Simian virus 40 protein VP1 is involved in spacing nucleosomes in minichromosomes

Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studied the quasi-regular large-scale segmentation in genomic sequences of different ssRNA, ssDNA, and dsDNA viruses. The particular representatives included satellite tobacco mosaic virus (STMV) and the strains of satellite tobacco necrosis virus (STNV), STNV-C, STNV-1, STNV-2, Escherichia phages MS2, ϕX174, α3, and HK97, and Simian virus 40. In all their genomes, we found the significant quasi-regular segmentation of genomic sequences related to the virion assembly and the genome packaging within icosahedral capsid. We also found good correspondence between our results and available cryo-electron microscopy data on capsid structures and genome packaging in these viruses. Fourier analysis of genomic sequences provides the additional insight into mechanisms of hierarchical genome packaging and may be used for verification of the concepts of 3-fold or 5-fold intermediates in virion assembly. The results of sequence analysis should be taken into account at the choice of models and data interpretation. They also may be helpful for the development of antiviral drugs.

Molecular biology, epidemiology, and pathogenesis of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain

Progressive multifocal leukoencephalopathy (PML) is a debilitating and frequently fatal central nervous system (CNS) demyelinating disease caused by JC virus (JCV), for which there is currently no effective treatment. Lytic infection of oligodendrocytes in the brain leads to their eventual destruction and progressive demyelination, resulting in multiple foci of lesions in the white matter of the brain. Before the mid-1980s, PML was a relatively rare disease, reported to occur primarily in those with underlying neoplastic conditions affecting immune function and, more rarely, in allograft recipients receiving immunosuppressive drugs. However, with the onset of the AIDS pandemic, the incidence of PML has increased dramatically. Approximately 3 to 5% of HIV-infected individuals will develop PML, which is classified as an AIDS-defining illness. In addition, the recent advent of humanized monoclonal antibody therapy for the treatment of autoimmune inflammatory diseases such as multiple sclerosis (MS) and Crohn's disease has also led to an increased risk of PML as a side effect of immunotherapy. Thus, the study of JCV and the elucidation of the underlying causes of PML are important and active areas of research that may lead to new insights into immune function and host antiviral defense, as well as to potential new therapies.

High cooperativity of the SV40 major capsid protein VP1 in virus assembly

SV40 is a small, non enveloped DNA virus with an icosahedral capsid of 45 nm. The outer shell is composed of pentamers of the major capsid protein, VP1, linked via their flexible carboxy-terminal arms. Its morphogenesis occurs by assembly of capsomers around the viral minichromosome. However the steps leading to the formation of mature virus are poorly understood. Intermediates of the assembly reaction could not be isolated from cells infected with wt SV40. Here we have used recombinant VP1 produced in insect cells for in vitro assembly studies around supercoiled heterologous plasmid DNA carrying a reporter gene. This strategy yields infective nanoparticles, affording a simple quantitative transduction assay. We show that VP1 assembles under physiological conditions into uniform nanoparticles of the same shape, size and CsCl density as the wild type virus. The stoichiometry is one DNA molecule per capsid. VP1 deleted in the C-arm, which is unable to assemble but can bind DNA, was inactive indicating genuine assembly rather than non-specific DNA-binding. The reaction requires host enzymatic activities, consistent with the participation of chaperones, as recently shown. Our results demonstrate dramatic cooperativity of VP1, with a Hill coefficient of ∼6. These findings suggest that assembly may be a concerted reaction. We propose that concerted assembly is facilitated by simultaneous binding of multiple capsomers to a single DNA molecule, as we have recently reported, thus increasing their local concentration. Emerging principles of SV40 assembly may help understanding assembly of other complex systems. In addition, the SV40-based nanoparticles described here are potential gene therapy vectors that combine efficient gene delivery with safety and flexibility.

Purification and Characterization of the Simian Virus 40 Transcription Elongation Complex

The transcriptional regulatory region of the simian virus 40 minichromosome that is being transcribed in the cell is nucleosome-free, while that of the non-transcribed minichromosome is nucleosome covered. Although additional studies have shown that the two structures are otherwise similar, the precision of these indirect studies has not been sufficient to determine if the transition between the two involves nucleosome displacement or nucleosome sliding. In order to address this question directly, we have developed a new function-based affinity isolation method that is capable of purifying the native transcription elongation complex of a single gene from mammalian cells. The simian virus 40 transcription elongation complex was purified by this method and the topological linking number of its DNA was compared directly to that of the bulk, non-transcribed minichromosome. The results show that the two types of minichromosome contain the same number of nucleosomes as well as nucleosomal structure. These findings indicate that interconversion between the non-transcribing and transcribing states is accomplished by a remodeling event involving nucleosome sliding rather than nucleosome displacement.

