Regulated replication of an episomal simian virus 40 origin plasmid in COS7 cells.

The replication of a simian virus 40 (SV40) origin-containing plasmid, pSLneo, stably transfected COS7 cells has been studied. pSLneo contains the SV40 origin of replication and encodes the positive selectable marker for G418 resistance. In transient replication assays, pSLneo replicates to a high copy number in COS7 cells. Uncontrolled SV40 plasmid replication has been reported to be lethal to such transfected cells. Thus, it was anticipated that extensive plasmid replication would preclude isolation of permanent cell lines containing pSLneo. However, significant number of G418-resistant colonies arose after transfection of COS7 cells with pSLneo. Cell lines established from these drug-resistant colonies contained between 100 and 1,000 extrachromosomal pSLneo copies per cell. Episomal plasmid DNA in pSLneo/COS7 lines was stably maintained after 2 months of continuous culture in selective medium. Bromodeoxyuridine labeling and density shift experiments demonstrated that replication of pSLneo closely paralleled that of cellular DNA. On average, plasmid DNA did not replicate more than once during a single cell generation period. Regulation of pSLneo replication appeared to be negatively controlled by a cis-acting mechanism. Endogenous copies of episomal pSLneo remained at a stable low copy number during the simultaneous, high-level replication of a newly transfected plasmid encoding SV40 large T antigen in the same cells. These results indicate that regulated replication of an SV40 origin plasmid can be acquired in a cell and does not require the presence of additional genetic elements. The molecular mechanism by which cells enforce this regulation on extrachromosomal SV40 plasmids remains to be defined.     

TT virus infection in nonhuman primates and characterization of the viral genome: identification of simian TT virus isolates

Newly discovered TT virus (TTV) is widely distributed in human populations. To understand more about the relationship between TTV and its hosts, we tested 400 sera from various nonhuman primates for the presence of TTV DNA by PCR assay. We collected serum samples from 24 different species of nonhuman primates. TTV DNA was determined by PCR with primers designed from the 5'-end region of the TTV genome. Nucleotide sequencing and phylogenetic analysis of viral genomes were also performed. TTV DNA was detected in 87 of 98 (89%) chimpanzees and 3 of 21 (14%) crab-eating macaques. Nucleotide sequences of the PCR products obtained from both animals were 80 to 100% identical between two species. In contrast, the sequences differed from TTV isolates in humans by 24 to 33% at the nucleotide level and 36 to 50% at the amino acid level. Phylogenetic analysis demonstrated that all TTV isolates obtained from simians were distinct from the human TTV isolates. Furthermore, TTV in simians, but not in humans, was classified into three different genotypes. Our results indicate that TTV in simians represents a group different from, but closely related to, TTV in humans. From these results, we tentatively named this TTV simian TTV (s-TTV). The existence of the s-TTV will be important in determining the origin, nature, and transmission of human TTV and may provide useful animal models for studies of the infection and pathogenesis of this new DNA virus.     

Certain properties of transcribed fragments of the mouse genome cloned in plasmid pBR322

Clones of total mouse DNA efficiently hybridized with mRNA (or cDNA) were selected by colony hybridization technique. The majority of selected fragments demonstrate hybridization with cDNA, dsRNA-B (isolated from pre-mRNA) and oligo(dT). The data obtained indicate that the base sequences hybridizing to these test-probes are contiguous within several individual cloned restriction DNA fragments. At least in two cases sequences hybridizing with cDNA belong to repetitive fraction of the mouse genome (presumptive repetitive structural genes). They are transcribed effectively, and respective mRNAs of abundant type. Two other clones contain structural genes which are expressed into mRNAs of non-abundant type.     

Isolation and characterization of a ColE1 plasmid containing the entire bio gene cluster of Escherichia coli K12.

