Studies of simian virus 40 DNA. VII. A cleavage map of the SV40 genome

Evolutionary variants of simian virus 40 which are impaired in early lytic functions but transform nonpermissive cells

From an undiluted passaged virus stock, two size classes of defective simian virus 40 (SV40) DNA were isolated from which two evolutionary variants were cloned. By means of restriction enzyme and heteroduplex analysis, physical maps of the mutants have been constructed. Both mutants contained the region of SV40 DNA coding for the early proteins plus some adjacent sequences (the region from 0.120 to 0.685 map unit, clockwise, on the standard SV40 DNA map). Furthermore, each mutant contained, in the form of two inverted repeats, four times the sequences from the region 0.625 to 0.685 map unit, clockwise. Some biological properties of the mutant DNA were examined, and we found that the mutant DNA (i) has, as compared with SV40 DNA, an impaired ability to induce T antigen in permissive and nonpermissive cells; (ii) does not complement a thermosensitive A mutant of SV40; (iii) replicates very inefficiently without a helper; and (iv), as an apparent contradiction, transforms nonpermissive baby rat kidney cells as well as SV40 DNA. A hypothetical mechanism for the expression of the mutant DNA that might explain the observed biological properties is presented.

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

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

Arrangement of the genome of the human papovavirus RF virus

DNA from plaque-purified RF virus, a variant of BK virus, was found to contain two species of molecules. Hybridization of each DNA species to the fragments of BK virus DNA revealed that one species had a deletion corresponding to at least 50% of the late region and the other had a deletion corresponding to at least 40% of the early region of BK virus DNA. Analysis by cleavage of each RF virus DNA species with restriction endonucleases EcoRI, HindIII, AvaII, and PvuII, when compared with BK virus DNA, revealed that the size and number of fragments were different. These results suggest the loss of some restriction sites and the appearance of new sites, probably as a result of base changes in each RF virus DNA species. Furthermore, analysis of the restriction map of each DNA molecule revealed in insertion(s) in both DNA species.

Construction of an SV40-derived cloning vector

A new reiterated variant of simian virus 40 (SV40; dl1142) has been constructed. It should be useful for the purpose of cloning foreign pieces of DNA in SV40 virions. Up to 80% of the SV40 genome has been made available for substitution with foreign DNA and the vector contains a number of unique (single-cut) restriction sites which will facilitate cloning. The 5' and 3' regions of both the SV40 early and late messenger RNAs are included in the vector. Prokaryotic DNA has been successfully cloned in the early region of the vector. The transcriptional properties of the recombinant have been studied, and it was found that both the vector and insert DNA are transcribed, mainly as non-adenylated RNA.

Nucleotide sequence of the Hind-I-proximal part of simian virus 40 HindII + III restriction fragment B (fifth part of the T antigen gene)

The nucleotide sequence of the simian virus 40 DNA segment that lies between the HindIII restriction endonuclease cleavage site at map position 0.324 and the AtuI cleavage site at 0.261 has been determined by the base-specific partial chemical degradation procedure of Maxam and Gilbert. This region comprises 335 base pairs and represents 6.4% of the total SV40 genome and 41% of the restriction fragment Hind-B. It connects in the clockwise direction to the restriction fragment Hind-I (described in the preceding paper). Hind-B is situated in the second half of the early transcription region of the SV40 genome and encodes information (including the termination signal) for the early protein large-T antigen. in the part of Hind-B described here, the DNA strand that has the same polarity as early 19-S mRNA defines only one open reading frame for translation; the other two are blocked by multiple triplets corresponding to termination codons. The open reading frame is part of one that runs throughout much of the early region: from the second splicing boundary of the large-T gene (position 0.534) to the information for the large-T stop signal (position 0.174) near the Hind-B/Hind-G junction, and which together with the non-contiguous DNA segment from position 0.65 (site of the information for the large-T start signal) to 0.69 (the first splicing boundary) codes for the entire large-T antigen.