Simian Virus-40 as a Gene Therapy Vector

Simian virus-40 (SV40), an icosahedral papovavirus, has recently been modified to serve as a gene delivery vector. Recombinant SV40 vectors (rSV40) are good candidates for gene transfer, as they display some unique features: SV40 is a well-known virus, nonreplicative vectors are easy-to-make, and can be produced in titers of 10(12) IU/ml. They also efficiently transduce both resting and dividing cells, deliver persistent transgene expression to a wide range of cell types, and are nonimmunogenic. Present disadvantages of rSV40 vectors for gene therapy are a small cloning capacity and the possible risks related to random integration of the viral genome into the host genome. Considerable efforts have been devoted to modifing this virus and setting up protocols for viral production. Preliminary therapeutic results obtained both in tissue culture cells and in animal models for heritable and acquired diseases indicate that rSV40 vectors are promising gene transfer vehicles. This article reviews the work performed with SV40 viruses as recombinant vectors for gene transfer. A summary of the structure, genomic organization, and life cycle of wild-type SV40 viruses is presented. Furthermore, the strategies utilized for the development, production, and titering of rSV40 vectors are discussed. Last, the therapeutic applications developed to date are highlighted.

Chromosome-protein interactions in polyomavirus virions

In this work, we sought to determine whether the components of the murine polyomavirus capsid establish specific interactions with the minichromosome encapsidated into the mature viral particles by using the cis-diamminedichloroplatinum(II) cross-linking reagent. Our data indicated that VP1, but not minor capsid proteins, interacts with the viral genome in vivo. In addition, semiquantitative PCR assays performed on cross-linked DNA complexes revealed that VP1 binds to all regions of the viral genome but significantly more to the regulatory region. The implications of such an interaction for viral infectivity are discussed.

The gene encoding the major viral structural protein stimulates recombination in polyomavirus DNA

RmI is a chimeric DNA molecule consisting of a polyoma genome in which a partly duplicated VP1-coding region brackets an insert of murine DNA (Ins); when transfected into mouse cells, RmI recombines intramolecularly to yield infectious, unit-length, polyoma DNA. We report here that RmI encodes a polypeptide of 337 amino acids (designated VmP1) which includes the N-terminal 328 amino acids of VP1 and 9 amino acids specified by Ins. Mutating the VmP1-coding sequence strongly reduces the ability of RmI to yield polyoma DNA. In contrast, mutating the portion of the VP1-coding sequence which is not part of the VmP1-coding sequence has little or no impact on the ability of RmI to yield polyoma DNA, even though it renders such DNA noninfectious. Thus, release of polyoma DNA from RmI involves a function of VP1 distinct from that ensuring virus assembly and propagation; since VP1 can arise only after recombination has occurred, VmP1, but not VP1, could carry such a function. We suggest that VmP1 acts in concert with VP2, which we have already reported to stimulate recombination in RmI.

Structural organization of the hepatitis B virus minichromosome

The replicative intermediate of hepatitis B virus (HBV), the covalently closed, circular DNA, is organized into minichromosomes in the nucleus of the infected cell by histone and non-histone proteins. In this study we investigated the architecture of the HBV minichromosome in more detail. In contrast to cellular chromatin the nucleosomal spacing of the HBV minichromosome has been shown to be unusually reduced by approximately 10 %. A potential candidate responsible for an alteration in the chromatin structure of the HBV minichromosome is the HBV core protein. The HBV core protein has been implicated in the nuclear targeting process of the viral genome. The association of the HBV core protein with nuclear HBV replicative intermediates could strengthen this role. Our findings, confirmed by in vivo and in vitro experiments indicate that HBV core protein is a component of the HBV minichromosome, binds preferentially to HBV double-stranded DNA, and its binding results in a reduction of the nucleosomal spacing of the HBV nucleoprotein complexes by 10 %. From this model of the HBV minichromosome we propose that the HBV core protein may have an impact on the nuclear targeting of the HBV genome and be involved in viral transcription by regulating the nucleosomal arrangement of the HBV regulatory elements, probably in a positive manner.

