Identification and characterization of a protein covalently bound to DNA of minute virus of mice

Nucleolin forms a specific complex with a fragment of the viral (minus) strand of minute virus of mice DNA

Nucleolin, a major nucleolar protein, forms a specific complex with the genome (a single-stranded DNA molecule of minus polarity) of parvovirus MVMp in vitro. By means of South-western blotting experiments, we mapped the binding site to a 222-nucleotide motif within the non-structural transcription unit, referred to as NUBE (nucleolin-binding element). The specificity of the interaction was confirmed by competitive gel retardation assays. DNaseI and nuclease S1 probing showed that NUBE folds into a secondary structure, in agreement with a computer-assisted conformational prediction. The whole NUBE may be necessary for the interaction with nucleolin, as suggested by the failure of NUBE subfragments to bind the protein and by the nuclease footprinting experiments. The present work extends the previously reported ability of nucleolin to form a specific complex with ribosomal RNA, to a defined DNA substrate. Considering the tropism of MVMp DNA replication for host cell nucleoli, these data raise the possibility that nucleolin may contribute to the regulation of the parvoviral life-cycle.

Characterization of linker insertion and point mutations in the NS-1 gene of minute virus of mice: effects on DNA replication and transcriptional activation functions of NS-1

The NS-1 gene of minute virus of mice encodes a multifunctional protein required for replication of the viral genome and for transcriptional regulation of the two MVM promoters. To study the localization of activities required for DNA replication and transactivation of the capsid gene promoter, insertion and point mutations were introduced into the NS-1 gene. The mutant NS-1 genes were expressed in COS-7 cells by using an SV 40 promoter driven NS-1 expression vector. The ability of the mutant proteins to complement a replication defective NS-1 mutant of the infectious MVM plasmid pMM984 and to activate transcription from the capsid gene promoter in chloramphenicol acetyl transferase expression assays was determined. Two point mutations Ser-249 to Ala and Lys-250 to Gln and a one amino acid insertion between Asp-606 and Leu-607 had no effect on viral DNA replication and transactivation activities. Six independent insertions of between 2 and 12 amino acids inhibited the DNA replication activity of NS-1 between 20- and at least 100-fold. There was no apparent correlation between the extent of inhibition of parvoviral DNA replication and the location of the mutations. The transcriptional activation function of NS-1 was inhibited between 1.5- and at least 20-fold and was therefore overall relatively less sensitive to mutagenesis than was its DNA replication function. An exception to this was a 5 amino acid insertion between Tyr-543 and Gln-544 that abolished transactivation as well as the ability of NS-1 to complement viral DNA replication.

Two spatially distinct genetic elements constitute a bipartite DNA replication origin in the minute virus of mice genome

Mutations were introduced into plasmid pMM984, a full-length infectious clone of the fibrotropic strain of minute virus of mice, to identify cis-acting genetic elements required for the excision and replication of the viral genome. The replicative capacity of these mutants was measured directly, using an in vivo transient DNA replication assay following transfection of plasmids into murine A9 cells and primate COS-7 cells. Experiments with subgenomic constructs indicated that both viral termini must be present on the same DNA molecule for replication to occur and that the viral nonstructural protein NS-1 must be provided in trans. The necessary sequences were located within 1,084 and 807 nucleotides of the 3' and 5' ends of the minute virus of mice genome, respectively. The inhibitory effect of deletions within the 206-bp 5'-terminal palindrome demonstrated that these sequences comprise a cis-acting genetic element that is absolutely essential for the excision and replication of viral DNA. The results further indicated a requirement for a stem-plus-arms T structure as well as for the formation of a simple hairpin. In addition, the removal of one copy of a tandemly arranged 65-bp repeat found 94 nucleotides inboard of the 5'-terminal palindrome inhibited viral DNA replication in cis by 10- and just greater than 100-fold in A9 and COS-7 cells, respectively. The latter results define a novel genetic element within the 65-bp repeated sequence, distinct from the terminal palindrome, that is capable of regulating minute virus of mice DNA replication in a species-specific manner.

