofuranosylbenzimidazole did not affect polymerases that stalled or terminated prematurely, but strongly reduced the presence of polymerases that normally transcribed throughout the entire E or L strand. Examination of the size of RNA chains produced during in vitro incubations showed that many polymerases stalled in vivo within 50 to 100 nucleotides downstream from the initiation sites on both DNA strands. The number of polymerases active in vitro at the E strand promoter was similar to the number of polymerases at the L strand promoter. However, in contrast to L-strand transcription, most of the polymerases that initiated at the E-strand promoter were incapable of extended transcription in vivo. These results suggest that large T antigen-mediated repression of E-strand transcription is not simply due to the exclusion of RNA polymerases from the early promoter. Stalling and/or premature termination by RNA polymerases shortly downstream from the early promoter appears to be a mechanism by which temporal regulation of polyomavirus gene expression can be effected.

Topological characterization of the simian virus 40 transcription complex

We have used sedimentation analysis as well as agarose gel electrophoresis to characterize the topological state of the DNA of the Simian Virus 40 (SV40) transcription complex. We found that the complex DNA contained constrained topological tension, presumably resulting from nucleosome-like structures, but no detectable unconstrained (i.e., relaxable) topological tension. These results contradict previous conclusions that the SV40 transcription complex contains only unconstrained topological tension. Our findings are also the opposite of what has been proposed to be the case for the 5S gene analyzed in Xenopus oocytes. Thus the proposal that expression from the 5S gene is associated with substantial topological tension is not valid for expression from the SV40 late gene.

Structure of in-vivo transcribing chromatin as studied in simian virus 40 minichromosomes

In order to study the structure of chromatin during transcription, individual in-vivo transcribing simian virus 40 (SV40) minichromosomes were analyzed in the electron microscope after crosslinking the nascent RNA strands with different psoralen derivatives to the template DNA. Since psoralen crosslinks the DNA between nucleosomes, spreading of the crosslinked DNA and DNA-RNA complexes reveals single-stranded bubbles at positions where nucleosomes were located. We found that the transcribing SV40 minichromosomes contained a similar number of nucleosomes as did the minichromosomes without crosslinked nascent RNA. The nascent RNA was crosslinked in about equal proportions either in single-stranded bubbles of nucleosomal length or in continuously crosslinked regions between bubbles, in contrast with control experiments with ribosomal chromatin of Dictyostelium. Treatment of SV40 minichromosomes with 1.2 M-NaCl before and during photocrosslinking with psoralen led to the disappearance of the single-stranded bubbles. Since no bubbles could be detected at the attachment sites of the RNA molecules when the nucleosomes were disrupted in high salt, and since in about half of the molecules the RNA was attached to fully crosslinked linker DNA, we assume that the single-stranded bubbles with crosslinked RNA are not due to protection by the elongating RNA polymerase II complex, but are rather due to nucleosome-like structures. At the resolution level of single nucleosomes, these results imply for the first time that nucleosome-like structures (perhaps modified compared with "normal" nucleosomes) on SV40 minichromosomes do not prevent transcription elongation by RNA polymerase II.

Large T antigen-rich viral DNA replication loci in SV40-infected monkey kidney cells

The nuclear distribution of the large T antigen (T-Ag) during lytic infection of CV1 monkey kidney cells with SV40 virus was studied by immunoelectron microscopy. The viral protein was associated with the cellular chromatin and also accumulated within a small number of clearly delimited areas of the nucleoplasm. These T-Ag-rich areas were devoid of viral particles but contain 3-10 nm DNA filaments in an amorphous matrix. We have named these areas 'viral DNA/T-Ag loci.' The combination of the immunostaining for T-Ag with ultrastructural autoradiography revealed that these viral DNA/T-Ag loci were the sites of active SV40 DNA synthesis. We suggest that the viral DNA/T-Ag loci may represent definite structural domains specifically involved in viral DNA replication regulated by SV40-T antigen.

Attenuation may regulate gene expression in animal viruses and cells

In eukaryotes, an abundant population of promoter-proximal RNA chains have been observed and studied, mainly in whole nuclear RNA, in denovirus type 2, and in SV40. On the basis of these results it has been suggested that a premature termination process resembling attenuation in prokaryotes occurs in eukaryotes. Moreover, these studies have shown that the adenosine analog 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) enhances premature termination, but its mode of action is not understood. The determination of the nucleotide sequences of SV40 and other viruses and cellular genes provide means for elucidating the nucleotide sequences involved in the attenuation mechanism. A model has recently been described in which attenuation and mRNA modulation in a feedback control system quantitatively regulate SV40 gene expression. The suggested mechanism described in this model opens up approaches to the investigation of attenuation and mRNA modulation as a possible mechanism whereby eukaryotes may regulate transcription in a variety of different circumstances.

