2-LTR circular viral DNA as a marker for human immunodeficiency virus type 1 infection in vivo

The unintegrated viral DNA found in human immunodeficiency virus type 1 infection includes linear and circular forms. We targeted the circular form containing two copies of the viral long terminal repeat (2-LTR circle) and developed specific assays to detect this molecule in peripheral blood mononuclear cells from HIV-infected patients. In vitro HIV-1 infection of peripheral blood mononuclear cells showed rapid accumulation and rapid decay of 2-LTR circular viral DNA. Examination of 2-LTR circular viral DNA levels provides a view of spreading infection based on a viral DNA form that is structurally distinct and has a known, short half-life in infected cells. In patients not receiving antiviral therapy, the levels of 2-LTR circular viral DNA and total viral DNA were significantly correlated to CD4 cell counts. Similar correlations were not observed in patients receiving zidovudine (AZT), didanosine (ddA), or zalcitabine (ddC).

Rolling circle DNA replication in vitro by a complex of herpes simplex virus type 1-encoded enzymes

Extracts of insect cells infected with baculoviruses recombinant for the herpes simplex virus 1 (HSV-1)-encoded enzymes that are required for its replication can promote the rolling circle replication of circular plasmid templates. Replication is independent of a HSV-1 origin of replication (oris) or the HSV-1 origin binding protein and is inhibited by the origin binding protein when the plasmid contains oris. Replication is dependent on a complex composed of the HSV-1-encoded DNA polymerase and its processivity enhancing factor (the UL42 protein), ICP8 (the HSV-1-encoded single-strand DNA binding protein), and the HSV-1-encoded helicase-primase. The complex can be purified by size-exclusion and anion-exchange chromatography.

Formation of extrachromosomal circular DNA in HeLa cells by nonhomologous recombination

Extrachromosomal circular DNA (eccDNA) generated from chromosomal DNA is found in all mammalian cells and increases with cell stress or aging. Studies of eccDNA structure and mode of formation provide insight into mechanisms of instability of the mammalian genome. Previous studies have suggested that eccDNA is generated through a process involving recombination between repetitive sequences. However, we observed that approximately one half of the small eccDNA fragments cloned from HeLa S3 cells were composed entirely of nonrepetitive or low-copy DNA sequences. We analyzed four of these fragments by polymerase chain reaction and nucleotide sequencing and found that they were complete eccDNAs. We then screened a human genomic library with the eccDNAs to isolate the complementary chromosomal sequences. Comparing the recombination junctions within the eccDNAs with the chromosomal sequences from which they were derived revealed that nonhomologous recombination was involved in their formation. One of the eccDNAs was composed of two separate sequences from different parts of the genome. These results suggest that rejoining of ends of fragmented DNA is responsible for the generation of a substantial portion of the eccDNAs found in HeLa S3 cells.

Characterization of a region of plasmid pBL1 of Brevibacterium lactofermentum involved in replication via the rolling circle model

The minimal region for autonomous replication of pBL1, a 4.5-kb cryptic plasmid of Brevibacterium lactofermentum ATCC 13869 that has been used to construct a variety of corynebacterium vectors, was shown to be contained on a 1.8-kb HindII-SphI DNA fragment. This region contains two open reading frames (ORFs) (ORF1 and ORF5) which are essential for pBL1 replication in B. lactofermentum. Accumulation of single-strand intermediates in some of the constructions indicates that plasmid pBL1 replicates via the rolling circle replication model; its plus strand and minus strand were identified by hybridization with two synthetic oligonucleotide probes complementary to each pBL1 strand. ORF1 seems to encode the Rep protein and showed partial homology with sequences for Rep proteins from Streptomyces plasmids which replicate via rolling circle replication such as pIJ101, pSB24, and pJV1.