Parvovirus replication

The members of the family Parvoviridae are among the smallest of the DNA viruses, with a linear single-stranded genome of about 5 kilobases. Currently the family is divided into three genera, two of which contain viruses of vertebrates and a third containing insect viruses. This review concentrates on the vertebrate viruses, with emphasis on recent advances in our insights into the molecular biology of viral replication. Traditionally the vertebrate viruses have been distinguished by the presence or absence of a requirement for a coinfection with a helper virus before productive infection can occur, hence the notion that the dependoviruses (adeno-associated viruses [AAV]) are defective. Recent data would suggest that not only is there a great deal of structural and genetic organizational similarity between the two types of vertebrate viruses, but also there is significant similarity in the molecular biology of productive replication. What differs is the physiological condition of the host cell that renders it permissive. Healthy dividing cells are permissive for productive replication by autonomous parvoviruses; such cells result in latent infection by dependoviruses. For a cell to become permissive for productive AAV replication, it must have been exposed to toxic conditions which activate a latent AAV genome. Such conditions can be caused by helper-virus infection or exposure to physical (UV light) or chemical (some carcinogens) agents. In this paper the molecular biology of replication is reviewed, with special emphasis on the role of the host and the consequences of viral infection for the host.

Replication of minute virus of mice DNA in adenovirus-infected or adenovirus-transformed cells

The effect of adenovirus infection or transformation on the DNA replication of Minute Virus of Mice (MVM) was studied in human fibroblast cell lines. In WI38, HeLa, and 293 cells MVM infection allowed production of viral NS-1 and capsid proteins with or without adenovirus 2 (Ad2) co-infection. However, MVM DNA replication varied markedly. In HeLa cells MVM DNA was replicated weakly in host nucleoli, and replication was increased markedly by Ad2 co-infection as well as recompartmentalized to Ad2 replication factories. In Ad-transformed 293 cells MVM DNA was replicated very efficiently when infected alone or with Ad2 co-infection although recompartmentalization from nucleoli to replication factories was also seen. In WI38 cells MVM DNA was not replicated under any conditions. The variation in DNA replication in WI38, HeLa, and 293 cells despite viral protein production in all cases suggests that MVM DNA replication is uncoupled from viral gene expression and that host factors required for MVM DNA replication are induced or recompartmentalized by adenovirus infection or transformation.

The terminal regions of adenovirus and minute virus of mice DNAs are preferentially associated with the nuclear matrix in infected cells

The interaction of viral genomes with the cellular nuclear matrix was studied by using adenovirus-infected HeLa cells and minute virus of mice (MVM)-infected A-9 cells. Adenovirus DNA was associated with the nuclear matrix both early and late in infection, the tightest interaction being with DNA fragments that contain the covalently bound 5'-terminal protein. Replicative forms of MVM DNA were also found to be exclusively matrix associated during the first 16 to 20 h of infection; at later times viral DNA species accumulated in the soluble nuclear fraction at different rates, suggesting a saturation of nuclear matrix-binding sites. MVM DNA fragments enriched in the matrix fraction were also derived from the terminal regions of the viral genome. However, only the subset of fragments which possess a covalently bound 5'-terminal protein (i.e., DNA fragments in which the 5' palindromic DNA sequences are in the extended duplex rather than the hairpin conformation) were matrix associated. These observations suggest that the DNA-matrix interactions are, at least in part, mediated by the viral terminal proteins. Since these proteins have previously been shown to be intimately involved in viral DNA replication, our results further indicate that an association with the nuclear matrix may be important for viral genome replication and possibly also for efficient gene transcription.

Characterization of replicative form DNA of the autonomous parvovirus mink enteritis virus

Characterization of replicative form (RF) DNA of mink enteritis virus (MEV) was carried out. Most of the RF DNA were bound to terminal protein but some were free from the protein. The protein-free RF DNA increased about 7 times from 30 to 50 hr post-infection, while the DNA with protein increased less. The molecules of the replicative intermediate which were partially single-stranded DNA and bound to terminal protein were present. Two terminal conformations, "extended" and "turnaround," were observed in both ends of both terminal protein-bound and protein-free RF DNA. The 5' end labeling revealed that 5' ends of protein-free RF DNA were not blocked to phosphorylation by an amino acid or an oligopeptide which attaches to 5' ends of proteolytically deproteinized RF DNA. Restriction analysis of incomplete RF DNA which was partially double-stranded DNA showed that extended conformation was dominant in such incomplete RF molecules.