Transcription of minute virus of mice, an autonomous parvovirus, may be regulated by attenuation

To characterize the transcriptional organization and regulation of minute virus of mice, an autonomous parvovirus, viral transcriptional complexes were isolated and cleaved with restriction enzymes. The in vivo preinitiated nascent RNA was elongated in vitro in the presence of [alpha-32P]UTP to generate runoff transcripts. The lengths of the runoff transcripts were analyzed by gel electrophoresis under denaturing conditions. On the basis of the map locations of the restriction sites and the lengths of the runoff transcripts, the in vivo initiation sites were determined. Two major initiation sites having similar activities were thus identified at residues 201 +/- 5 and 2005 +/- 5; both of them were preceded by a TATAA sequence. When uncleaved viral transcriptional complexes or isolated nuclei were incubated in vitro in the presence of [alpha-32P]UTP or [alpha-32P]CTP, they synthesized labeled RNA that, as determined by polyacrylamide gel electrophoresis, contained a major band of 142 nucleotides. The RNA of the major band was mapped between the initiation site at residue 201 +/- 5 and residue 342. We noticed the potential of forming two mutually exclusive stem-and-loop structures in the 142-nucleotide RNA; one of them is followed by a string of uridylic acid residues typical of a procaryotic transcription termination signal. We propose that, as in the transcription of simian virus 40, RNA transcription in minute virus of mice may be regulated by attenuation and may involve eucaryotic polymerase B, which can respond to a transcription termination signal similar to that of the procaryotic polymerase.

Unwinding of the DNA helix in simian virus 40 chromosome templates by RNA polymerase

We measured the distortion of the DNA helix by RNA polymerase transcribing simian virus 40 (SV40) chromosome templates and compared it with the distortion caused by the enzymes as it transcribes naked SV40 DNA, using RNA polymerase from Escherichia coli. Purified DNA topoisomerase I was added to the transcription reactions and the number of supercoil turns in DNA, after deproteinising and removal of RNA, was determined by gel electrophoresis and band-counting. The number of polymerase molecules bound per naked DNA molecule was determined by electron microscopy. Each bound RNA polymerase distorted the template in such a way as to lead to on apparent average of 0.6-0.7 negative superhelical turn in the extracted DNA. Thus only few base-pairs are melted per RNA polymerase molecule. When SV40 chromosomes were transcribed the extracted DNA had a higher number of supercoil turns than DNA extracted from the initial chromosomes. We conclude that the polymerase deforms the DNA in chromatin in the same way as it deforms pure DNA. From control experiments with inhibitors of initiation we estimated that on average 9-10 RNA polymerase molecules were bound per SV40 chromosome. This suggests that transcription can proceed while the majority or all the nucleosomal structures are intact on an SV40 DNA molecule. We discuss the implications of these findings for the mechanism of transcription of chromatin.

Electron microscopic studies of transcriptional complexes released from vaccinia cores during RNA-synthesis in vitro: methods for fractionation of transcriptional complexes

Electron microscopic (EM) and biochemical methods were employed to study the transcriptional complexes present in detergent lysates of vaccinia virus cores actively synthesizing RNA in vitro. When processed and examined in the EM, 14 'transcriptional sites' could be observed on full-length DNA templates. Fractionation of lysates by equilibrium density centrifugation in CsSO4, chromatography on hydroxyapatite columns or by sedimentation in sucrose gradients, allowed isolation of DNA templates associated with transcripts but these manipulations often resulted in fragmentation of the DNA template or promoted the release of transcripts from the template. It is suggested that RNA transcripts remain associated with the template in regions of supercoiling. These regions, in turn, may be maintained by DNA-protein interactions which are compromised as the transcriptional complexes are fractionated and purified.

Separation and properties of two kinds of simian virus 40 late transcription complexes

Simian virus 40 (SV40) transcription complexes were labeled in cells with 3-min pulses of [(3)H]uridine 48 h after infection and were extracted from nuclei in isotonic buffer or in a buffer containing Sarkosyl. In sucrose gradients, the labeled complexes sedimented faster than both free RNA and most SV40 nucleoproteins. Most of the pulse-labeled nascent RNA hybridized to the entire late region of SV40, remained bound to viral DNA in Cs(2)SO(4) gradients, and ranged in size from a few nucleotides to about 5,000 nucleotides, with a peak at about 700. In contrast, the SV40-associated RNA polymerase activity in the same preparations sedimented near the major peak of SV40 nucleoproteins and was clearly separated from the transcription complexes bearing pulse-labeled nascent RNA. The two kinds of transcription complexes were released from isolated nuclei at different rates. Complexes bearing pulse-labeled RNA were released immediately when the nuclei were agitated in a Dounce homogenizer in isotonic buffer, whereas most of the complexes bearing RNA polymerase active in vitro were released more slowly, during subsequent incubation of the nuclei at 0 degrees C. Since the complexes bearing pulse-labeled nascent RNA were virtually inactive in vitro, the blocked complexes described by Laub et al. (Proc. Natl. Acad. Sci. U.S.A. 77:3297-3301, 1980) probably account for almost all the SV40-associated RNA polymerase activity studied previously by many investigators. New procedures must be developed to preserve the activity of the pulse-labeled complexes if the many advantages of the SV40 system for studying transcription by nucleoprotein complexes in vitro are to be realized fully.

