Purification and molecular characterization of adenovirus type 2 DNA-binding protein

Stimulation of the adenovirus major late promoter in vitro by transcription factor USF is enhanced by the adenovirus DNA binding protein

Previous studies have shown that the sequence-independent adenovirus DNA binding protein (DBP) increases transcription from several promoters, notably from the adenovirus major late promoter (MLP) and the adeno-associated virus P5 promoter, both of which contain a USF/MLTF binding site. In order to study this mechanism, we have investigated the effects of DBP on the binding of USF/MLTF to MLP and on transcription from MLP by a reconstituted in vitro system. As shown by gel retardation and DNase I footprinting, upon saturation of DNA, DBP enhances the binding affinity of USF43 to the promoter three- to fourfold without changing the footprint pattern. In contrast, the binding of the TATA box binding protein to the promoter is not influenced by DBP. No protein-protein interactions between DBP and USF43 could be observed in the absence of DNA, suggesting that enhanced binding is caused by a change in DNA structure induced by the DBP-DNA complex. Employing a transcription system reconstituted with purified general transcription factors, we show that USF43 enhances basal transcription and that USF43-dependent transcription is further increased by DBP, while DBP alone does not have an effect on basal transcription. Our results suggest that transcription enhancement by DBP is based on a specific increase in the binding of a transcription factor to a promoter through subtle changes in DNA structure, similar to the mechanism by which DBP stimulates the initiation of DNA replication.

Role of the adenovirus 72-kDa DNA binding protein in the rapid decay of early viral mRNA

Previous experiments have shown that the early adenovirus E1A and E1B mRNAs decay with a half-life of 20 min in a lytic infection dependent on the action of the viral 72-kDa DNA binding protein. In contrast, the same E1A and E1B mRNAs are stable when synthesized in 293 cells, an adenovirus-transformed cell line that is devoid of the 72-kDa protein. If 293 cells are infected with the E1A deletion mutant dl312, the endogenous E1A RNA disappears after 4 hr of infection, a time coincident with the appearance of the 72-kDa protein. The induction of decay is specific since there is no decrease in the level of actin or certain other cellular mRNAs. Thus, the stability of the early RNAs is variable and correlates with the presence of the 72-kDa protein. An interaction of the 72-kDa DNA binding protein with RNA inside the cell has been demonstrated by in vivo crosslinking of protein to RNA. However, the protein is found in association with actin mRNA as well as E1A mRNA. Thus, although the 72-kDa protein appears to be required for the rapid decay of viral mRNA it apparently does not impart specificity to the process.

Characterization of the chymotryptic core of the adenovirus DNA-binding protein

A fragment of the DNA-binding protein of adenovirus type 5 has been obtained by controlled chymotryptic digestion of the entire molecule. Partial sequence determination indicates that the fragment consists of amino acids 174-525. The fragment is biologically active as measured by its ability to substitute for the entire molecule in a reconstituted DNA replication system. Crystals have been obtained that show diffraction to 2 A.

Identification of a herpes simplex virus function that represses late gene expression from parental viral genomes

The expression of herpes simplex virus gamma 2 (late) genes is inhibited before the onset of viral DNA replication. We report that the block in the expression of certain gamma 2 genes is relieved, at least in part, by defects in the beta ICP8 protein. We have examined the expression of the gamma 2 gene encoding glycoprotein C (gC) in cells infected with a temperature-sensitive ICP8 mutant. Under conditions in which viral DNA replication is inhibited, cells infected with the ICP8 mutant overproduce the gC family of mRNAs relative to the level observed in cells infected with a wild-type virus. The gC mRNA synthesized in cells infected with the ICP8 mutant virus is correctly initiated and spliced and is translated with the same relative efficiency as in cells infected with a replicating wild-type virus. These results suggest that ICP8 is involved in the negative regulation of gamma 2 genes expressed from parental viral genomes. The level of gC expression was greatest in cells infected with a replicating wild-type virus. These data suggest that DNA replication and genome amplification are not absolute requirements for gamma 2 gene expression but may facilitate full-level expression of these genes.