A genome-linked copy of the NS-1 polypeptide is located on the outside of infectious parvovirus particles

The 5' ends of all newly synthesized single-stranded (s1) DNA genomes of the autonomous parvovirus minute virus of mice are covalently linked to the major virally coded nonstructural protein NS-1, but later in infection this association is disrupted, giving rise to an abbreviated form of single-stranded DNA designated s2. Both s1 and s2 forms are encapsidated and migrate in velocity gradients as 110S particles, and, as such, both appear to be infectious. Most virions are released from A9 cells as s1 particles, but the NS-1 molecules are located on the outside of the virion where they are accessible to both antibodies and enzymes. These polypeptides are cleaved from the encapsidated DNA by nucleolytic or proteolytic digestion, which can occur either in the culture medium or upon subsequent entry into further host cells. Since the s1 to s2 cleavage can be minimized by blocking viral reentry, it is likely that most of the processing occurs after entry into the host cell. Incoming virus is rapidly converted to the s2 form when it is used to infect new host cells, but in vitro removal of the NS-1 molecules with proteases or nucleases fails to influence the infectivity of s1 particles under normal culture conditions. Limited proteolysis of s1 particles with trypsin demonstrates that NS-1 is linked to the DNA via its amino-terminal domain. Analysis of the 5' ends of s1 and s2 forms indicates that there are approximately 24 externally located nucleotides linking the NS-1 molecules to the 5.1-kilobase nuclease-resistant DNA core of the virion.

Interactions of minute virus of mice and adenovirus with host nucleoli

Biochemical evidence is presented that both minute virus of mice (MVM) and adenovirus interact with the nucleolus during lytic growth and that MVM can also target specific changes involving nucleolar components in adenovirus-infected cells. These virus-nucleolus interactions were studied by analysis of intranuclear compartmentalization of both viral DNAs and host nucleolar proteins: (i) MVM in mouse cells (its normal host) replicates its DNA in the host nucleoli; (ii) specific nucleolar proteins as well as small nuclear ribonucleoprotein antigens are recompartmentalized to multiple intranuclear foci in adenovirus-infected HeLa cells; and (iii) when adenovirus helps MVM DNA replication in a nonpermissive human cell (HeLa), the MVM DNA is also recompartmentalized for synthesis. The data suggest mechanisms for disruption of nucleolar function common to oncogenic or oncolytic virus lytic growth and cell transformation.

A novel primase-free form of murine DNA polymerase alpha induced by infection with minute virus of mice

Two species of DNA polymerase alpha free of primase activity were identified in extracts of Ehrlich mouse cells that had been infected with minute virus of mice. Primase-free forms of DNA polymerase alpha eluted with 150 and 180 mM NaCl during ion-exchange chromatography on DEAE-cellulose columns, exhibited sedimentation coefficients of 11 S and 8.2 S, respectively, and were inhibited by aphidicolin, N2-(p-n-butylphenyl)-9-(2-deoxy-beta-D-ribofuranosyl)guanine 5'-triphosphate, and 2-(p-n-butylanilino)-9-(2-deoxy-beta-D-ribofuranosyl)adenine 5'-triphosphate. The ratio of primase-free DNA polymerase alpha to the DNA polymerase alpha-primase complex increased from 1.5 to greater than 100 during the course of infection, and free primase was produced during the MVM replicative cycle.

Sequence organization in regulatory regions of DNA of minute virus of mice

Analysis of the nucleotide sequence of minute virus of mice (MVM) DNA indicates that the DNA termini contain clusters of potential DNA regulatory elements and that there are repetitive DNA elements highly reiterated throughout the entire genome, which may also have a role in DNA function. The left end of MVM DNA, which contains the promoter for the nonstructural genes, has a cluster of DNA elements that includes homologies to the polyoma virus enhancer, three copies of an E1A-inducible transcription factor (ATF) binding site, and a potential Z-DNA element. The MVM right end, which contains the origin of DNA replication, has a cluster of DNA elements that includes several homologies to the polyoma virus replication origin and a potential Z-DNA element. In addition, oligonucleotide frequency analysis indicates the presence of highly recurring sequence elements throughout the entire MVM genome that may be involved in regulation. This computer-aided analysis suggests similarities and significant differences in regulatory sequence organization between MVM and polyoma virus, and identifies specific DNA elements for future genetic characterization.

