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

Heterogeneity in state and expression of viral DNA in polyoma virus-induced tumors of the mouse

We have examined the state and expression of polyoma viral DNA in representative epithelial and mesenchymal tumors, using a combination of biochemical and in situ methods. Results showed wide variations among tumor types and also in different regions within individual tumors, with respect to copy number of viral DNA, presence or absence of deletions, and expression of early and late viral proteins. Epithelial tumors showed the greatest heterogeneity. High copy free viral DNA, frequently with deletions, was found in all such tumors. A portion of free viral DNA was recoverable as transcriptionally active minichromosomes. Three distinct subpopulations of cells were distinguished by in situ analyses. Type 1 cells showed high copy free viral DNA and expressed the major viral capsid protein VP1; these cells appeared to be at various stages of productive (lytic) viral infection. Some productively infected cells were able to undergo mitosis; in a portion of these cells, VP1 was found in close association with the mitotic spindle. Type 2 cells contained high copy free DNA but did not express VP1; by some unknown mechanism, these cells manifest a post-replication block to late gene expression and lytic infection. Type 3 cells contained only low copy, presumably integrated, viral DNA and expressed no VP1; they thus resemble cells transformed in vitro by the virus. Epithelial tumors contained variable mixtures of these subpopulations, while mesenchymal tumors were composed of Type 3 cells only. Differences in virus-cell interactions are discussed in terms of their possible implications in tumor development.

High rotational mobility of DNA in animal cells and its modulation by histone acetylation

DNA rotational mobility in a bovine papilloma virus (BPV)-based minichromosome, autonomously replicating in mouse cells, was studied using topoisomer analysis in temperature shift experiments. It was found that in live cells the average number of topological turns increased by six in the course of temperature shift through a range of 37 degrees C. This comprised approximately 85% of the total potential mobility of naked plasmid DNA. DNA rotation in isolated nuclei was found to be 3.5-4.0 turns per 37 degrees C in 100 mM NaCl - much higher than in all experiments with animal cells reported thus far. In low salt mobility was considerably lowered. Attempts to extract minichromosomes from nuclei allowed isolation of no more than 10% of minichromosomal DNA, with could indicate a very high proportion of transcriptionally active minichromosomes in the intracellular population. Growing cells in the presence of sodium butyrate resulted not only in an increase in the level of plasmid superhelicity and a decrease of its transcription (as we report in the accompanying publication) but also reduced rotational mobility of plasmid DNA threefold (from 6 to 2 turns per 37 degrees C). The decrease in DNA rotational mobility after butyrate treatment was also partially manifested in isolated nuclei (especially at lower ionic strength). To check whether histone acetylation is directly responsible for DNA immobilization, we performed in vitro acetylation of histones using acetyl adenylate. This resulted in severe DNA immobilization in experiments using both up and down temperature shifts.

Restriction enzyme accessibility and RNA polymerase localization on transcriptionally active SV40 minichromosomes isolated late in infection

The transcriptionally active SV40 minichromosomes isolated late in infection contain a nucleosome-free ORI region or gap. To analyze the chromatin structure of this subpopulation of minichromosomes extracted at different ionic strengths in the early and late coding regions, minichromosomes were isolated in the presence of a 5, 50, or 130 mM concentration of monovalent cations and subjected to in vitro RNA elongation in either the presence or the absence of high salt and anionic detergent. The minichromosomes isolated at low ionic strength were transcriptionally more active than those isolated at physiological ionic strength. Nevertheless, in each case, the in vitro elongation complexes were present essentially on the late strand of the SV40 genome and localized preferentially in the late and 3' early coding regions. These regions were transcribed similarly in either the presence or the absence of chromatin denaturing agents. In contrast, the in vitro elongation activity of the RNA polymerase molecules present on the late strand in the middle and 5' end of the early coding region was inhibited in the absence of treatments to disrupt chromatin structure. In addition, as probed by restriction enzyme digestion, the ORI and late coding regions of the transcriptionally active minichromosomes were found to be more sensitive than the 5' region of the early genes. Taken together, these results suggest that the 5' and middle regions of the early genes of the SV40 transcriptional complexes isolated late in infection at low or physiological ionic strength are packaged in a more compact conformation than the rest of the genome.

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.

Transcriptionally active SV40 minichromosomes are restriction enzyme sensitive and contain a nucleosome-free origin region

A nucleosome-free region or gap containing the origin of replication and the transcriptional promoter elements is observed on 20 to 25% of the SV40 minichromosomes isolated at physiological ionic strength late in infection. We used the preferential sensitivity of the gapped minichromosomes to restriction enzymes to obtain sucrose gradient fractions containing 50 to 80% of gapped molecules. The same fractions are also enriched in RNA polymerase B (II) molecules engaged in transcription. Using electron microscopy, we demonstrate here that the transcriptional complexes are preferentially sensitive to restriction enzyme digestion, which indicate that they represent a subpopulation of the gapped minichromosomes.

Isolation and characterization of polyoma nucleoprotein complexes

A method for the isolation of polyoma nucleoprotein complexes has been developed using neuraminidase treatment of infected cell lysates. At least three distinct forms of polyoma virion intermediates were identified by their [3H]thymidine labeling kinetics and sedimentation coefficients: a rapidly labeled 95 S "replicating complex" which chases to a 75 S minichromosome and then to a 240 S virion structure. The general properties of these distinct intermediates were similar to those found for SV40. In contrast to SV40, however, a continuum of labeled polyoma viral DNA sedimented between 240 S and 95 S. These complexes were characterized by their release from cell debris with neuraminidase, precipitation with antivirion antibody, complete disruption in 1 M NaCl, and association with hemagglutinating (HA) activity. These intermediates may represent incremental capsid protein additions to the 75 S minichromosome, hypothesized in the current models for SV40 assembly. The ability to isolate a complete complement of polyoma subviral complexes provides a basis for studying the growth defect of polyoma host-range mutants, and the properties of neuraminidase release, hemagglutination, and specific immunoprecipitation suggest purification steps for further characterization of these virion assembly intermediates.