P nucleotide insertions and the resolution of hairpin DNA structures in mammalian cells

Two lines of evidence point to a hairpin DNA intermediate in V(D)J joining (V, variable; D, diversity; J, joining) [Lieber, M.R. (1991) FASEB J. 4, 2934-2944]. One is the presence of P nucleotide insertions (short inverted-repeat sequence) in V(D)J junctions [Lafaille, J. J., DeCloux, A., Bonneville, M., Takagaki, Y. & Tonegawa, S. (1989) Cell 59, 859-870]; a second is the detection of site-specifically broken DNA molecules with covalently closed (hairpin) termini in thymus DNA [Roth, D. B., Menetski, J. P., Nakajima, P., Bosma, M. J. & Gellert, M. (1989) Cell 70, 983-991]. However, P nucleotide insertions could be generated in ways not involving a hairpin structure, and because physical evidence for hairpin-ended DNA fragments has been obtained only with mutant mice, there is some uncertainty regarding the role of hairpin molecules in the normal V(D)J joining pathway. To determine whether mammalian cells are capable of metabolizing this odd type of DNA terminus and whether, in doing so, junctions with P insertions are in fact created, a linear DNA molecule with a hairpin closure at each end was transfected into several murine cell lines. The hairpin-ended molecules were recircularized, and the junctions exhibited P insertions at a high frequency. This result directly links the presence of P insertions to a hairpin precursor, providing strong evidence for the notion that a hairpin DNA intermediate exists in V(D)J recombination. A comparison of hairpin end joining in various cells, including those derived from mice with the severe combined immunodeficiency (scid) mutation, is presented.

Decatenating activity of Escherichia coli DNA gyrase and topoisomerases I and III during oriC and pBR322 DNA replication in vitro

oriC and pBR322 DNA replication, reconstituted with purified replication proteins, has been used to study the functional activities of Escherichia coli topoisomerase I, DNA gyrase, and topoisomerase III during the final stages of DNA replication. In the oriC system, DNA gyrase-catalyzed decatenation of daughter DNA molecules was very inefficient, whereas topoisomerase III could catalyze complete decatenation. In the pBR322 DNA replication system, almost all the daughter DNA molecules could be decatenated by DNA gyrase alone in the absence of salt. Decatenation by DNA gyrase in the pBR322 system was completely inhibited, without a concomitant inhibition of DNA synthesis, by the addition of physiological concentrations of salt. Topoisomerase III, however, could decatenate all of the daughter DNA molecules in the pBR322 system, even in the presence of high concentrations of salt. A similar effect could not be observed in the oriC system, because the addition of salt inhibited DNA synthesis. Topoisomerase I was incapable of catalyzing decatenation under any conditions examined in either the oriC or pBR322 replication system. The addition of topoisomerase I to the replication systems resulted only in an inhibition of DNA synthesis.

Passage through mitosis is required for oncoretroviruses but not for the human immunodeficiency virus

The human immunodeficiency virus productively infects and integrates into cells that have been arrested in the cell cycle with either gamma irradiation or aphidicolin. Integration by oncoretroviruses such as the murine leukemia virus (MuLV), on the other hand, depends on cell proliferation. Although the entire cell cycle is not necessary for MuLV infection, it is essential that the infected cells pass through mitosis. The long terminal repeat circle junction, a marker for nuclear entry, is first observed in MuLV-infected cells immediately after mitosis. These results suggest that mitosis is necessary for nuclear entry of MuLV, but not human immunodeficiency virus, unintegrated proviral DNA.

ATP-independent loading of the proliferating cell nuclear antigen requires DNA ends

The proliferating cell nuclear antigen (PCNA) is a processivity subunit for eukaryotic DNA polymerase delta. We present biochemical evidence that yeast PCNA likely adopts a toroidal structure containing an inside cavity through which double-stranded DNA slides. A comparative study of DNA replication reactions on circular versus linear model substrates shows that PCNA can only interact productively with DNA polymerase delta if the substrate is linear. This combined with the observation that a large molar excess of PCNA is required for maximal stimulatory activity is consistent with a model in which PCNA slips onto the end of the DNA in an ATP-independent manner.