Nucleotide sequence of the simian virus 40 HindII + III restriction fragment I (fourth part of the T antigen gene)

The HindII + III restriction fragment I (Hind-I) from simian virus 40 DNA represents 4.96% of the genome and maps in the early transcription region. Hind-I is an internal segment of the A gene and its information is expressed as part of the early 19-S mRNA, which codes for T antigen. We report here the nucleotide sequence of the 259-base-pair Hind-I fragment. The sequence was determined and confirmed by RNA and DNA sequencing methods: by analysis of oligonucleotides resulting from T1 and pancreatic RNase digestion of labeled RNA transcribed from SV40 DNA with Escherichia coli DNA-dependent RNA polymerase, by partial degradation of RNA transcripts with snake venom phosphodiesterase, and by base-specific chemical degradation of 5'-end-labeled subfragments of Hind-I according to the procedure of Maxam and Gilbert. Multiple triplets corresponding to termination codons occur in two of the three reading frames of the DNA strand that has the same polarity as early mRNA. The open reading frame connects in phase with the one of the Hind fragments flanking Hind-I, and the amino acid sequence specified by Hind-I lies in the middle part of the large-T antigen. Some features of the primary nucleotide sequence and of early transcription are discussed.

Localization of the binding sites of prokaryotic and eukaryotic RNA polymerases on simian virus 40 DNA

The binding sites of calf thymus RNA polymerase (B) II, wheat germ RNA polymerase B and of the Escherichia coli RNA polymerase were mapped on the simian virus 40 genome by observation of enzyme-linear DNA complexes by electron microscopy. Three to four major sites and several minor sites are observed for each enzyme; common binding sites for the three enzymes are found in positions 0.17, 0.53 and 0.90 of the viral physical map. Initiation complexes with these enzymes can be stabilized with specific ribodinucleotides and a single ribonucleoside triphosphate. Whereas ApA and ATP greatly enhances the binding of the E. coli enzyme at position 0.17, they stabilize the binding of the eukaryotic enzyme at many sites, some of them located in close proximity of the origin of replication.

Characterization of plant satellite DNA using restriction nucleases

The structural organization of satellite DNAs of mustard Brassica nigra and lemon Citrus limon has been studied by digestion with restriction nucleases. Analysis of DNA products produced by EcoRI and Bam I shows that two satellite DNAs contain long range periodicities belonging to several repeated sequences. The periodicities in two satellite DNAs differ characteristically, however, they have been found to contain common homologous sequences. Using the restriction nuclease Bsp I, a highly periodical fractions has been found in Citrus satellite DNA, composed of Bsp I fragments ranging from 80 to 1240 basepain. The major repeat units comprise five Bsp I fragments ranging from 80 to 200 bp. These fractions characterized by a high content of 5-methyl-cytosine.

Coding potential and regulatory signals of the polyoma virus genome

The complete DNA sequence of the A2 strain of polyoma virus has been determined. It consists of 5,292 base pairs. The sequence is analysed in terms of its coding potential and sites of possible functional significance or structural interest. The polyoma virus genome is compared with those of related tumour viruses, simian virus 40 and BK virus.

BK virus DNA: complete nucleotide sequence of a human tumor virus

The complete DNA sequence of the human papovavirus BK is presented. From the 4963 base-pair sequence of BK virus (MM strain), the amino acid sequence of at least five proteins can be deduced: a T antigen and a t antigen, which share amino terminal peptides; proteins VP2 and VP3, which share 232 amino acids; and protein VP1, whose coding sequence overlaps those for VP2 and VP3 by 113 nucleotides but is read in a different frame. The gene loci and the arrangement of genes are strikingly similar in BK virus and simian virus 40 (SV40). The sequence of the deduced proteins in BK virus shares 73 percent amino acid homology with those in SV40, whereas the DNA sequence of the two viruses shares 70 percent homology, suggesting close evolutionary relationship. However, the repeated DNA sequences in the noncoding regions of these viruses are different.