Involvement of minor structural proteins in recombination of polyoma virus DNA

We have previously observed that a polyoma-mouse chimeric DNA molecule (RmI) in which the murine DNA insert is flanked by directly repeated viral sequences is effectively converted into unit-length polyoma DNA upon transfection of permissive mouse cells. This intramolecular recombination event appears to be dependent on VmP1, a protein encoded by RmI which includes the 328 N-terminal amino acids of polyoma VP1, and nine amino acids of murine origin carrying the C-terminus of the protein. We report here that introducing mutations into the VP2/VP3 coding sequence reduces the ability of RmI to generate polyoma DNA, even though the same mutations seem to exert little or no effect on the ability of polyoma DNA to either replicate or accumulate inside transfected cells. A mutation affecting VP2 alone being as effective as one that affects both VP2 and VP3, VP2 appears to be playing a critical role in recombination.

Production of polyomavirus structural protein VP1 in yeast cells and its interaction with cell structures

The gene for mouse polyomavirus major structural protein VP1 was expressed in Saccharomyces cerevisiae from the inducible GAL7 promoter. VP1 pseudocapsids were purified from cell lysates. Their subpopulation contained fragments of host DNA, which, in contrast to those of VP1 pseudocapsids produced in insect cells, did not assemble with cellular histones into pseudonucleocores. VP1 pseudocapsids accumulated in the yeast cell nuclei. A strong interaction of VP1 with tubulin fibres of the mitotic spindle was observed. The fibres of spindles were larger in diameter, apparently due to tight VP1 binding. Substantial growth inhibition of yeast cells producing VP1 was observed.

A mutation in the DE loop of the VP1 protein that prevents polyomavirus transcription and replication

Natural mutants of the DE loop of the Polyomavirus (Py) major coat protein VP1 have been previously shown to display an altered host specificity (L. Ricci, R. Maione, C. Passananti, A. Felsani, and P. Amati, 1992, J. Virol. 66, 7153-7158). To better understand the role of this outfacing loop of the VP1 protein in Py infectivity, we constructed and characterized a Py mutant (Py M17) harboring a deletion of 7 AA within the tip of the DE loop. The mutant virions obtained after DNA transfection were unable to replicate and initiate early transcription in fibroblast cells. Complementation experiments performed to rescue the deficient M17 replication by means of wt functions revealed the cis-dominance of the mutation. In situ cell fractionation experiments demonstrated that the Py mutant, like the Py wt, enters the cells, reaches the nucleus and that both the viral DNA and VP1 protein are found tightly bound to the nuclear matrix. These data suggest that the VP1 protein, associated to the viral DNA, conditions early viral gene expression and that the DE loop of the protein must be involved in this process.

How do animal DNA viruses get to the nucleus?

Genome and pre-genome replication in all animal DNA viruses except poxviruses occurs in the cell nucleus (Table 1). In order to reproduce, an infecting virion enters the cell and traverses through the cytoplasm toward the nucleus. Using the cell's own nuclear import machinery, the viral genome then enters the nucleus through the nuclear pore complex. Targeting of the infecting virion or viral genome to the multiplication site is therefore an essential process in productive viral infection as well as in latent infection and transformation. Yet little is known about how infecting genomes of animal DNA viruses reach the nucleus in order to reproduce. Moreover, this nuclear locus for viral multiplication is remarkable in that the sizes and composition of the infectious particles vary enormously. In this article, we discuss virion structure, life cycle to reproduce infectious particles, viral protein's nuclear import signal, and viral genome nuclear targeting.

Conserved nucleoprotein structure at the ends of vertebrate and invertebrate chromosomes

Eukaryotic chromosomes terminate with telomeres, nucleoprotein structures that are essential for chromosome stability. Vertebrate telomeres consist of terminal DNA tracts of sequence (TTAGGG)n, which in rat are predominantly organized into nucleosomes regularly spaced by 157 bp. To test the hypothesis that telomeres of other animals have nucleosomes, we compared telomeres from eight vertebrate tissues and cell cultures, as well as two tissues from an invertebrate. All telomeres have substantial tracts of (TTAGGG)n comprising 0.01-0.2% of the genome. All telomeres are long (20-100 kb), except for those of sea urchin, human, and some chicken chromosomes, which are 3-10 kb in length. All of the animal telomeres contained nucleosome arrays, consistent with the original hypothesis. The telomere repeat lengths vary from 151 to 205 bp, seemingly uncorrelated with telomere size, regularity of nucleosome spacing, species, or state of differentiation but surprisingly correlated with the repeat of bulk chromatin within the same cells. The telomere nucleosomes were consistently approximately 40 bp smaller than bulk nucleosomes. Thus, animal telomeres have highly conserved sequences and unusually short nucleosomes with cell-specific structure.