The majority of simian immunodeficiency virus/mne circle junctions result from ligation of unintegrated viral DNA ends that are aberrant for integration

SIV/Mne circle junctions were amplified by the polymerase chain reaction (PCR) and cloned in a bacterial plasmid. Sequence analysis of clones isolated from 11 independent PCRs reveals that the start site for plus DNA synthesis is 5' ACTG. . ., and thus an asymmetric cleavage must occur during viral integration. In addition, most of the sequences found resulted from the ligation of aberrant proviral DNA ends that were apparently generated by priming errors, primer removal errors, or integrase processing errors. The results suggest that in this virus, as in Moloney murine leukemia virus, two good ends may be required for efficient integration.

The E1 protein of bovine papilloma virus 1 is an ATP-dependent DNA helicase

For efficient DNA replication of papillomaviruses, only two viral-encoded proteins, E1 and E2, are required. Other proteins and factors are provided by the host cell. E2 is an enhancer of both transcription and replication and is known to help E1 bind cooperatively to the origin of DNA replication. E1 is sufficient for replication in extracts prepared from permissive cells, but the activity is enhanced by E2. Here we show that purified E1 can act as an ATP-dependent DNA helicase. To measure this activity, we have used strand displacement, unwinding of topologically constrained DNA, denaturation of duplex fragments, and electron microscopy. The ability of E1 to unwind circular DNA is found to be independent of origin-specific viral DNA sequences under a variety of experimental conditions. In unfractionated cellular extracts, E1-dependent viral DNA replication is origin-dependent, but at elevated E1 concentrations, replication can occur on non-origin-containing DNA templates. This conversion from an origin-dependent replication system to a nonspecific initiator system is discussed in the context of the current understanding of the initiation of chromosomal DNA replication.

Nuclear and kinetoplast DNA synthesis in Trypanosoma cruzi, autoradiographical study with DNA polymerase inhibitors

DNA synthesis in epimastigote forms of Trypanosoma cruzi was studied autoradiographically by incorporation of [3H]thymidine in the nuclear and kinetoplast DNA. Both DNA were heavily labelled. Three eukaryotic DNA polymerase inhibitors (aphidicolin, aracytidine, and dideoxythimidine) were chosen to study the nuclear and kinetoplast DNA synthesis in vivo. Inhibition was mainly observed with the nuclear DNA.

Structural organization of the maxicircle variable region of Trypanosoma brucei: identification of potential replication origins and topoisomerase II binding sites

The maxicircle of the parasitic protozoan Trypanosoma brucei, one component of the mitochondrial genome, has size differences among isolates that localize to the variable region (VR) between the ND5 and 12S rRNA genes. We present here the nucleotide sequence of this entire region, thus completing the sequence of the maxicircle genome. We also find heterogeneously sized transcripts from throughout most of the VR. The VR has three distinct sections, each with characteristic repeated sequences. The repeated sequences in two sections are short and highly reiterated; the intraspecies size variation occurs within this region. The third section contains non-repetitive sequences and a large duplication immediately upstream of the 12S rRNA gene. Two repeat units within section I contain a sequence that has homology to the DNA replication origin of minicircles. This region also contains sequences with homology to topoisomerase II binding and cleavage sites. These findings suggest a role for the VR in DNA replication of the maxicircle.

Tumor necrosis factor-alpha induces circular forms of human immunodeficiency virus type-1 DNA in the persistently infected low-level expressing cell line, ACH-2

The low human immunodeficiency virus type-1 (HIV-1) expressing T-cell line, ACH-2, was used to investigate accumulation of the circular, extrachromosomal form of HIV DNA (HD) after tumor necrosis factor-alpha (TNF-alpha) induction. We chose the 2 long terminal repeat (LTR) circular form to analyze unintegrated HD by polymerase chain reaction (PCR), using primer pairs which flank the 2 LTR HD. Approximately a 10-fold increase in 2 LTR HD was detected intracellularly in the TNF-alpha-induced ACH-2 cells using an end point-dilution assay. To examine the cellular compartment location of the 2 LTR HD accumulation, ACH-2 cells were fractionated into cytoplasmic and nuclear components and further subjected to PCR. A 4- to 5-fold increase in the 2 LTR HD signal was observed in the nuclear fraction. These results indicate that unintegrated HD increases in a chronically infected cell line after TNF-alpha induction. This phenomenon, which previously had been observed only with acute infections, may offer insight into basic pathogenic mechanisms.