Mutations in the major DNA-binding protein gene of herpes simplex virus type 1 result in increased levels of viral gene expression

We have examined the effect of temperature-sensitive mutations in the herpes simplex virus 1 DNA-binding protein gene on viral gene expression. We have found that at the nonpermissive temperature, the synthesis of certain immediate early, early, and late viral polypeptides was greater in cells infected with the temperature-sensitive mutants than in cells infected with the wild-type virus. This effect was independent of the requirement for this viral protein for viral DNA replication. The altered rate of synthesis of viral proteins was due to a thermolabile gene product. Cells infected with these mutants at the permissive temperature and then shifted to the nonpermissive temperature exhibited enhanced levels of viral gene expression. The addition of actinomycin D at the time of the temperature shift prevented the alteration in viral protein synthesis. Therefore, continuing transcription is required for this change in gene expression. Northern blot analysis of cytoplasmic RNA showed that the steady-state level of specific viral transcripts expressed from parental virus genomes was greater in cells infected by these mutants at the nonpermissive temperature. These results indicate that the major DNA-binding protein of herpes simplex virus type 1 acts as a negative regulator of viral gene expression by affecting the abundance of cytoplasmic viral mRNAs.

Late nonstructural 100,000- and 33,000-dalton proteins of adenovirus type 2. I. Subcellular localization during the course of infection

We analyzed the subcellular locations of the late adenovirus type 2 nonstructural 100,000-dalton (100K) and 33K proteins in adenovirus type 2-infected HeLa cells both by biochemical cell fractionation and by immunofluorescence microscopy, using specific antisera against purified sodium dodecyl sulfate-denatured 100K and 33K polypeptides. Both methods showed that the 100K protein was present in the cytoplasm as well as in the nuclei of infected cells and that it accumulated in the nuclei during the course of infection. Phosphorylated 100K protein also was found both in the cytoplasm and in nuclei. However, the nuclear 100K protein pool was phosphorylated to a higher degree than the cytoplasmic pool. In all experiments the 33K protein, which also is a phosphoprotein, was present exclusively in the nuclei of infected cells. The 100K and 33K proteins were associated with different nuclear substructures; this was demonstrated serologically by an analysis of infected cells in which double color immunofluorescence microscopy was used. In these experiments antibodies against the 100K protein decorated different nuclear structures than antibodies against the 33K protein.

The stability of early adenovirus mRNA is controlled by the viral 72 kd DNA-binding protein

H5ts125, a temperature-sensitive mutant of adenovirus type 5, is restricted to the early phase of infection when grown at the nonpermissive temperature. One phenotype of the virus is the overproduction of early viral mRNA at the nonpermissive temperature relative to levels found in wild-type-infected cells, although normal levels are found at the permissive temperature. We have analyzed this phenomenon for the production of RNA from two specific early viral transcription units, E1A and E1B. Transcription rates from both of these regions were found to be the same in ts125-infected cells as in wild-type-infected cells at the nonpermissive temperature. However, when the cytoplasmic stabilities of the E1A and E1B mRNAs were measured in wild-type- and ts125-infected cells, it was found that at the nonpermissive temperature, the RNAs were 3 to 5 times more stable in a ts125 infection than in a wild-type infection. Since the mutation in ts125 maps to the gene for the 72 kd DNA-binding protein, these results imply that a functional 72 kd protein is required for the rapid turnover of early viral mRNA in wild-type-infected cells, indicating that the abundance of early viral mRNA is controlled by the 72 kd DNA-binding protein.