Association of nucleosome-free regions and basal transcription factors with in vivo-assembled chromatin templates active in vitro

Using SV40 minichromosomes assembled in vivo, we have studied the relationship between a nucleosome-free promoter-region and initiation of transcription by RNA polymerase II on chromatin templates in vitro. Our data suggest that accessibility of DNA to transcription factors, programmed into the structure of the chromatin, is crucial for initiation of transcription. First, minichromosomes competent to be transcribed in vitro contained nucleosome-free promoter regions. Second, tsC219 minichromosomes, most of which contain the nucleosome-free promoter region, supported transcription more efficiently both in vivo and in vitro than wild-type minichromosomes, in which only a subset contain the nucleosome-free region. We have also identified basal transcription factors associated with the in vivo-assembled chromatin templates. A striking correlation was observed between minichromosomes associated with in vivo initiated RNA polymerases and those associated with the basal transcription factors TFIID and TFIIE/F, and to a lesser extent, TFIIB. Of these associated factors, only TFIID was poised for ready assembly into preinitiation complexes and therefore for subsequent initiation of transcription. However, an active chromatin template could also be maintained in the absence of the binding of TFIID. Finally, our data are consistent with the presence of TFIIF in elongating ternary complexes on the chromatin templates.

Host range analysis of a chimeric simian virus 40 genome containing the BKV capsid genes

Simian virus 40 (SV40) propagates poorly in cells from human embryonic kidney (HEK) and human fetal fibroblasts (HFF) while BK virus grows well in many human cell types. It has been suggested that sequences within the SV40 late region but not within the BKV late region may act to inhibit growth of virus in HEK and HFF cells. In order to test this and to identify a late region host range function, we have replaced the late region of wtSV40 DNA with the late region of RFV (a variant of BKV) to produce an intermolecular hybrid or chimera. The constructed SV40/RFV chimeric genome contained approx. 5900 base pairs, more than 650 base pairs greater than wtSV40. Nevertheless, when introduced by transfection the chimera appeared to be infectious. Three chimeric genomes were recovered from infected cells and all contained deletions of nearly 600 base pairs, exclusively at the region of the 3' terminal junction. Since all three chimeras propagated in human HFF and HEK cells, the RFV late region and not the RFV regulatory region possesses a host range function required for growth in human cells. Analysis of T-antigen gene expression suggests that the replacement of the SV40 late region with the BKV late region leads to full expression of the SV40 early region in human cells. Two chimeras exhibited a BKV-like host range and the third exhibited both a BKV and an SV40-like host range. We determined precisely which sequences were deleted in each chimera and we exchanged 3' terminal junction fragments containing these deletions, between two chimeras with different host ranges. From these experiments we demonstrated that: (1) The 3' terminus of the SV40 large T-antigen gene is required for growth of SV40/RFV in TC-7 and CV-1 simian cells but not for growth in human cells; (2) while the SV40 late region is refractory for growth in human cells, the RFV late region is not refractory for growth in simian cells; (3) the 3' terminus of the RFV T-antigen gene is not required for growth in human cells. The results of the 3' terminal junction exchanges and studies of early gene expression also demonstrate that BKV and SV40 can penetrate human and simian cells, even when they failed to grow in one cell type.

Nucleosome spacing is compressed in active chromatin domains of chick erythroid cells

We have cleaved the chromatin of embryonic and adult chicken erythroid cells using a novel nuclease that is capable of resolving clearly the nucleosomes of active chromatin. We found that in active chromatin, nucleosomes are spaced up to 40 base pairs closer together than in inactive chromatin. This was true for both "housekeeping" and "luxury" genes and was observed whether the digestion was carried out on isolated nuclei in vitro or by activating the endogenous nuclease in vivo. The close spacing extended several kilobases into flanking chromatin, indicating that this is a domain property of active chromatin, not just a characteristic of regions disrupted by transcription. A simple interpretation of our results is that the nucleosomes of active chromatin are mobile in vivo and, not being constrained by linker histones, freely move closer together.

