Organization of Plasmodium falciparum genome: 1. Evidence for a highly repeated DNA sequence

Plasmodium falciparum DNA, isolated from the merozoite stage, was cleaved with HindIII and cloned in pBR322 and lambda L47.1 vectors. Plasmid clones containing 13.4, 7.0, 4.3, 4.1 and 1.5 kb inserts were characterized in some detail. The inserts contain several repeating units of smaller size. Nucleic acid hybridization studies showed that the repeat element is present in the Plasmodium DNA at a very high copy number and appears to be distributed widely throughout the genome.

An upstream regulatory domain of avian tumor virus long terminal repeat is required for the expression of a procaryotic neomycin gene in eucaryotic cells

The regulatory elements present in the long terminal repeat (LTR) of avian sarcoma virus DNA were analyzed by recombinant DNA techniques coupled with DNA-mediated gene transfer in avian as well as mammalian cells. For this purpose, the neomycin resistance gene from transposon Tn5 was inserted downstream from the avian sarcoma virus LTR, and the recombinant plasmid DNA was introduced into cells by the calcium phosphate technique. Cells resistant to the drug G-418 were selected. Analysis of the RNA transcripts made in vivo in these transformants indicated that initiation and termination of the transcripts occurred in the LTR sequences. Deletions were then introduced into the LTR, and their effect on transcription was also studied. These results allowed us to identify a strong regulatory sequence between nucleotides -299 and -114 in the LTR of avian sarcoma virus.

Studies on the structure and organization of avian sarcoma proviruses in the rat XC cell line

The structure and arrangement of the multiple provirus copies of avian sarcoma virus in a rat XC cell line were studied by restriction endonucleases. The following observations were made: (i) the majority of the proviruses integrated randomly with respect to cell DNA; (ii) no gross deletions or rearrangements in the proviruses were observed; (iii) two types of proviruses (type I and type II) could be distinguished on the basis of restriction endonuclease cleavage sites; (iv) the virus rescued from these cells was derived from type II provirus, which has a novel EcoRI site between the env and pol genes; (v) most of the provirus units contained the src gene.

Evidence for a prokaryotic promoter in the murine mammary tumor virus long terminal repeat

The long terminal repeat (LTR) of C3H murine mammary tumor virus (MuMTV) is approx. 1.3 kb long. HaeIII digestion of a cloned PstI fragment containing the left-end LTR generated four fragments of sizes 0.56, 0.41, 0.34 and 0.14 kb, one of which (0.41 kb) had a promoter activity in Escherichia coli. This was demonstrated by replacing the bacterial promoter for the neomycin-resistance (NmR) gene in the plasmid pKC56 with the HaeIII fragments. Only the 0.41-kb fragment that contains sequences from the U3 region of the LTR was found to contain a promoter, as shown by the expression of the drug-resistance phenotype in the recombinant plasmid. The strength of this promoter was comparable to or greater than that found with the parental NmR gene promoter. S1 nuclease mapping of the NmR gene transcript indicated that the initiation of this transcript occurred within the 0.41-kb LTR fragment from a site approx. 10 bp upstream from the 3' end. A comparison of the known DNA sequences in the MuMTV LTR with those found in bacterial promoters revealed that a 'Pribnow box', the initiation signal for the prokaryotic promoters, is present in the 0.41-kb LTR fragment upstream from the initiation site. Furthermore, in a recombinant plasmid that contained the complete LTR the same promoter sequences appeared to be involved in the initiation of RNA transcription. The 0.34-kb LTR fragment, which contains sequences derived from the U3 and U5 regions of the LTR, did not possess promoter activity in E. coli. However, it was found to induce deletions of adjacent plasmid DNA sequences. The deletions were specifically initiated from the downstream end of the LTR-fragment insert. The presence of a prokaryotic promoter in the MuMTV LTR, together with the observation that certain LTR sequences can induce deletions, analogous to those caused by transposable elements, in recombinant plasmids suggest that the MuMTV LTR may have evolved from such elements.

Localization of active promoters for eucaryotic RNA polymerase II in the long terminal repeat of avian sarcoma virus DNA

The nucleotide sequences in the long terminal repeat of avian sarcoma virus that are recognized in vitro by HeLa cell RNA polymerase II have been identified. For this purpose, various 5' and 3' deletions were introduced into a cloned long terminal repeat fragment. The effects of these deletions on transcription initiation in HeLa whole-cell extracts were then studied. Three specific transcripts have been identified. The major transcript is initiated at nucleotide +1 (relative to the cap site). Deletion of the upstream sequence between -299 and -55 has no effect on the level of transcription from this start site, whereas deletion of the sequence downstream of -14 drastically reduces the levels of transcription. In contrast, deletion of the sequence downstream from the TATA box has no effect on the initiation or efficiency of synthesis of the two minor RNA species, which are initiated at around nucleotides -260 and -105. The transcription of these RNA products, however, is abolished by an upstream deletion between -299 and -55. These results suggest that HeLa cell RNA polymerase II recognizes in vitro more than one promoter site present in the long terminal repeat of the avian sarcoma virus genome and defines the sequences required for initiation of the major transcript.