Characterization of the effect of aphidicolin on adenovirus DNA replication: evidence in support of a protein primer model of initiation

Adenovirus DNA replication is inhibited by aphidicolin but the inhibition clearly has different parameters than the inhibition of purified DNA polymerase alpha. In adenovirus infected Hela cells, 10 micrograms/ml of aphidicolin reduced viral DNA synthesis by 80%. Cellular DNA synthesis was inhibited by 97% at 0.1 microgram/ml. 10 micrograms/ml of drug had no effect on virus yield or late protein synthesis though higher concentrations of drug (50 micrograms/ml) caused an abrupt cessation of late protein synthesis and 100 micrograms/ml reduced virus yield by 3 logs. Concentrations of the drug from 0.5 microgram/ml to 10 micrograms/ml were found to dramatically slow the rate of DNA chain elongation in vitro but not stop it completely, so that over a long period of time net incorporation was reduced only slightly compared to the control. 50 micrograms/ml or 100 micrograms/ml of drug completely inhibited incorporation in vitro. Initiation of viral DNA replication - covalent attachment of dCMP to the preterminal protein - occurs in vitro. This reaction was found to be insensitive to inhibition by aphidicolin. We thus conclude that aphidicolin exerts its effect on adenovirus DNA chain elongation, but not on the primary initiation event of protein priming.

Adenovirus early gene products may control viral mRNA accumulation and translation in vivo

The mechanisms controlling early adenovirus gene expression in vivo have been studied using inhibitors of protein synthesis. When inhibitors were added shortly before or at the onset of infection, viral mRNA from all early regions was transcribed, spliced and accumulated over a 7 hr period. After longer pretreatment, accumulation of several early mRNAs were suppressed. Addition of inhibitors 1 hr after infection enhanced the accumulation of viral mRNA in the cytoplasm. Translation of early mRNA selected on adenovirus DNA in a cell-free system reflected the amount of viral mRNA present. A viral coded product may therefore control accumulation of viral mRNA. A different pattern emerged when inhibitors of protein synthesis were removed at 5 hr postinfection and cells were removed at 5 hr postinfection and cells were pulse-labeled in vivo. If inhibitors were introduced at or before infection, early viral proteins were synthesized only after a lag of 1-3 hr. However, if treatment was introduced 1 hr postinfection, reversion of the protein synthesis block was instantaneous. It appears that protein synthesis inhibitors reveal an in vivo translational block for viral mRNA. This block could be overcome by preinfection with a related virus. Furthermore, no block was observed in a virus-transformed human embryonic kidney cell line (293) which expresses early region 1 of the viral genome. Viral gene product(s) encoded in early region 1 may control translation of early adenovirus messenger RNA in vivo.

Immunoautoradiographic detection of proteins after electrophoretic transfer from gels to diazo-paper: analysis of adenovirus encoded proteins

We describe a method by which complex protein mixtures are fractionated by standard one-dimensional Na-DodSO4/polyacrylamide gel electrophoresis or O'Farrell two-dimensional gel electrophoresis and then are efficiently and rapidly transferred electrophoretically to diazobenzyloxymethyl- or diazophenylthioether-paper and analyzed by immunoautoradiography. The method is illustrated with protein extracts of human KB cells infected with adenovirus type 2. Proteins were transferred from gels without decrease in resolution and with an increase in the sensitivity of detection by autoradiography when [35S]-methionine-labeled proteins were used. When unlabeled proteins were transferred, low levels of virus encoded proteins could be detected by sequential treatment of diazobenzyloxymethyl-paper with anti-adenovirus type 2 virion or anti-73,000 DNA binding protein and 125I-labeled Staphyloccus aureus protein A. Covalently bound viral proteins retained immunologic reactivity after dissociation of the protein A and antibody, By one-dimensional gel transfer/immunoautoradiography, seven virion proteins were detected as prominent bands and several others as weaker bands. By two-dimensional gel transfer/immunoautoradiography, several additional viral proteins were detected. By use of anti-DNA binding protein serum, the Mr 73,000 protein and Mr 41,000-48,000 subspecies were detected. A protein present at a concentration of approximately 1 part in 100,000 of the total protein can be identified in cell extracts. This method may be applicable to various biological problems requiring resolution and detection of small amounts of specific proteins that can be recognized immunologically or that can be detected by binding to specific radiolabeled DNA or RNA sequences or hormones.