The effect of the simple repeating d(CG.GC)n, d(CA.GT)n, and d(A.T)n DNA sequences on the nucleosomal organization of SV40 minichromosomes

The effect of several simple repeating DNA sequences--d(CG.GC)5, d(CA.GT)30, and d(A.T)60--on the nucleosomal organization of the SV40 minichromosome is analyzed. These three different sequences were cloned at the Hpa II site of SV40 (position 346) which occurs at the 3' border of the nucleosome-free SV40 control region. Our results show that neither the d(A.T)60 sequence nor the d(CG.GC)5 sequence appear to have any relevant effect on the nucleosomal organization of the region of the minichromosome surrounding the inserted repeated sequence. Both sequences are hypersensitive to micrococcal nuclease cleavage in the minichromosome, indicating that they are not organized into nucleosomes. On the other hand, the d(CA.GT)30 sequence is found organized as nucleosomes and causes the delocation of nucleosomes in the minichromosomal region close to the inserted repeated sequence.

In vitro assembly of a positioned nucleosome near the hypersensitive region in simian virus 40 chromatin

Previous studies have identified a nucleosome near a potential late boundary for the nuclease-hypersensitive region in simian virus 40 chromatin. We have performed in vitro reconstitution analysis to determine whether the underlying DNA sequence encodes for the assembly of this nucleosome and applied hydroxyl radical and DNase I footprinting techniques to examine the structure of the reconstituted nucleosome. Both methods revealed the formation of a precisely positioned nucleosome in vitro, on a fragment spanning the strong in vivo nucleosome location site determined previously in the viral chromatin. The center of the positioned nucleosome maps between nucleotide 384 and 387 on simian virus 40 DNA. The corresponding nucleosome core includes the major-late transcription site (12 base-pairs within the core), the MspI site, and a segment shown previously to adopt a bent structure in the absence of proteins. The hydroxyl radical produces a strikingly well-defined cleavage pattern over the bent DNA incorporated in nucleosomes. The dominant periodicity of DNA in this nucleosome is 10.26 base-pairs per turn. The distribution of the .OH cut sites in the positioned nucleosome provides strong support for models in which the minor grooves of the A/T-rich tracts are oriented toward the histone core while the minor grooves of the G/C-rich sequences are facing outward.

Characterization of the DNA-binding properties of the polyomavirus capsid protein VP1

The major capsid protein of polyomavirus, VP1, has been expression cloned in Escherichia coli, and the recombinant VP1 protein has been purified to near homogeneity (A. D. Leavitt, T. M. Roberts, and R. L. Garcea, J. Biol. Chem. 260:12803-12809, 1985). With this recombinant protein, a nitrocellulose filter transfer assay was developed for detecting DNA binding to VP1 (Southwestern assay). In optimizing conditions for this assay, dithiothreitol was found to inhibit DNA binding significantly. With recombinant VP1 proteins deleted at the carboxy and amino termini, a region of the protein affecting DNA binding was identified within the first 7 amino acids (MAPKRKS) of the VP1 amino terminus. Southwestern analysis of virion proteins separated by two-dimensional gel electrophoresis demonstrated equivalent DNA binding among the different VP1 isoelectric focusing subspecies, suggesting that VP1 phosphorylation does not modulate this function. By means of partial proteolysis of purified recombinant VP1 capsomeres for assessing structural features of the protein domain affecting DNA binding, a trypsin-sensitive site at lysine 28 was found to eliminate VP1 binding to DNA. The binding constant of recombinant VP1 to polyomavirus DNA was determined by an immunoprecipitation assay (R. D. G. McKay, J. Mol. Biol. 145:471-488, 1981) to be 1 x 10(-11) to 2 x 10(-11) M, which was not significantly different from its affinity for plasmid DNA. McKay analysis of deleted VP1 proteins and VP1-beta-galactosidase fusion proteins indicated that the amino terminus was both necessary and sufficient for DNA binding. As shown by electron microscopy, DNA inhibited in vitro capsomere self-assembly into capsidlike structures (D. M. Salunke, D. L. D. Caspar, and R. L. Garcea, Cell 46:895-904, 1986). Thus, VP1 is a high-affinity, non-sequence-specific DNA-binding protein with the binding function localized near its trypsin-accessible amino terminus. The inhibitory effects of disulfide reagents on DNA binding and of DNA on capsid assembly suggest possible intermediate steps in virion assembly.