Computer-assisted dissection of rolling circle DNA replication

A comparative analysis of the proteins involved in initiation and termination of rolling circle replication (RCR) was performed using computer-assisted methods of data based screening, motif search and multiple amino acid sequence alignment. Two vast classes of such proteins were delineated, one of these being associated with RCR proper, and the other with mobilization (conjugal transfer) of plasmid DNA. The common denominator of the two classes was found to be a conserved amino acid motif that consists of the sequence HisUHisUUU (U--bulky hydrophobic residue; hereafter HUH motif). Based on analogies with metalloenzymes, it is hypothesized that the two conserved His residues this motif may be involved in metal ion coordination required for the activity of the RCR and mobilization proteins. The proteins of the replication (Rep) class contained two additional conserved motifs, with the motif around the Tyr residue(s) forming the covalent link with nicked DNA being located C-proximally of the HUH motif. This class further split into two large superfamilies and several smaller families, with the proteins belonging to a single but not to different (super)families demonstrating statistically significant similarity to each other. Superfamily I, prototyped by the gene A proteins of small isometric single-stranded (ss) DNA bacteriophages, included also Rep proteins of P2-related double-stranded (ds) DNA bacteriophages, the small phage-plasmid hybrid phasyl, and several cyanobacterial and archaebacterial plasmids. These proteins contained two invariant Tyr residues separated by three partially conserved amino acids, suggesting that they all may share the cleavage-ligation mechanism proposed for phi X174 A protein and involving alternate covalent binding of both tyrosines to DNA (Van Mansfeld, A.D., Van Teeffelen, H.A., Baas, P.D., Jansz, H.S., 1986. Nucl. Acids Res. 14, 4229-4238). Superfamily II included Rep proteins of a number of ssDNA plasmids replicating mainly in gram-positive bacteria that unexpectedly were shown to be related to the Rep proteins of plant geminiviruses. Conservation of the "HUH" motif and a motif around the putative DNA-linking Tyr residue was observed also in the Rep proteins of animal parvoviruses containing linear ssDNA with a terminal hairpin and replicating via the rolling hairpin mechanism. The class of plasmid mobilization (Mob) proteins was characterized by the opposite orientation of the conserved motifs, with the (putative) DNA-linking Tyr being located N-proximally of the "HUH" motif.(ABSTRACT TRUNCATED AT 400 WORDS)

In vivo resolution of circular plasmids containing concatemer junction fragments from minute virus of mice DNA and their subsequent replication as linear molecules

During replication of their linear, single-stranded DNA genomes, parvoviruses generate a series of concatemeric duplex intermediates. We have cloned, into Escherichia coli plasmids, junction fragments from these palindromic concatemers of minute virus of mice DNA spanning both the right end-to-right end (viral 5' to 5') and left end-to-left end (viral 3' to 3') fusions. When mouse cells were transfected with these circular plasmids and superinfected with minute virus of mice, the viral junctions were resolved and the plasmids replicated as linear chromosomes with vector DNA in their centers and viral DNA at their termini. Resolution did not occur when the concatemer joint was replaced by a different palindromic sequence or when the transfected cells were not superinfected, indicating the presence of latent origins of replication which could only be activated by a viral trans-acting factor(s). Moreover, the products of resolution and replication from the two termini were characteristically different. Analysis of individual terminal fragments showed that viral 5' (right-end) sequences were resolved predominantly into "extended" structures with covalently associated copies of the virally encoded NS-1 polypeptide, while bridges derived from the 3' (left) end resolved into both NS-1-associated extended termini and lower-molecular-weight "turn-around" forms in which the two DNA strands were covalently continuous. This pattern of resolution exactly coincides with that seen at the two termini of replicative-form intermediates in normal virus infections. These results demonstrate that the bridge structures are authentic substrates for resolution and indicate that the frequency with which extended versus turn-around forms of each terminus are generated is an intrinsic property of the telomere.