Adenovirus-specific DNA-binding protein inhibits the hydrolysis of DNA by DNase in vitro

The adenovirus-specific DNA-binding protein was isolated from adenovirus type 5-infected KB cells and shown to possess DNase inhibitor activity. The protein decreased the rate of hydrolysis of single-strand DNA proportionately to its concentration in the reaction. Two peaks of activity were obtained upon sedimentation in a glycerol gradient, probably corresponding to the two major adenovirus-specific polypeptides in the preparation (molecular weights, 72,000 and 44,000). The DNase inhibitor activity of the adenovirus DNA-binding protein was distinguishable from that of the cellular DNA-binding protein, which we have described previously (K, Nass and G. D. Frenkel, J. Biol. Chem. 254:3407-3410, 1979), by its pattern of sedimentation and by the effect of temperature on the two activities. For the adenovirus DNA-binding protein, the ratio of DNase inhibitor activity at 43 degrees C to that at 30 degrees C was approximately 14, whereas for the cellular protein this ratio was less than 3. The DNase inhibitor activity with the temperature coefficient of 14 was absent from cells infected with adenovirus type 5 ts125 at 40 degrees C. DNase inhibition is a simple, sensitive, quantitative method for assay of the adenovirus DNA-binding protein.

Adenovirus type 2 early polypeptides immunoprecipitated by antisera to five lines of adenovirus-transformed rat cells

We have identified adenovirus type 2 (Ad2)-induced early polypeptides (EPs) and have attempted to determine which EPs are coded by each of the four early gene blocks. [35S]methionine-labeled EPs were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Cycloheximide pretreatment followed by labeling in hypertonic medium (210 to 250 mM NaCl) facilitated the detection of EPs. Seven major (reproducible bands in autoradiograms) EPs were detected with molecular weights of 74,000 (74K), 21K, 19K, 15K, 13.5K, 11.5K, and 11K. Minor (weaker bands) EPs of 55K, 52K, 42K, 18K, 12K, 8.8K, and 8.3K were also often seen. To identify and map the genes for virus-coded EPs, we prepared antisera against five lines of adenovirus-transformed cells that retain different fractions of the viral genome. The lines were F17, 8617, F4, and T2C4 transformed by Ad2 virions and 5RK (clone I) transformed by transfection with the Ad5 HsuI-G fragment (map position 0 to 8). The early gene blocks retained and expressed (in part) as RNA in these cells were as follows: 5RK(I), block 1 (70% of left 8% of genome); F17, block 1; 8617, blocks 1 and 4; F4 blocks 1, 2, and 4; T2C4, blocks 1, 2, 3, and 4. The following major EPs were immunoprecipitated: 15K by all antisera; 53K and 14.5K by F17, T2C4, 8617, and F4 antisera; 11.5K by T2C4, 8617, and F4 antisera; 44K, 42K, 19K, and 13.5K by T2C4 antisera; 11K by 8617 antisera. Minor EPs of 28K, 18K, and 12K were precipitated by all antisera except 5RK(I). The 53K and 15K EPs were precipitated also from Ad2 early infected monkey cells by the F17 antiserum and by sera from hamsters bearing tumors induced by Ad1-simian virus 40. The relationships between some of the immunoprecipitated EPs were investigated by the partial proteolysis procedure. All 53K EPs are the "same" (i.e., highly related), all 15K EPs are the "same," and all 11.5K EPs are the "same." The 15K EP is highly related to the 14.5 K EP. Although less certain, all 28K EPs appeared related, as did all 18K EPs. The T2C4-specific 44K EP is probably a dimer of the 21K glycopolypeptide. The T2C4-specific 13.5K EP and the 8617-specific 11K EP appear unrelated to any other polypeptides. These immunoprecipitation data provide evidence that early gene block I (map position 1 to 11) may encode major 53K, 15K, and 14.5K polypeptides, and minor 28K, 18K, and 12K polypeptides, and that all or some of the gene for 15K and 14.5K lies within map position 1 to 8. The surprisingly complex pattern of polypeptides coded by early gene block I raises the possibility that some polypeptides may be coded by overlapping "spliced" mRNA's. The possible block locations of the genes for the 21K, 13.5K, and 11.5K polypeptides are discussed.