A restriction map of cauliflower mosaic virus DNA (strain PV 147). Mapping of the cleavage sites of HhaI, SacI, AvaI, PvuII, PstI, XbaI, EcoRI, Bg/II, HincII, HpaII and HindII + III

The virion-extracted DNA (Mr5 x 10(6)) of cauliflower mosaic virus (CaMV) has three single-stranded interruptions. The mapping of this DNA using eleven restriction endonucleases (HhaI, SacI, AvaI, PvuII, PstI, XbaI, EcoRI, Bg/II, HincII, HpaII and HindII + III) is reported here. The existence of the three single-stranded breaks complicates the identification and the molecular weight determination of fragments produced by HpaII, HindIII and HindII + III. Indeed the electrophoretic mobility of some fragments in which a single-stranded discontinuity is located is modified, and the fluorescence of ethidium bromide complexed with these fragments is reduced as compared to that observed for the other fragments existing in a molar ratio. These drawbacks were overcome by performing experiments of nick-translation of CaMV DNA with Escherichia coli DNA polymerase I. FRom the data it follows that the CaMV DNA molecule bears bears 1 site for HhaI and SacI, 2 for AvaI and PvuII, 3 for PstI, 4 for XbaI, 5 for EcoRI, 6 for Bg/II and HincII, 11 for HpaII and 15 for HindII + III. The corresponding fragments have all been ordered and precisely located providing a suitable map for further investigations connected with the study of the fine structure and the function of the CaMV genome.

A DNA-dependent ATPase of calf-thymus

A DNA-dependent ATPase has been purified from calf thymus. The enzyme hydrolyses ATP and dATP in the presence of heat-denatured DNA. It does not hydrolyse the corresponding nucleoside triphosphates of guanine, uridine and cytosine. The Km values for ATP and dATP are both 0.62 mM. The enzyme requires magnesium or manganese ions. Its sedimentation coefficient is about 4.4 S. The catalytic activity is inhibited by N-ethylmaleimide but is not sensitive to novobiocin and nalidixic acid which are potent inhibitors of bacterial DNA gyrase. In some cases, during purification, chromatographically distinct additional DNA-dependent ATPase activities were detected. Limited proteolysis or covalent modification of the enzyme in the tissues, or during the first steps of its extraction, are probably responsible for the appearance of these chromatographically distinct forms.

Persistence of phage lambda DNA in genomes of mouse cells transformed by lambda-carrying SV40 vectors

To test the suitability of simian virus 40 (SV40) DNA as a vector for inserting DNA segments into the chromosomes of mammalian cells, an EcoRI-A fragment of bacteriophage lambda DNA was covalently joined to a fragment of SV40 DNA and used to transform mouse cells in culture. Three independent, morphologically transformed clones were obtained that were positive for SV40 T-antigen by immunofluorescence staining. DNA from each transformant was examined by restriction enzyme analysis and found to contain both lambda and SV40 sequences. Co-migration of some fragments containing lambda and SV40 sequences following digestion of transformed cell DNA by each of four different restriction enzymes indicated that part of the retained lambda and SV40 DNA was linked in two of the three lines. In the third line, however, none of the restriction fragments had both lambda and SV40 sequences. Although the presence of non-integrated lambda DNA was not excluded, at least some of the lambda DNA appeared to be linked to host cell DNA. Results of digestion by EcoRI suggested that in some cases the transforming linear molecule had probably circularized prior to integration.

Mapping of restriction sites in the argF gene of Escherichia coli by partial endonuclease digestion of end-labeled DNA

A detailed physical map depicting the cleavage sites generated by ten different restriction endonucleases was prepared for the argF region of the Escherichia coli K-12 genome carried on a 1650 base pair fragment capable of directing the in vitro synthesis of ornithine transcarbamylase (OTCase; ec 2.1.3.3) under the control of arginine holorepressor. The method employed was originally developed by Smith and Birnstiel (1976), and involved the electrophoretic sizing of partial endonuclease digestion products of DNA radiolabeled at one end. This novel technique proved to be rapid, simple, amenable to the simultaneous mapping of numerous cleavage sites, and provided the essential information for determining the map order of restriction fragments. A facile method which involved magnesium phosphate as the DNA-binding agent was presented for the isolation of DNA fragments. The discovery of a 117 base pair leader sequence in the argF gene is also discussed.