Location of nucleosomes in simian virus 40 chromatin

Over the past decade, the results of numerous indirect mappings analyses have not clarified whether or not nucleosomes occupy preferred positions in simian virus 40 (SV40) chromatin. To address this question more directly, we followed a shotgun cloning approach and determined the nucleotide sequences of over 400 cloned nucleosomal DNA fragments obtained from digestion of SV40 chromatin with micrococcal nuclease. Our results demonstrate and establish that nucleosomes do not occupy unique positions in SV40 minichromosomes and thus indicate the existence of at least several types of chromatin molecules having different nucleosome organization patterns. We developed two types of statistical analysis in order to examine the cloning data in greater detail. One type, overlap analysis, revealed the distribution of the cloned fragments with respect to SV40 DNA. The distribution exhibits an oscillating pattern, dividing the genome into regions of weak or strong nucleosome density. The other analysis determined the distribution of the midpoints of the cloned fragments and revealed potential strong and weak nucleosome location sites, and an early versus late distinction in organization of nucleosomes in SV40 chromatin. The late region appears to contain more strong nucleosome location sites (8) than the early region (4). The strongest nucleosome abuts the late side of the nuclease-hypersensitive region and includes the major transcription initiation site of the late genes. Another strong site precedes this nucleosome and includes sequences implicated in controlling the expression of the SV40 early and late genes. A strong or weak nucleosome location site is not apparent near the early side of the nucleosome-hypersensitive region. Only weak and overlapping nucleosome location sites are found in the region where replication terminates in the SV40 minichromosomes.

BK virus terminates tolerance to dsDNA and histone antigens in vivo

In order to characterize the immune response to BK virus, a human polyomavirus containing dsDNA and host cell histones, we followed the appearance of antibodies in five outbred rabbits after intravenous inoculation with purified infectious BK virus without any adjuvant. The animals were followed for 15 weeks after the first inoculation and booster doses were given after four and eight weeks. Antibodies were studied by ELISA techniques with the BK virus particle, dsDNA, ssDNA or the individual histones as test antigens. Antibodies to BK virus structural proteins were detected in all rabbits. Two out of five rabbits produced antibodies to dsDNA, ssDNA, nucleosomes and histones H1 and H3. Even a weak reactivity to H2B was detected in one serum. The autoantibody response was transient as it declined after a few weeks, but it reappeared after a second boost in one of the rabbits. The other animals did not respond in the same manner. The specificity of the antibodies against dsDNA was ascertained by inhibition studies employing S1 nuclease treated DNA as inhibitor. Furthermore, the dsDNA used as coating antigen was not recognized by a human reference serum with known specificity for ssDNA. The rabbit antisera did not show any reactivity to a panel of other (in this context irrelevant) autoantigens. This suggests that the anti-DNA and -histone antibodies are not a result of non-specific polyclonal B cell activation. Thus, inoculation of dsDNA viruses may represent a new model that allows us to investigate mechanisms responsible for circumvention of tolerance to self molecules.

Locations of nucleosomes on the regulatory region of simian virus 40 chromatin

We have asked where the nucleosomes are located with respect to the replication origin and regulatory region of simian virus 40 DNA, what would be the possible functional consequences of the identified locations, and to what extent these locations correlate with the current views on mechanisms involved in establishing nucleosome-free regions in chromatin. To identify the precise location of nucleosomes, we have shot-gun cloned and sequenced nucleosomal DNA obtained from micrococcal nuclease digestion of wt776 chromatin prepared late in infection. Our results indicate that nucleosomes do not occupy unique positions over the replication origin or the elements involved in transcriptional control. However, it appears that the nucleosome distribution is not random, since several nucleosomes are represented by two or more independently generated clones. Two nearly identical cloned fragments map over the replication origin; five include 1.5 copies of the 72 base-pair enhancer sequences; and eight map to a region that spans a DNA bending locus and the major transcription initiation site of the late genes. The complex nucleosome distribution pattern observed in our direct analysis suggests that disparate nucleosome-free regions may be involved in controlling replication, and selective expression of the viral early or late genes.

cis-acting sequences that control the level of viral DNA synthesis in the polyomavirus late region

A deletion in the polyomavirus late region results in a drastic reduction of viral replication, as shown after transfection of viral DNA into 3T6 cells. This mutation is cis acting, since cotransfection with wild-type DNA did not restore the normal phenotype. Viral DNA synthesis returned to normal levels only after reintroduction of the authentic sequences in either orientation. The data presented here suggest that these sequences are involved in the binding of a factor(s) that controls the level of viral replication.