Parvovirus replication in normal and transformed human cells correlates with the nuclear translocation of the early protein NS1

The parvovirus H-1 infection of the normal human diploid fibroblast strain MRC-5 produces a cytopathic effect, but no increase in infectious virus has been observed. Previously, we reported that large amounts of empty capsids are assembled in the nucleus of H-1 infected MRC-5 cells (S. Singer and S. Rhode, in D. Ward and P. Tattersall, ed., Replication of Mammalian Parvoviruses, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1978). The level of viral replicative-form DNA synthesis as shown by metabolic labeling is markedly reduced in these cells. Synthesis of the early protein NS1 is normal or slightly decreased, and the usual amount of the 92,000-molecular-weight (92K) posttranslationally modified NS1 was seen. The second deficient parameter that we have observed in the abortive infection is the nuclear translocation of NS1. In contrast, the simian virus 40-transformed MRC-5 cell line MRC-5 V1 and the simian virus 40-transformed human kidney cell line NB undergo a productive infection by H-1 accompanied by more efficient translocation of NS1 to the nucleus. The results indicate that there is an association between defective translocation of the NS1 rep protein to the nucleus and defective amplification of parvovirus replicative-form DNA. The nuclear translocation of specific proteins seems to be a function that is altered by development or neoplastic transformation.

Characterization of novel populations of MVM virions containing covalent DNA-protein complexes

Virions of minute virus of mice were purified by sedimentation in sucrose gradients and chromatography on DEAE-cellulose columns and shown to consist of single-stranded viral DNA and the viral capsid polypeptides VP-1 (83 kDa) and VP-2 (64.5 kDa). A 63-kDa polypeptide distinct from the viral capsid polypeptide VP-3 (61.4 kDa) was found in some virion preparations. Virions sedimented at 135 and 110 S. The genomic single strands associated with purified 135 and 110 S virions were covalently bound to a protein as judged by the anomalous electrophoretic mobility of the DNA in agarose gels at pH 12.5. The protein was removed from the DNA by Pronase but remained bound after heating at 98 degrees in the presence of 0.1% sodium dodecyl sulfate. Nuclease digestion of the purified DNA-protein complex released several polypeptides ranging in size from 58 to 65 kDa. Restriction enzyme analysis of the purified DNA protein complex following its conversion to a duplex RF DNA in vitro showed that the protein was attached to the 5' termini of the DNA.

The terminal protein of minute virus of mice is an 83 kilodalton polypeptide linked to specific forms of double-stranded and single-stranded viral DNA

A new assay (label transfer from DNA to protein) enabled the identification of a terminal protein (TP) in nucleoprotein complexes extracted from cells infected with the parvovirus, minute virus of mice, MVM. In SDS-PAGE, TP migrates as a major band at 83 kDa, with a minor 65 kDa component, each of which exactly co-migrates with the cellular forms of the virally coded polypeptide NS-1. In parallel, the analysis of nucleoproteins by SDS-agarose gel electrophoresis allowed us to observe that the major species of viral DNA molecules (mRF, dRF and ssDNA) are all present in the form of DNA-protein complexes. Three forms of mRF DNA were identified, two of which are protein-associated and one which appears to be protein-free.