Purification and characterization of an early glycoprotein from adenovirus type 2-infected cells

An adenovirus type 2 early glycoprotein with an apparent molecular weight of 19,000 (E19K) in sodium dodecyl sulfate-polyacrylamide gels has been extensively purified. Purification involved detergent solubilization of membrane fractions from infected cells, followed by affinity chromatography on a lectin column and DEAE-Sephadex chromatography. The purified material contained three polypeptides (E40K, E19K, E17.5K), with approximately 90% of the material in the E19K moiety. All three polypeptides yielded identical tryptic peptide maps. The E19K polypeptide contained glucosamine as revealed by [3H]glucosamine labeling of infected cells and amino acid analysis of the purified protein. Immunoprecipitation with a monospecific antiserum showed that the E19K polypeptide started to be synthesized at 2 h, with a maximal rate at 4 h after infection. It was also synthesized at a low rate late in the infectious cycle (12 to 24 h postinfection). Immunoprecipitation from three adenovirus type 2-transformed hamster embryo cell lines and two adenovirus type 2-transformed rat cell lines revealed that one of the hamster cell lines (ad2HE4) and one of the rat cell lines (A2T2C4) expressed this protein.

Purification and characterization of an early protein (E14K) from adenovirus type 2-infected cells

One adenovirus type 2 (Ad2) early protein, with an apparent molecular weight of 14,000 in sodium dodecyl sulfate-polyacrylamide gels (E14K), was purified to homogeneity. Purification involved fractionation of cytoplasmic extracts, precipitation at low pH, and DEAE-cellulose, phosphocellulose, and hydroxylapatite chromatography. The yield was around 12 microgram of purified protein per 10(9) HeLa cells. The two Ad2 DNA binding proteins with molecular weights of 75,000 and 45,000 (E75K and E45K) were purified by the same procedure. Tryptic peptide analyses indicated that the E14K protein is unrelated to the DNA binding proteins. The purified E14K protein has a high content of basic amino acids and a sedimentation coefficient of 5.5S in the native state, corresponding to a molecular weight of around 95,000. Pulse-chase experiments suggest that the E14K polypeptide is a primary translation product. Immunoprecipitation with a monospecific antiserum against the E14K protein revealed that it is exclusively localized in the cytoplasm of infected cells. E14K started to be synthesized at 2 hpostinfection, with a maximal rate of synthesis at 4 to 6 h postinfection. Immunoprecipitation of cell extracts from four different Ad2-transformed hamster embryo cell lines revealed that only one (Ad2HE4) of them expresses this protein. The adenovirus-simian virus 40 hybrid virus (Ad2ND1) does not express this protein, suggesting that the gene for the E14K protein is located in the part of the Ad2 genome which is deleted in this hybrid virus.

Temperature-sensitive replication of H5ts125 adenovirus DNA in vitro

A soluble adenovirus DNA replication system has been prepared in extracts of HeLa cells infected with the temperature-sensitive mutant H5ts125. These nuclear extracts synthesize full-sized viral DNA at 30 degrees but are temperature sensitive in this function at 38 degrees. A 72,000-dalton DNA-binding protein purified from cells infected with wild-type virus complements the temperature-sensitive defect and restores viral DNA replication to 74% of normal values.

Structure of the adenovirus 2 early mRNAs

We have defined the structure of adenovirus 2 (Ad2) cytoplasmic RNAs produced during the early phase of infection. Hybrids between cytoplasmic RNA and DNA restriction fragments of the viral genome were digested with endonuclease S1 or exonuclease VII, and the products were analyzed by gel electrophoresis. Seven abundant cytoplasmic RNAs (assumed to be mRNAs) were identified, and all have a spliced structure. Different mRNAs produced from a single transcriptional unit contain extensively overlapping sequences, and differ from each other by the pattern in which genome sequences are spliced together. The structures of the early Ad2 mRNAs are consistent with a model for mRNA biosynthesis in which an initial transcript is processed into a mature mRNA by "splicing out" internal sequences. The pattern of spliced mRNAs produced from the early region responsible for the transforming activity of Ad2 resembles the splicing pattern of the oncogenic early mRNAs of simian virus 40 (SV40). This fact, in conjunction with recent DNA sequencing results, leads us to suggest that, like the SV40 tumor antigens, the polypeptides encoded by these Ad2 mRNAs have an identical amino acid sequence at their N terminal ends, but have different C terminal sequences.