Summary Temperature-sensitive mutants of Tetrahymena pyriformis which had previously been selected for their inability to grow at 38°C but which grew normally (or near normally) at 30°C were characterized with respect to their patterns of RNA and protein accumulation at both the permissive and nonpermissive temperatures. Out of 116 such mutants, the majority (72) acted like wild type for these accumulations during a 3 h labelling period although some of them stopped dividing during this time. The remainder exhibited a variety of altered phenotypes for the rate, extent, and timing of RNA and/or protein accumulation. Those mutants which exhibited selective inhibition of RNA accumulation, and were thus potential ribosomal RNA (rRNA) mutants, were further characterized by examining patterns of protein and RNA synthesis in cells starved at the permissive temperature, but re-fed at the permissive and non-permissive temperatures. At least five different types of mutants as defined by patterns of protein and RNA synthesis in refed cells were identified. Direct analysis of the RNA synthesized in cells from 2 of these types of mutants showed that in 5 out of 6 cases rRNA synthesis and/or processing was inhibited within 30 min after shifting to the non-permissive temperature. The other mutant examined was found to show a delayed inhibition of rRNA synthesis.     

Evaluation of intra-host variants of the entire hepatitis B virus genome

Genetic analysis of hepatitis B virus (HBV) frequently involves study of intra-host variants, identification of which is commonly achieved using short regions of the HBV genome. However, the use of short sequences significantly limits evaluation of genetic relatedness among HBV strains. Although analysis of HBV complete genomes using genetic cloning has been developed, its application is highly labor intensive and practiced only infrequently. We describe here a novel approach to whole genome (WG) HBV quasispecies analysis based on end-point, limiting-dilution real-time PCR (EPLD-PCR) for amplification of single HBV genome variants, and their subsequent sequencing. EPLD-PCR was used to analyze WG quasispecies from serum samples of patients (n = 38) infected with HBV genotypes A, B, C, D, E and G. Phylogenetic analysis of the EPLD-isolated HBV-WG quasispecies showed the presence of mixed genotypes, recombinant variants and sub-populations of the virus. A critical observation was that HBV-WG consensus sequences obtained by direct sequencing of PCR fragments without EPLD are genetically close, but not always identical to the major HBV variants in the intra-host population, thus indicating that consensus sequences should be judiciously used in genetic analysis. Sequence-based studies of HBV WG quasispecies should afford a more accurate assessment of HBV evolution in various clinical and epidemiological settings.     

Transposition of a Ds element from a plasmid into the plant genome in Nicotiana plumbaginifolia protoplast-derived cells

Nicotiana plumbaginifolia haploid protoplasts were co-transformed with two plasmids, one with a NPT-II/Ds element and one with a gene encoding an amino-terminal truncated Ac transposase. It is shown that Ds can efficiently transpose from extrachromosomal DNA to N. plumbaginifolia chromosomes when the Ac transposase gene is present in trans. Ds has been shown to have transposed into the plant genome in a limited number of copies (1.9 copies per genome), for 21/32 transgenic lines tested. The flanking sequences present in the original plasmid are missing in these 21 plants. In only two of 21 plants was part of the transposase construct integrated. By segregation analysis of transgenic progeny, Ds was shown to be present in the heterozygous state in 10 lines even though haploid protoplasts had been originally transformed. This observation could indicate that integration occurred after or during DNA replication that leads to protoplast diploidization.     

Rescue of the adeno-associated virus genome from a plasmid vector: evidence for rescue by replication

In cultured cells, adeno-associated virus (AAV) replication requires coinfection with a helper virus, either adenovirus or herpesvirus. In the absence of helper virus coinfection AAV can integrate its genome site specifically into the AAVS1 region of chromosome 19. Upon subsequent infection with a helper virus, the AAV genome is released from chromosome 19 by a process termed rescue, and productive replication ensues. The AAV genome cloned into a plasmid vector can also serve to initiate productive AAV replication. When such constructs are transfected into cells and those cells are simultaneously or subsequently infected with a helper virus, the AAV genome is released from the plasmid. This process is thought to serve as a model for rescue from the human genomic site. In this report we present a model for rescue of AAV genomes by replication. A hallmark of this model is the production of a partially single-stranded and partially double-stranded molecule. We show that the AAV2 Rep 68 protein, together with the UL30/UL42 herpes simplex virus type 1 DNA polymerase and the UL29 single-strand DNA binding protein ICP8, is sufficient to efficiently and precisely rescue AAV from a plasmid in a way that is dependent on the AAV inverted terminal repeat sequence.     