Generation of a nucleosome-free promoter region in SV40 does not require T-antigen binding to site I

The relationship between T-antigen interactions at Site I and the presence of a nucleosome-free promoter in SV40 chromatin was examined by analyzing chromatin from mutants defective for T-antigen interaction at site I (cs 1085, scs111, and tsA58) and their parental wild-type strains (776, SVS, and VA45-54, respectively). As judged by sensitivity to digestion with restriction endonucleases that recognize unique sequences within the promoter region (BglI, KpnI, and MspI), a nucleosome-free promoter was observed in a substantially larger proportion of chromosomes from the defective mutants than their wild-type parents. This result demonstrates that T-antigen binding to site I is not necessary for setting the early boundary of the nucleosome-free region, although it may function directly or indirectly in determining the proportion of chromosomes containing this feature.

Formation, stability and core histone positioning of nucleosomes reassembled on bent and other nucleosome-derived DNA

DNA originating from chicken erythrocyte mononucleosomes was cloned and sequenced. The properties of nucleosome reconstruction were compared for two cloned inserts, selected on account of their interesting sequence organization, length and difference in DNA bending. Cloned fragment 223 (182 base-pairs) carries alternatively (A)3-4 and (T)4-5 runs approximately every ten base-pairs and is bent; cloned fragment 213 (182 base-pairs) contains a repeated C4-5ATAAGG consensus sequence and is apparently not bent. Our experiments indicate the preference of the bent DNA fragment 223 over fragment 213 to associate in vitro with an octamer of histones under stringent conditions. We provide evidence that the in vitro nucleosome formation is hampered in the case of fragment 213, whereas the reconstituted nucleosomes were equally stable once formed. For the correct determination of the positioning of the histone octamer with regard to the two nucleosome-derived cloned DNA sequences, the complementary use of micrococcal nuclease, exonuclease III and DNase I is a prerequisite. No unique, but rotationally related, positions of the histone octamer were found on these nucleosome-derived DNA fragments. The sequence-dependent anisotropic flexibility, as well as intrinsic bending of the DNA, resulting in a rotational setting of the DNA fragments on the histone core, seems to be a strong determinant for the allowed octamer positions, Exonuclease III digestion indicates a different histone-DNA association when oligo(d(C.G)n) stretches are involved. The apparent stagger near oligo(d(A.T)n) stretches generated by DNase I digestion on reconstituted nucleosome 223 was found to be inverted from the normal two-base 3' overhang to a two-base 5' overhang. Two possibilities of the oligo(d(A.T)n) minor groove location relative to the histone core are envisaged to explain this anomaly in stagger.

Analysis of temperature-sensitive mutations in the simian virus 40 gene encoding virion protein 1

Temperature-sensitive (ts) assembly mutants of the tumorigenic virus simian virus 40 (SV40) fail to follow the normal pathway of virion morphogenesis at 40 degrees C. The mutations were previously mapped to the gene coding for the major virion protein VP1 and fall into three groups: tsB, tsBC, and tsC. We have determined the tsB/C mutations by DNA sequence analysis and deduced the corresponding amino acid substitutions. We find that the mutations are global and span 68% of the VP1 gene. They result predominantly in single amino acid substitutions. The B mutations are localized between nucleotides 1667 and 2091, spanning the VP1 amino acid residues 54-195. With the exception of one mutation in tsC260, the C group mutations occur between the nucleotides 2141 and 2262, spanning VP1 residues 212-252. The tsBC substitutions are not localized within a distinct region. We present a model for the VP1 structure. The model correlates the distribution of ts assembly mutations in the SV40 VP1 gene with the VP1 functional domains, deduced form the phenotypes exhibited by the assembly mutants, and the VP1 structural domains, deduced recently from the cryoelectron microscopic studies of the SV40 virions. We summarize the behavior of the SV40 ts mutants and discuss the possible relationship between the ts phenotype and amino acid substitutions.