Adenovirus type 2 coded single-stranded DNA binding protein: in vivo phosphorylation and modification

The adenovirus type 2-coded single-stranded DNA binding protein (DBP) was shown to be a phosphoprotein and to exist in at least two forms that differ in mobility by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. After a 30-min pulse with [35S]methionine or 32PO4, 35S- or 32P-labeled DBP had a nominal molecular weight of 74,000 whereas after a 30-min label followed by a 20-h chase, 35S- and 32P-labeled DBP had a nominal molecular weight of 77,000. Both large and small forms of 35S- and 32P-labeled DBP bound to single-stranded DNA-cellulose columns and were eluted by 0.4 to 0.6 M NaCl; both forms also were immunoprecipitated by antiserum against adenovirus type 1-simian virus 40-induced tumor cells (this antiserum contains antibodies against DBP) and by monospecific antiserum against 95 to 99% purified DBP. With highly purified 32P-DBP labeled 7 to 10 h postinfection, it was shown that the 32P radioactivity was firmly associated with protein material (i.e., not contaminating nucleic acids or phospholipids) and had properties expected of a phosphoester of an amino acid; paper electrophoresis of acid hydrolysates of this preparation identified phosphoserine but not phosphothreonine. Phosphoserine but not phosphothreonine was also identified in acid hydrolysates of another preparation of 32P-DBP labeled for 30 min, chased for 20 h, and then immunoprecipitated by adenovirus type 1-simian virus 40 antiserum.

Immunofluorescence study of the adenovirus type 2 single-stranded DNA binding protein in infected and transformed cells

High-titer monospecific antiserum against highly purified adenovirus 2 (Ad2) single-stranded DNA binding protein (DBP) was used to study, by indirect immunofluorescence (IF), the synthesis of DBP in Ad2-infected human cells and adenovirus-transformed rat, hamster, and human cell lines. In infected cells the synthesis of DBP was first detected in the cytoplasm at 2 to 4 h postinfection and reached a maximum intensity at 6 h postinfection. At this time DBP began to accumulate in the nucleus, where it reached maximum intensity at about 14 h postinfection. The cytoplasmic IF was diffuse, whereas nuclear IF appeared as dots that coalesced into large globules as infection progressed. In cells treated with 1-beta-d-arabinofuranosylcytosine to inhibit viral DNA synthesis, strong nuclear IF was observed in the form of dots, but the large fluorescent globules were not observed. The Ad2 (oncogenic group C) anti-DBP serum reacted very strongly by IF with Ad5 (group C)-infected, to a lesser extent with Ad7 and Ad11 (group B)-infected, and weakly with Ad12 and Ad18 (group A)-infected KB cells (treated with 1-beta-d-arabinofuranosylcytosine). These results may indicate that Ad2 DBP is closely related immunologically to DBPs induced early after infection by adenovirus serotypes in oncogenic group C, moderately related to DBPs of serotypes in oncogenic group B, and perhaps distantly related to DBPs of serotypes in oncogenic group A. The following adenovirus-transformed cell lines were examined for DBP synthesis by IF with the Ad2 anti-DBP serum: six rat cell lines (T2C4, F17, 8662, 8638, 8617, and F161) transformed by Ad2 virus, three hamster cell lines transformed by Ad2 virus (Ad2HT1) and Ad2-simian virus 40 hybrid virus (ND1HK1 and ND4HK4), and one rat (5RK) and one human (293-31) cell line transformed by transfection with Ad5 DNA. T2C4 and 8662 appeared weakly positive, whereas Ad2HT1 and ND4HK1 were strongly positive. The other transformed cell lines did not produce DBP detectable by IF. Thus, some but not all transformed cell lines produce DBP, which indicates that DBP is not required for maintenance of cell transformation and that transformed cells can express "nontransforming" viral genes as protein.