Restriction map of the region surrounding the EcoRI site in the pCR1 plasmid and analysis of an inserted ovalbumin gene

We have determined a restriction map of a 1650 base pair region surrounding the EcoRI site of the bacterial plasmid, pCR1. We have used pCR1 as a vector in cloning synthetic ovalbumin double-stranded cDNA. Using the pCR1 restriction map, we have characterized the ovalbumin sequences inserted in one recombinant plasmid, pOvE12. POvE12 appears to contain all, or nearly all, of the sequences found in full length, double-stranded cDNA synthesized in vitro.

malB region in Escherichia coli K-12: specialized transducing bacteriophages and first restriction map

By starting from an Escherichia coli K-12 strain with a lambda phage integrated in the malB region, series of transducing phages carrying part or all of the malB region have been isolated. Genetic mapping of the transduced malB fragments was accomplished by complementation and recombination with known mutations in the region. By using the DNA of these phages, it was found that the malB region is cleaved by the restriction enzymes BglII, EcoRI, HaeII, HincII, SalI, and SstI, but not BamHI, HindIII, KpnI, PstI, XbaI, or XhoI. A physical map was constructed and tentatively correlated with the genetic map.

Tandem integration of complete and defective SV40 genomes in mouse-human somatic cell hybrids

We have analyzed the arrangement of SV40 DNA sequences integrated in human chromosome 7 in two lines of mouse-human somatic cell hybrids: one containing only one human chromosome 7 per cell and the other containing an average of about three. We found that the integration site differs in both the viral and host sequences in the two clones. However, the sites of integration into the several copies of human chromosome 7 of one clone are identical. Each chromosome 7 in both clones carries approximately six viral genomes tandemly linked. Some of these genomes lack about 20% of the DNA from the late region, including the Eco RI site.

Biochemical studies on bovine adenovirus type 3. III. Cleavage maps of viral DNA by restriction endoncleases EcoRI, BamHI, and HindIII

Cleavage of bovine adenovirus type 3 (BAV3) DNA by restriction endonucleases EcoRI, BamHI, and HindIII yielded 7 (A to G), 5 (A to E), and 12 (A to L) fragments, respectively. The order of these fragments has been determined to be GDACBFE for EcoRI fragments, AEBDC for BamHI fragments, and JEBKACDHFGIL for HindIII fragments, and cleavage sites of these enzymes have been mapped on the genome of BAV3. BAV3 preparation contains incomplete virus whose genome has a deletion of about 13% of complete virus genome. Restriction endonuclease digestion of the incomplete virus DNA revealed that EcoRI E and F, BamHI C and HindIII G, I, and L fragments were deleted. Therefore, the deleted region of incomplete virus DNA is located near the right-hand end of the BAV3 DNA molecule, a result consistent with our previous electron-microscopic observations on heteroduplex molecules formed between complete and incomplete BAV3 DNA.

Studies on the single-stranded discontinuities of the cauliflower mosaic virus genome

The Cauliflower Mosaic Virus (CaMV) genome is a double-stranded DNA molecule of about 5 million daltons. Native DNA molecules appear heterogeneous when analysed by gel electrophoresis. We have examined the nature of this apparent heterogeneity. Besides, this genome is shown here to contain three single-stranded breaks, as revealed by different denaturation experiments: heating at 75 degrees C, treatment with NaOH or dimethyl sulfoxide (DMSO). Labelling with terminal transferase proves that the 3' ends at these interruptions all have free hydroxyl groups. Electron microscopy and alkaline gel electrophoresis indicate that these three discontinuities are shared by both strands, and that they are not randomly located. S1 nuclease is active on CaMV DNA and generates three fragments. The comparison between the sizes of these fragments and of the products of denaturation leads us to consider that S1 acts at the level of the interruptions. We have determined that two of them, distant by one third genome unit, are in the same strand; the other is in the opposite strand, distant by one sixth genome unit from the nearest other one. The combined use of restriction enzymes and S1 nuclease has enabled us to locate these three discontinuities on the restriction map of the CaMV genome that we have otherwise established.

Comparative study of kinetoplast DNA in culture, blood and intracellular forms of Trypanosoma cruzi

A comparative study has been made on the kinetoplast DNA (kDNA) from I in culture epimastigote, blood trypomastigote and intracellular amastigote stages of Trypanosoma cruzi. The basic properties of the kDNA in all 3 forms were identical. Thus the DNA was in the form of networks of density 1.698-9 g/cm3 and with sedimentation coefficients (S20w) of approximately 5500, the networks being composed of large complexes of minicircular and apparently linear molecules, the former having contour lengths of 0.45 MICROMETer. Several differences were noted. The ultrastructural arrangement of the kDNA in the kinetoplast of the blood stage consisted of three to four double rows of DNA as compared to one double layered row in the other two stages. There was proportionately more kDNA in the blood stages, suggesting that, since the networks have apparently the same size (see above), more than one is present. DNA loops situated at the periphery of the kDNA networks were observed in higher proportion in blood and intracellular forms. Dimeric and oligomeric circles were present in the kDNA of the blood and intracellular stages in much greater proportion than in culture epimastigote stages. Few large circular molecules, heterogeneous in size, were also observed in intracellular blood stages. There were some differences, mainly quantitative, in the gel electrophoresis patterns after endonuclease digestion.