Presence of TT virus DNA in bone marrow cells from hematologic patients

Recent observations suggest that TT virus (TTV), in addition to liver, may also infect bone marrow. In this study, bone marrow samples and sera from 33 patients with haematological disorders and sera from 16 healthy controls were investigated for TTV DNA presence. Altogether TTV DNA sequences were demonstrated in bone marrow cells of 84.84% of patients. Moreover TTV DNA was detected in sera from 72.72% of patients and from 93.75% of controls. N22 sequences amplified from bone marrow cells and serum of 3 patients were analysed, after cloning: all these isolates were of type 2c and 2 or 3 variants were present in each isolate. After single strand DNA degradation, replicative forms were detectable in BM cells. This finding, in addition to the detection of variants similar in the BM and in the serum of the same patient could suggest that BM is a site of TTV replication (or one of the sites) from which the virus is spread in blood.     

Characterization of the major mRNAs transcribed from the genes for glycoprotein B and DNA-binding protein ICP8 of herpes simplex virus type 1.

The structural genes encoding the herpes simplex virus type 1 glycoprotein B and the major DNA-binding protein ICP8 have been mapped previously within the EcoRI-F restriction fragment (map coordinates 0.314 to 0.420) of the viral genome. In this study the mRNAs transcribed from these DNA sequences were identified by hybridization selection of 32P-labeled RNA and by Northern blot analysis of polyadenylated cytoplasmic RNA. A 3.4-kilobase RNA was the major mRNA homologous to the DNA sequences between coordinates 0.343 and 0.386 in which mutations in the glycoprotein B gene have been mapped. A 4.5-kilobase RNA was the major mRNA homologous to the viral DNA sequences between coordinates 0.361 and 0.417 in which mutations in the ICP8 gene have been mapped. Hybridization-selected mRNAs were translated in vitro to determine the primary translation products encoded in each region. The glycoprotein B- and ICP8-specific polypeptides were identified by immunoprecipitation with specific antisera. The translation products encoded by the glycoprotein B gene were 103,000 and 99,000 in molecular weight. The translation products encoded by the ICP8 gene were 125,000 and 122,000 in molecular weight.     

Multiple leader RNAs and messenger RNAs are transcribed from the la crosse virus small genome segment

Nucleotide sequencing has demonstrated that the Small genome segment of Bunyaviruses contains the genetic information for two viral proteins (N and NS_s) in overlapping reading frames (Akashi and Bishop, 1983; Cabradilla et al., in press). Using 3′ end-labeled genome probes, La Crosse virus (LAC) infected cells were shown to contain three leader RNAs, which start at position 1 and terminate at approximate positions 74, 95, and 115 from the 3′ end of the genome. Primer extension and S1 mapping studies have shown that LAC-infected cells contain seven mRNAs, five of which initiate at positions 1, 74, 101, 117, and 123 and two more which initiate at approximate positions 147 and 159 from the 3′ end of the Small genome segment. The existence of multiple leader RNAs and mRNAs from the Small genome segment may allow access to both overlapping reading frames by ribosomes that still initiate only at 5′ proximal AUGs, without the need to splice the mRNA.     

Mouse immunoglobulin genes: a bacterial plasmid containing the entire coding sequence for a pre-gamma 2a heavy chain

A DNA sequence complementary to the entire coding part of a mouse gamma 2a immunoglobulin heavy chain mRNA isolated from a myeloma producing a levan binding protein (UPC 10), has been cloned in the PstI site of pBR 322. Transformants containing sequences complementary to purified gamma 2a heavy chain mRNA were selected. One transformant, pG2a-10-21, containing a 1750 nucleotide insert, has been characterized by hybrid-arrested translation and purification of gamma 2a heavy chain mRNA on DNA-DBM cellulose filters. Restriction enzyme analysis and partial sequencing demonstrate that the pG2a-10-21 contains the complete structural sequence for the gamma 2a heavy chain and predicts the sequence of a 18 amino acid hydrophobic amino terminal extra piece segment.