Initiation of SV40 DNA replication in vivo: location and structure of 5' ends of DNA synthesized in the ori region

Initiation sites for DNA synthesis were located at the resolution of single nucleotides in and about the genetically defined origin of replication (ori) in replicating SV40 DNA purified from virus-infected cells. About 50% of the DNA chains contained an oligoribonucleotide of six to nine residues covalently attached to their 5' ends. Although the RNA-DNA linkage varied, the putative RNA primer began predominantly with rA. The data reveal that initiation of DNA synthesis is promoted at a number of DNA sequences that are asymmetrically arranged with respect to ori: 5' ends of nascent DNA are located at several sites within ori, but only on the strand that also serves as the template for early mRNA, while 5' ends of nascent DNA with the opposite orientation are located only outside ori on its early gene side. This clear transition between discontinuous (initiation sites) and continuous (no initiation sites) DNA synthesis defines the origin of bidirectional replication at nucleotides 5210--5211 and demonstrates that discontinuous synthesis occurs predominantly on the retrograde arms of replication forks. Furthermore, it appears that the first nascent DNA chain is initiated within ori by the same mechanism used to initiate nascent DNA ("Okazaki fragments") throughout the genome.

Stable association of viral protein VP1 with simian virus 40 DNA

Mild dissociation of simian virus 40 particles releases a 110S virion core nucleoprotein complex containing histones and the three viral proteins VP1, VP2, and VP3. The association of viral protein VP1 within this nucleoprotein complex is mediated at least partially through a strong interaction with the viral DNA. Treatment of the virion-derived 110S nucleoprotein complex with 0.25% Sarkosyl dissociated VP2, VP3, and histones, leaving a stable VP1-DNA complex. The VP1-DNA complex had a sedimentation value of 30S and a density of 1.460 g/cm3. The calculated molecular weight of the complex was 7.9 x 10(6), with an average of 100 VP1 molecules per DNA. Agarose gel electrophoresis of the VP1-DNA complex demonstrated that VP1 is associated not only with form I and form II simian virus 40 DNAs but also with form III simian virus 40 DNA generated by cleavage with EcoRI.

Two deletions within genes for simian virus 40 structural proteins VP2 and VP3 lead to formation of abnormal transcriptional complexes

The procedure developed by R. M. Fernandez-Muñoz et al. (J. Virol. 29:612-623, 1979) for isolating simian virus 40 (SV 40) chromatin free of disrupted previrions was optimized for preparing late transcriptional complexes, and these complexes were partially characterized. Transcriptional complexes derived from wild-type virus and from several deletion and temperature-sensitive mutants could be activated more than five-fold either by the anionic detergent Sarkosyl or by 300 mM ammonium sulfate, in agreement with the properties of SV40 transcriptional complexes prepared by other procedures. In contrast, complexes from cells infected with deletion mutants dl1261 or dl1262 were not activated at all by a high salt concentration, even though the extent of their activation by Sarkosyl was normal. Mutants dl1261 and dl1262 carry deletions of 54 and 36 base pairs, respectively, at an approximate map position of 0.91, which is within the overlapping genes for the virion proteins VP2 and VP3. The effects of these deletions on transcription in vitro indicate that VP2 or VP3 or both are bound to late transcriptional complexes in a way that affects the progress of initiated RNA polymerase. The properties of late transcriptional complexes derived from wild-type SV40 can be explained by the presence of the following two different kinds of complexes: (i) a minority class (about 20%), which is free of VP2 or VP3, active at low concentrations of ammonium sulfate in vitro, and responsible for late transcription in vivo, and (ii) a majority class (about 80%) with VP2 or VP3 bound, which is inactive at low salt concentrations both in vitro and in vivo but capable of being activated by high salt concentrations or by Sarkosyl. We propose that mutant VP2 and VP3 proteins from dl1261 and dl1262 bind to the majority class of late transcriptional complexes in a way that can be reversed by Sarkosyl but not by a high salt concentration.