Location of the cleavage sites on the SV 40 DNA map produced by the restriction endonucleases Pst 1 and Bam 1

Restriction endonucleases from Providencia stuartii (Pst 1) and Bacillus amyloliquefaciens H (Bam 1) cleave SV 40 DNA at two and one specific sites, respectively. Using EcoRI and Hind III endonuclease restriction sites as reference, the two Pst I sites were mapped at 0.050; 0.265 and the Bam I site was mapped at 0.170 of the genome length, clockwise, from the single EcoRI cleavage site.

Association of the folded chromosome with the cell envelope of Escherichia coli: nature of the membrane-associated DNA

Membrane-associated folded chromosomes isolated from Escherichia coli in the presence of spermidine sedimented at about 5,800S. The folded chromosome and the membrane fragment were each stable in the absence of the other; a 1,700S folded chromosome was obtained after removal of the membrane by a Sarkosyl treatment, and a 4,000S membrane fragment remained after digestion of the chromosomal DNA with deoxyribonuclease I. The interaction between the folded chromosome and the membrane fragment was stable, and, even when the DNA was unfolded, both components remained associated and cosedimented. The large frictional effect of the unfolded DNA reduced the sedimentation rate of the complex to about 2,000S. Partial removal of this unfolded DNA with restriction endonucleases caused the membrane fragments and the remaining associated DNA to sediment faster, at about 3,500S. The DNA remaining associated with the membrane fragments after restriction endonuclease treatment, about 4.5% of the total DNA when EcoRI was used, was indistinguishable from the DNA released from the membranes by three criteria: (i) DNA size distribution in agarose gels after electrophoresis, (ii) reassociation kinetics, and (iii) thermal elution from hydroxylapatite. This finding, that random DNA sequences rather than specific ones were responsible for the majority of the DNA-membrane interactions, argues against the folded chromosome's being a static structure with specific DNA sequences interacting with the cell envelope.

Complete nucleotide sequence of the simian-virus 40 Hind-G fragment and localisation of the carboxyl terminus of the VP1 protein

The restriction fragment Hind-G represents 7.0% of the simian virus 40 (SV40) genome. The information present in fragment Hind-G is expressed as part of the major, late 16-S messenger RNA. The complete nucleotide sequence of the fragment Hind-G has now been determined by application of the procedure of Maxam and Gilbert [Proc. Natl Acad. Sci. U.S.A. (1977) 74, 560-564]. It contains 369 nucleotide base pairs. On the basis of the termination code words in the strand with the same polarity as the late mRNA, two illegitimate reading frames can be defined. Therefore the third, open frame must code for the carboxyl terminal part of the VP1 protein. It terminates within fragment Hind-G with a TGA signal. This stop codon is followed by a non-translated region of the mRNA of about 83 nucleotides. The latter contains the sequence A-A-U-A-A-A, common to all other eukaryotic mRNA molecules so far studied. The Hind-G fragment also contains sequences which presumably play a role in the synthesis, processing and/or expression of early mRNA; these aspects are discussed in the following paper.

Nucleotide sequence of the restriction fragment Hind-F-EcoRI1 of simian-virus-40 DNA (part of the VP1 gene)

The nucleotide sequence of the simian virus 40 (SV40) genome region between the cleavage sites for restriction endonucleases EcoRI (map position 0) and HindII (map position 0.05) has been determined mainly by the partial chemical DNA degradation procedure of Maxam and Gilbert. This fragment represents 5.3% of the genome of SV40 and is located in the late region, internally in the VP1 gene. The message strand shows only one open reading frame for translation into protein, which connects to the one for the preceding fragment. On this basis part of the amino acid sequence of the VP1 protein is presented.