Capsid protein VP1 (p85) of Aleutian disease virus is a major DNA-binding protein

The interaction between Aleutian disease virus (ADV) DNA and proteins isolated from ADV-infected cells or ADV virions, respectively, was examined. Proteins were separated on SDS-polyacrylamide gels, transferred to nitrocellulose, and probed with 32P-labeled restriction fragments of replicative form (RF) DNA or with single-stranded virion DNA. The ADV capsid protein VP1 was found to bind the 3'-terminal BamHI fragment of RF DNA extending from map units (m.u.) 0 to 15. No binding was observed with the fragment extending from m.u. 15 to 63 and only minor amounts of label were detected with the 5'-terminal EcoRV fragment extending from m.u. 63 to 100. With the latter fragment, small amounts of label were also detected bound to higher-molecular-weight proteins of about 100,000 Da. No binding of DNA to the ADV nonstructural protein NS1 or to the ADV capsid protein VP2 was detected. Additionally, single-stranded virion DNA was found to bind to VP1.

Evidence that developmentally regulated control of gene expression by a parvoviral allotropic determinant is particle mediated

An infectious molecular clone of the immunosuppressive strain of the autonomous parvovirus minute virus of mice [MVM(i)] was constructed deriving left-hand terminal sequences from a rare encapsidated plus strand. Progeny virus was shown to package the same proportions of plus and minus strands as did authentic MVM(i) virions. Rescue of virus from this clone also resulted in the repair of a 21-base truncation at the junction between the right-hand end of the viral insert and the vector and generated the same heterogeneous 5' end as is present in standard MVM(i) DNA. Progeny virus rescued by transfection of this clone into mouse cell lines displayed the lymphotropic phenotype characteristic of the parental MVM(i) virus from which it was derived. However, analysis of viral RNA from transfected mouse fibroblasts revealed that the MVM(i) and MVM(p) genomic clones are transcribed at the same low level. Furthermore, transfected fibroblasts yielded similar numbers of infectious centers regardless of which MVM clone was introduced. These results contrast markedly with the different infectivities of MVM(i) and MVM(p) particles and with the observation that viral transcription in fibroblasts productively infected with MVM(p) virions is 100-fold greater than that seen in the restrictive MVM(i) particle-mediated infection. These results suggest that the developmentally regulated intracellular factors controlling host cell susceptibility at the level of viral transcription interact with a component of the incoming viral capsid, rather than with a sequence within the viral DNA.

The NS-1 polypeptide of minute virus of mice is covalently attached to the 5' termini of duplex replicative-form DNA and progeny single strands

When A9 cells are infected with minute virus of mice, a small proportion of the virally coded NS-1 polypeptide becomes covalently attached to newly synthesized viral DNA. Antisera directed against NS-1 will specifically precipitate two forms of monomer duplex replicative-form DNA, multimeric duplex intermediates and progeny single strands, and restriction analysis of the duplex forms in these precipitates reveals that NS-1 is exclusively associated with extended-form conformers of the genomic termini. Pulse-labeled viral DNA, harvested at various times in a highly synchronized infection, can be almost quantitatively precipitated with any one of a series of antisera directed against different protein domains distributed throughout the NS-1 molecule but not with antibodies directed against other viral proteins. In each case the interaction with NS-1 can be shown to involve both termini of duplex DNA and single-strand forms, suggesting that in each case a full-length (83-kilodalton) copy of NS-1 is present. Precipitation of the replicating viral DNA with an antibody directed against a synthetic 16-amino-acid peptide containing the sequence at the extreme carboxy terminus of NS-1 can be quantitatively and specifically inhibited with the immunizing peptide in its unconjugated form, showing that the antibodies responsible for precipitating viral DNA are directed against the NS-1 sequence itself and not against a trace contaminant. Exonuclease digestion studies show that the association effectively blocks the 5' ends of the DNA molecules. Very little (less than 0.1%) of the newly synthesized [35S]methionine-labeled NS-1 made in highly synchronized cells during a 15-min pulse early in infection (6.25 to 6.5 h into the S phase) becomes associated with viral DNA immediately. However, pulse-chase experiments show that later in infection (10 to 13 h into the S phase), when viral DNA replication is reaching its peak, a few percent of the molecules in these preexisting pools of NS-1 do become covalently attached to the newly replicated DNA. Isolated viral DNA-protein complexes labeled with [35S]methionine in this way can be obtained by fractionation of the immunoprecipitated complexes on Sepharose CL4B in sodium dodecyl sulfate. Digestion of the purified complexes with nuclease releases an 83-kilodalton molecule which exactly comigrates with authentic NS-1 in sodium dodecyl sulfate-polyacrylamide gels.