In vitro assay for protein-protein interaction: carboxyl-terminal 40 residues of simian virus 40 structural protein VP3 contain a determinant for interaction with VP1

Intermolecular interactions between polypeptide chains play essential roles in the functioning of proteins. We describe here an in vitro assay system for identifying and characterizing such interactions. Such interactions are difficult to study in vivo. We have translated synthetic, nonmethyl-capped RNAs in a cell-free protein-synthesizing system. The translation products were allowed to interact posttranslationally to form protein-protein complexes. The chemical nature of the protein interaction(s) was determined by coimmunoprecipitation of associating proteins, sedimentation through sucrose gradients, followed by NaDodSO4/polyacrylamide gel electrophoresis or by nonreducing NaDodSO4/polyacrylamide gel electrophoresis. The system has been utilized to show the self-assembly of monomeric VP1, the major structural protein of simian virus 40, into disulfide-linked pentamers and to show the noncovalent interaction of another structural protein, VP3, with VP1 at low monomer concentrations. Additionally, we show that the carboxyl-terminal 40 amino acids of VP3 are essential and sufficient for its interaction with VP1 in vitro. The in vitro assay system described here provides a method for identifying the domains involved in, and the molecular nature of, protein-protein interactions, which play an important role in such biological phenomena as replication, transcription, translation, transport, ligand binding, and assembly.

Reconstruction of the three-dimensional structure of simian virus 40 and visualization of the chromatin core

The three-dimensional structure of the capsid and the nucleohistone core of simian virus 40 (SV40) has been reconstructed by image analysis of electron micrographs of frozen hydrated samples. The 72 prominent capsomere units that comprise the T = 7d icosahedral surface lattice of the capsid are clearly resolved. Both the pentavalent and hexavalent capsomeres appear with pentameric substructure, indicating that bonding specificity in the shell is not quasi-equivalent. There is a remarkable similarity between the structure of the SV40 virion capsid and the structure reported for the polyoma empty capsid. This result establishes that (i) the unexpected pentameric substructure of the hexavalent capsomeres is also present in virions and (ii) the arrangement of the 72 pentamers in the capsid lattice may be a characteristic feature of the entire papova family of viruses. The center of the SV40 reconstruction reveals electron density corresponding to the nucleohistone core. This density is smeared, suggesting that the minichromosome is not organized with icosahedral symmetry matching the capsid symmetry. The visualization of the virion chromatin provides a basis for invoking new models for the higher order structure of the encapsidated minichromosome.

Supercoiling in prokaryotic and eukaryotic DNA: changes in response to topological perturbation of plasmids in E. coli and SV40 in vitro, in nuclei and in CV-1 cells

Changes in DNA linking number have been observed in plasmid DNA purified from E. coli cells after the cells were treated with chloroquine. Chloroquine, a DNA intercalating drug, unwinds the DNA, decreasing the levels of negative supercoiling. Following this in vivo topological perturbation, within minutes DNA gyrase decreases DNA linking number producing more negatively supercoiled DNA topoisomers. Following the removal of the drug from cells, within minutes topoisomerase 1 or DNA gyrase increases the linking number restoring the original level of supercoiling. Analogous changes in DNA linking number after addition of chloroquine are observed in purified plasmid DNA, and in purified SV40 minichromosomes in the presence of exogenous topoisomerase. Changes in linking number are also observed in SV40 chromosomes in isolated nuclei and in SV40 DNA purified from CV-1 cells following topological perturbation with chloroquine. These results suggest that eukaryotic cells may have mechanisms to maintain a defined level of DNA supercoiling.

The flexibility and topology of simian virus 40 DNA in minichromosomes

The linking number of DNA in minichromosomes increases by 2 turns during SV40 assembly. Changes in temperature also influence the average linking number of the total intracellular forms of SV40 DNA. When the isolated minichromosomes assembled in vivo are incubated with topoisomerase I at 33 degrees C in vitro, the linking number of SV40 DNA decreases. This decrease is about: -1.1 turns for minichromosomes with an average nucleosome spacing of 198 base pairs (bp), wt776; and -0.6 turns for minichromosomes containing a shorter average nucleosome repeat (177 bp), tsC219. The difference between the average linking number of naked SV40 DNA relaxed with topoI at 33 degrees C and minichromosomes relaxed with the enzyme at the same temperature indicates that SV40 chromatin contains on the average 26 nucleosomes. However, the results of studies obtained both on DNA flexibility in chromatin and in naked DNA, and on the shape of the topoisomer distribution curves, indicate that all of the minichromosomes, regardless of their overall structure, do not contain the same number of nucleosomes; this heterogeneity may be as large as 8 nucleosomes. We find no apparent correlation between the amount of minichromosomes containing unconstrained torsional stress and the abundance of the molecules with a structure characteristic of transcriptionally active chromatin.