Evidence for extensive methylation of ribosomal RNA genes in a rat XC cell line

XC cell line was established from a rat fibrosarcoma induced by avian sarcoma virus. Analysis of ribosomal RNA genes in the DNA of this cell line indicated that there was a 3- to 4-fold increase in the number of the rDNA repeating units. [methyl-14C]Methionine labeling experiments as well as Southern blot analysis of the restriction endonuclease fragments showed extensive methylation of the cytosine residues in the rDNA. Further analysis by HpaII, HhaI and MspI suggested that the entire rDNA repeat unit was uniformly methylated in the recognition sequence for these enzymes. Parallel experiments with two other rat cell lines (rat embryo fibroblasts and adenovirus-transformed rat embryo cells) indicated no evidence of methylation in the rDNA.

Studies on the methylation of avian sarcoma proviruses in permissive and non-permissive cells

The extent of methylation of several avian oncogenic proviruses was determined by using the restriction endonucleases HpaII and MspI. The results indicated that the transformation-defective proviruses (RAV-O or B77-td), which are exogenously introduced into avian host cells, were not methylated. However, endogenous proviruses (RAV-O) or ASV proviruses present in non-permissive host cells were found to be partly or completely methylated. The methyl-sensitive restriction endonuclease PvuI, which recognizes a unique site within the long terminal repeat in the ASV genome, failed to cleave proviruses present in several non-permissive host cells. From these results we suggest that modification of the sequence around the PvuI site results in reduced levels of transcription.

Restriction endonuclease and nucleotide sequence analyses of molecularly cloned unintegrated avian tumor virus DNA: structure of large terminal repeats in circle junctions

Avian tumor virus supercoiled DNA was isolated from infected quail tumor cells and molecularly cloned in pBR322. Four different recombinant clones denoted pATV-6, pATV-7, pATV-8, and pATV-9 were characterized in detail by restriction endonuclease mapping and by DNA sequencing. The results of these studies indicate that (i) the two large terminal repeats (LTRs) present in PATV-6, are different sizes, (ii) pATV-8 and pATV-9 contain only one LTR, (iii) pATV-7 contains an inversion of 0.6 kilobase in the env gene and a deletion of the U3 region and the src gene, and (iv) the src gene is deleted in pATV-6 and pATV-9. Circle formation from linear molecules was also examined in several of the clones by DNA sequencing through the circle joint. pATV-6 is an example of one class of circular molecules and contains a partially repeated LTR similar to that reported by Ju and Skalka (Cell 22:379-386, 1980). A second class of circles was exemplified by pATV-8 and pATV-9, which contain a single copy of the LTR with no base changes or deletions. This is in contrast to a class of circles containing a complete double LTR structure described by Swanstrom et al. (Proc. Natl. Acad. Sci. U.S.A. 78:124-128, 1981) and suggests that circles containing a single intact LTR may be formed by a homologous recombinational event in which an entire LTR or complementary regions from both LTRs are removed from the linear DNA molecule during circularization.

An avian tumor virus promoter directs expression of plasmid genes in Escherichia coli

A sequence in the long terminal repeat (LTR) of avian tumor virus (ATV) DNA was shown to contain a promoter acute in Escherichia coli. For this analysis the bacterial promoters for the tetracycline (Tc) and neomycin (Nm) resistance genes were deleted from different plasmids and replaced with various fragments derived from the ATV DNA. Expression of the drug-resistant phenotype in the recombinant plasmids at levels comparable to or greater than those found with parental bacterial promotes was shown to be dependent on the presence of an intact sequence ranging from nucleotide +19 to -23 (relative to the cap site) in the ATV DNA. Comparison of the consensus bacterial promoter with the nucleotide sequence in this region revealed strong similarities.