Quantitation of transcribing native simian virus 40 minichromosomes extracted from CV1 cells late in infection

Simian virus 40 transcriptional complexes could be extracted from CV1 cells late in infection and separated from the bulk of inactive viral chromatin. Sucrose gradient sedimentation, cesium sulfate equilibrium density gradient centrifugation, and electron microscopy indicated that the viral transcriptional complexes corresponded to at least 0.5 to 1% of the viral minichromosomes extracted, about 5,000 copies per cell.

The SV40 early region TATA box is required for accurate in vitro initiation of transcription

The SV40 early region TATA box functions in vitro to fix initiation of transcription within a narrow region identical to that in vivo. In the absence of the TATA box region initiation occurs at multiple specific sites, as in vivo. However, certain sequences far upstream, crucial for efficient in vivo expression, are not essential in vitro.

Characterization of supercoiled nucleoprotein complexes released from detergent-treated vaccinia virions

Treatment of vaccinia virions with 1% sodium dodecyl sulfate in the absence of reducing agents resulted in the release of subviral particles termed "subnucleoids," which contained viral DNA in combination with four polypeptides with molecular weights of 90,000, 68,000, 58,000 and 10,000. Biochemical and electron microscopic studies showed that viral DNA in combination with these polypeptides was maintained in a superhelical configuration. When subnucleoids were "fixed" with glutaraldehyde and formaldehyde and then examined by electron microscopy, spherical particles were observed, in which the supercoiled DNA was folded into globular structures that were 20 to 60 nm in diameter and were interconnected by DNA-protein fibers resembling the nucleosome structures described for eucaryotic chromatin.

Simian virus 40 transcriptional complexes incorporate mercurated nucleotides into RNA in vitro

Simian virus 40 Sarkosyl transcriptional complexes incorporated mercurated nucleotide precursors into preinitiated RNA chains. Synthesis with mercurated precursors was three- to fivefold slower than with nonmercurated nucleotides (12 to 20 pmol per 10(6) cells per h at 25 degrees C), and 50 to 70% of the RNA product bound specifically to sulfhydryl-agarose. The amount of mercurated CMP incorporated into RNA was measured by specific binding of [35S]cysteine to the mercury residues. More than 90% of the mercurated RNA hybridized to simian virus 40 DNA.

DNA replication and the early to late transition in adenovirus infection

Expression of the late genes of adenovirus is only detectable after virus DNA synthesis has occurred. Using a superinfection protocol, we show that replication of the template per se is required for expression of late regions L2--L5 (mapping to the right of position 39) and that the accumulation of early gene products does not suffice. This regulation is probably exerted at the level of transcription rather than by control of processing or selective stabilization of late mRNA or its precursors. The promoter-proximal late gene block L1, however, appears to be subject to processing control. At early times a single member of this gene family (tripartite leader plus coordinates 29--39, encoding the 52,55K polypeptide pair) is expressed, whereas at late times an additional, differently spliced mRNA species is generated from this region (tripartite leader plus coordinates 34--39, encoding polypeptide IIIa).

Extraction of transcribing SV40 chromosomes in very low salt

SV40 chromosomes capable of continued RNA synthesis in vitro have been extracted from infected cells in solutions of very low ionic strength (5 mM HEPES, 0.25 mM MgCl2). The RNA made is of high molecular weight, and synthesis is sensitive to alpha-amanitin. More RNA is made than from previously described (high salt-extracted) transcription complexes. Transcribing SV40 chromosomes sediment at a rate intermediate between replicating and mature chromosomes, and have a higher ratio of protein to nucleic acid than either. They retain proteins that are lost during exposure to high salt, and might prove valuable in identifying proteins involved in SV40 transcription.

Characterization of simian virus 40 transcriptional intermediates in infected CV1 cell nuclei

Simian Virus (SV40) transcriptional intermediates (T.I.) were isolated from infected cell nuclei incubated in vitro in the presence of the four ribonucleoside triphosphates. The nascent mRNA strands in the viral DNA-RNA hybrid molecules were hydrogen bonded to their template by 200-250 nucleotides on the average, as judged from the extent of their RNase resistance and the aspect of T.I. under electron microscope after treatment with 50 per cent formamide. The RNA polymerase involved (RNA polymerase II) synthesized up to full length transcripts at a rate of approximately 150 nucleotides/min. at 25 degrees C. Each SV40 infected cell was found to contain about 200 active T.I. molecules at the peak of late transcription. The DNA in the T.I. molecules was exclusively form I DNA only in cell infected with the tsA30 mutant of SV40 that had been transferred to non-permissive temperature in order to arrest DNA replication, but both form I DNA and molecules behaving as replicative intermediates (R.I.) in wild type infected cells.