Genomic clones of bovine parvovirus: construction and effect of deletions and terminal sequence inversions on infectivity

Genomic clones of the autonomous parvovirus bovine parvovirus (BPV) were constructed by blunt-end ligation of reannealed virion plus and minus DNA strands into the plasmid pUC8. These clones were stable during propagation in Escherichia coli JM107. All clones tested were found to be infectious by the criteria of plaque titer and progressive cytopathic effect after transfection into bovine fetal lung cells. Sequencing of the recombinant plasmids demonstrated that all of the BPV inserts had left-end (3')-terminal deletions of up to 34 bases. DNA isolated from progeny virions arising from transfected infectious clones was found to be indistinguishable from wild-type DNA by restriction enzyme analysis. Defective genomes could also be detected in the progeny DNA even though the infection was initiated with homogenous, cloned DNA. Full-length genomic clones with 3' flip and 3' flop conformations were constructed and were found to have equal infectivity. Analysis of low-molecular-weight DNA isolated from lysates of cells transfected with these clones demonstrated that rescue and replication of BPV DNA could be detected 3 to 8 days after transfection. Expression of capsid proteins from transfected genomes was demonstrated by hemagglutination, indirect immunofluorescence, and immunoprecipitation of [35S]methionine-labeled cell lysates. Use of appropriate antiserum for immunoprecipitation showed the synthesis of BPV capsid and noncapsid proteins after transfection. Independently, a series of genomic clones with increasingly larger 3'-terminal deletions was prepared from separately subcloned 3'-terminal fragments. Transfection of these clones into bovine fetal lung cells revealed that deletions of up to 34 bases at the 3' end lowered but did not abolish infectivity, while deletions of greater than 52 bases were lethal. End-label analysis showed that the 34-base deletion was repaired to wild-type length in the progeny virus.

A nonstructural protein of feline panleukopenia virus: expression in Escherichia coli and detection of multiple forms in infected cells

Sequences coding for the nonstructural protein NS1 of the autonomous parvovirus feline panleukopenia virus were expressed in Escherichia coli as fusion proteins. The fusion proteins were specifically bound by antisera from canine parvovirus-infected dogs. Antisera against one of the fusion proteins bound to several proteins found only in feline panleukopenia virus-infected feline cells.

Nonhomologous recombination in the parvovirus chromosome: role for a CTATTTCT motif

The mechanism of nonhomologous recombination in murine cells infected with the parvovirus minute virus of mice (MVM) has been investigated by analysis of DNA sequences at recombination junctions in naturally occurring deletion variants of the virus. We report here that nonhomologous recombination in the MVM chromosome is characterized by short homologies, by insertion at recombination junctions of foreign DNA sequences that are enriched for preferred eucaryotic topoisomerase I cleavage sites, and by an association with a common DNA sequence motif of the type 5'-CTATTTCT-3'. Additional analyses of broken MVM chromosomes provided evidence for specific enzymatic cleavage within 5'-CTTATC-3' and 5'-CTATTC-3' sequences. The results indicate that the 5'-CTATTTCT-3' motif is an important genetic element for nonhomologous recombination in the parvovirus chromosome.

Nonhomologous recombination in the parvovirus chromosome: role for a CTATTTCT motif

The mechanism of nonhomologous recombination in murine cells infected with the parvovirus minute virus of mice (MVM) has been investigated by analysis of DNA sequences at recombination junctions in naturally occurring deletion variants of the virus. We report here that nonhomologous recombination in the MVM chromosome is characterized by short homologies, by insertion at recombination junctions of foreign DNA sequences that are enriched for preferred eucaryotic topoisomerase I cleavage sites, and by an association with a common DNA sequence motif of the type 5'-CTATTTCT-3'. Additional analyses of broken MVM chromosomes provided evidence for specific enzymatic cleavage within 5'-CTTATC-3' and 5'-CTATTC-3' sequences. The results indicate that the 5'-CTATTTCT-3' motif is an important genetic element for nonhomologous recombination in the parvovirus chromosome.