Amplified ribosomal RNA genes in a rat hepatoma cell line are enriched in 5-methylcytosine

In a rat hepatoma cell line, H4-IIE-C3, a 10-fold excess of 18S and 28S rRNA genes has been found in amplified chromosome regions. Antibodies to 5-methylcytidine bound extensively to the DNA of these regions, indicating a high level of DNA methylation. Most of the amplified rRNA genes were transcriptionally inactive, as shown by their failure to stain with silver. DNAs from the tumor cells and control rat hepatocytes grown with L-[methyl-14C]methionine were digested with restriction endonuclease EcoRI; the DNA fragments were separated by agarose gel electrophoresis, denatured, transferred to nitrocellulose filters, and hybridized to 32P-labeled rRNA or cDNA. Fragments containing the 18S or 28S rRNA coding sequences occurred in three major size classes; all three were rich in 5-methylcytosine. Analysis of EcoRI fragments of DNA from the tumor and control cells after digestion with Hpa II or Msp I endonuclease indicated that the 5'-C-C-G-G-3' sequences in most of the amplified rRNA genes were methylated. Analysis of the fragments produced by digestion with Hha I endonuclease indicated a high degree of methylation within its recognition sequence in the amplified rRNA genes as well. The association of hypermethylation with restricted transcriptional activity suggests that DNA methylation may regulate the activity of the rRNA genes.

Cloning of avian tumor virus DNA fragments in plasmid pBR322: evidence for efficient transcription in E. coli from a virus-coded promoter

Two avian tumor virus DNA fragments of 4.2 and 3.2 kb were inserted into pBR322 in the two possible orientations for each fragment. In the Escherichia coli host cells, RNA polymerase initiates transcription of large quantities (up to 0.5 to 1% of total E. coli RNA) of virus-specific RNA in the recombinant plasmids carrying the 4.2-kb fragment (pATV-6) but not in pATV-2 which contains the 3.2-kb fragment. Two SacI cleavage sites flank the putative promoter in the 4.2-kb viral insert. Deletion in the 1.2-kb SacI fragment obliterated the ability of pATV-6 to synthesize viral RNA. Digestion of the 1.2-kb SacI fragment with PvuI generates two fragments of 0.63 and 0.57 kb. Deletion of the 0.57-kb but not the 0.63-kb PvuI-SacI fragment completely eliminated the ability of the recombinant to synthesize viral RNA. These results strongly suggest that viral RNA in E. coli transcription is indeed initiated at a size present in the viral genome and that this site is localized in the 0.57-kb PvuI-SacI fragment.

Amyotrophic lateral sclerosis: search for poliovirus by nucleic acid hybridization

Radioactive-labeled complementary DNA (cDNA) probes specific for either poliovirus type I or type II were hybridized with cellular RNA from the brains of patients dying of amyotrophic lateral sclerosis. In 11 brains examined, the percentage of hybridization for either polio type was the same as the percentage in normal brains. Although hybridization is a sensitive method for detection of viral genome material in infected cells, inability to detect viral nucleic acid by current techniques does not preclude the presence of viral genetic material in the tissue examined.

Binding of Escherichia coli RNA polymerase to a specific site located near the 3'-end of the avaian sarcoma virus genome

We have isolated a unique 35 base pair region of avian tumor virus DNA that binds specifically to Escherichia coli RNA polymerase holoenzyme. Studies with various size classes of viral DNA coupled with restriction enzyme mapping data indicate that the binding site is located in the large terminal repeat of the viral genome and is within the first 50 nucleotides of the heteropolymeric region corresponding to the 3'-end of the virion RNA.

Modification of avian sarcoma proviral DNA sequences in nonpermissive XC cells but not in permissive chicken cells

For the first time, we present evidence with restriction enzymes HpaII and MspI which indicates that the proviral DNA sequence of avian sarcoma virus is modified by methylation in a nonpermissive rat cell line but not in permissive chicken cells. Some of the endogenous viral sequences in the permissive cells were also methylated. No 5-methylcytosine could be detected in the unintegrated viral DNA.

Effect of 5-methylcytidine on virus production in avian sarcoma virus-infected chicken embryo cells

5-Methylcytidine (5mC) is a minor constituent of RNA in procaryotes as well as eucaryotes. The function of this modified nucleoside is not known. We studied the effect of this compound on virus production in avian sarcoma virus-infected chicken embryo fibroblasts. We found, surprisingly, that virus release into the medium was severely reduced in cultures treated with 5mC. In contrast to the effect of 5mC on virus release, intracellular levels of virus-specific RNA transcripts as well as the proteins were slightly elevated. Analysis of intracellular RNA transcripts on velocity gradients and virus-specific proteins in polyacrylamide gels did not reveal any qualitative differences in 5mC-treated cells compared to cytidine-treated cells. From these results we conclude that the effect of 5mC is probably at the level of virus maturation or packaging.

Mapping unintegrated avian sarcoma virus DNA: termini of linear DNA bear 300 nucleotides present once or twice in two species of circular DNA

Three major species of viral DNA have been observed in cells infected by retroviruses: a linear, double-stranded copy of a subunit of viral RNA; closed circular DNA; and proviral DNA inserted covalently into the genome of the host cell. We have studied the structures of the unintegrated forms of avian sarcoma virus (ASA) DNA using agarose gel electrophoresis in conjunction with restriction endonucleases and molecular hybridization techniques. The linear duplex DNA is approximately the same length as a subunit of viral RNA (approximately 10 kb) and it bears natural repeats of approximately 300 nucleotides at its termini. The repeats are composed of sequences derived from both the 3' and 5' termini of viral RNA in a manner suggesting that the viral DNA polymerase is transferred twice between templates. Thus the first end begins with a sequence from the 5' terminus of viral RNA and is permuted by about 100 nucleotides with respect to the 3' terminus of viral RNA; the linear DNA terminates with a sequence of about 200 nucleotides derived from the 3' end of viral RNA. We represent this structure, synthesized from right to left, as 3'5'-----3'5'. Two closed circular species of approximately monomeric size have been identified. The less abundant species contain all the sequences identified in linear DNA, including two copies in tandem of the 300 nucleotide 3'5' repeat. The major species lacks about 300 base pairs (bp) mapped to the region of the repeated sequence; thus it presumably contains only a single copy of that sequence. The strategies used to determine these structures involved the assignment of over 20 cleavage sites for restriction endonucleases on the physical maps of ASV DNA. Several strains of ASV were compared with respect to these sites, and the sites have been located in relation to deletions frequently observed in the env and src genes of ASV.

Analysis of unintegrated avian RNA tumor virus double-stranded DNA intermediates

Previous studies by Guntaka et al. have shown that the unintegrated DNA intermediates of avian RNA tumor virus replication can be readily isolated from cultures of the quail tumor line QT-6 at 1 day after infection. The intermediates include double-stranded linear and covalently closed circular DNA species. Using the analysis procedure of Southern together with previously obtained information regarding the sites of action of certain restriction endonucleases on avian sarcoma virus DNA, we have further characterized the viral DNA intermediates. Evidence is presented that, relative to the RNA genome, most of the linear species possess a direct terminal sequence redundancy equivalent to 0.5 X 10(6) +/- 0.3 X 10(6) daltons of double-stranded DNA. Some of the circular forms also possess a sequence redundancy of 0.21 X 10(6) +/- 0.03 X 10(6) daltons.

Specific site of action for single-strand specific nuclease on the double-stranded circular DNA intermediates of an avian RNA tumor virus

Circular viral DNA intermediates obtained from the quail tumor line, QT6, at 1 day after infection, were opened at one specific location by the single-strand specific nuclease, S1, of Aspergillus oryzae. This site was no longer accessible to the S1 nuclease when circles were first opened at another location with a restriction endonuclease.

Ethidium bromide inhibits appearance of closed circular viral DNA and integration of virus-specific DNA in duck cells infected by avian sarcoma virus

The DNA of avian sarcoma virus assumes a closed circular configuration before integration into the host cell chromosomal DNA. Ethidium bromide reduces the formation of superhelical viral DNA and concurrently blocks integration of the viral genome. Inhibition of integration of viral DNA results in the inhibition of virus replication.

Synthesis of viral DNA in the cytoplasm of duck embryo fibroblasts and in enucleated cells after infection by avian sarcoma virus

TWO LINES OF EVIDENCE INDICATE THAT SYNTHESIS OF VIRAL DNA OCCURS IN THE CYTOPLASM OF DUCK EMBRYO FIBROBLASTS INFECTED WITH AVIAN SARCOMA VIRUS: (i) viral DNA is detected first in the cytoplasmic fraction of infected cells and subsequently in the nuclear fraction; and (ii) viral DNA is synthesized at a normal rate in cells infected after enucleation with cytochalasin B. The presence of viral DNA in the cytoplasmic fraction is not a consequence of leakage of newly synthesized viral DNA from the nucleus, since it remains in nuclear fractions late after infection when integration of viral DNA into the host genome is inhibited by ethidium bromide.

Synthesis, structure and function of avian sarcoma virus-specific DNA in permissive and nonpermissive cells

We have reviewed our recent evidence for the following scheme for synthesis and integration of viral DAN after infection of permissive cells by ASV: Within the first 3 hours of infection, duplex, virus-specific DNA the length of a subunit of the viral genome (3 times 10(6) daltons) is synthesized in the cytoplasm of infected cells by a virion-associated DNA polymerase; viral DNA probably forms a covalently closed circular duplex prior to integration into host nuclear DNA. Integration and the usual consequences of viral infection can be inhibited by ethidium bromide. We have described a number of features of viral DNA prior to its integration and have indicated how these features can be exploited in the purification of viral DNA. Viral DNA has also been measured in nonpermissive (mammalian) cells in which the variable expression of viral genes is controlled by unknown mechanisms.