Rolling circle replication of DNA in yeast mitochondria

The conformation of mitochondrial DNA (mtDNA) from yeasts has been examined by pulsed field gel electrophoresis and electron microscopy. The majority of mtDNA from Candida (Torulopsis) glabrata (mtDNA unit size, 19 kb) exists as linear molecules ranging in size from 50 to 150 kb or 2-7 genome units. A small proportion of mtDNA is present as supercoiled or relaxed circular molecules. Additional components, detected by electron microscopy, are circular molecules with either single- or double-stranded tails (lariats). The presence of lariats, together with the observation that the majority of mtDNA is linear and 2-7 genome units in length, suggests that replication occurs by a rolling circle mechanism. Replication of mtDNA in other yeasts is thought to occur by the same mechanism. For Saccharomyces cerevisiae, the majority of mtDNA is linear and of heterogeneous length. Furthermore, linear DNA is the chief component of a plasmid, pMK2, when it is located in the mitochondrion of baker's yeast, although only circular DNA is detected when this plasmid occurs in the nucleus. The implications of long linear mtDNA for hypotheses concerning the ploidy paradox and the mechanism of the petite mutation are discussed.

Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: a physical map and identification and location of ARS elements

DNA was isolated from a circular derivative of chromosome III to prepare a library of recombinant plasmids enriched in chromosome III sequences. An ordered set of recombinant plasmids and bacteriophages carrying the contiguous 210-kilobase region of chromosome III between the HML and MAT loci was identified, and a complete restriction map was prepared with BamHI and EcoRI. Using the high frequency transformation assay and extensive subcloning, 13 ARS elements were mapped in the cloned region. Comparison of the physical maps of chromosome III from three strains revealed that the chromosomes differ in the number and positions of Ty elements and also show restriction site polymorphisms. A comparison of the physical map with the genetic map shows that meiotic recombination rates vary at least tenfold along the length of the chromosome.

Replication of tomato golden mosaic virus DNA B in transgenic plants expressing open reading frames (ORFs) of DNA A: requirement of ORF AL2 for production of single-stranded DNA

Tomato golden mosaic geminivirus has a genome of two single-stranded (ss) DNA components, A and B. An almost identical 'common' region in DNA A and DNA B is thought to contain sequence elements controlling replication and transcription. Hence investigation of sequences important for DNA replication by in vitro mutagenesis is complicated by possible effects on the transcription of genes for replication proteins. To overcome this problem, transgenic plants expressing open reading frames (ORFs) of DNA A from an enhanced cauliflower mosaic virus 35S RNA promoter were constructed and tested for their ability to support the replication of DNA B and DNA B mutants. The results show that plants transgenic for ORF AL1 are able to support the replication of the double-stranded (ds) forms of DNA B, but that ORF AL2 is required in addition to produce ssDNA B. ORFs AL3, BL1 or BR1 were not required for replication of ds or ssDNA B. To the best of our knowledge this is the first time that essential replication proteins of a geminivirus have been expressed constitutively from a plant genome without giving rise to replicating DNA A molecules, thereby allowing DNA B to replicate alone. Such transgenic plants should enable not only the mutational analysis of sequence elements within the replication origin region, but also the construction of a new generation of vectors for gene amplification in plants, based on a minimal virus replicon.

Minichromosome assembly accompanying repair-type DNA synthesis in Xenopus oocytes

Minichromosomes were assembled by injection of circular DNA into the nucleus of Xenopus oocytes. We observed that, in the course of DNA supercoiling and chromatin assembly, a small percentage of the injected DNA molecules incorporated a radioactive precursor. This DNA synthesis was carried out by aphidicolin-sensitive DNA polymerase, and generated short repair-like patches covalently linked to the injected DNA. We found that the DNA thus repaired was rapidly supercoiled almost to completion within 15 to 30 min after injection, whereas 60 to 120 min were required to supercoil the intact, bulk DNA molecules. Such differential supercoiling kinetics was also observed when UV-damaged DNA was injected. Chromatin assembly, which was characterized by DNA fragment sizes protected from micrococcal nuclease digestion, was consistent with the rapid DNA supercoiling and proceeded more efficiently on the repaired DNA. These results indicate that there are at least two kinetically distinct ways of assembling minichromosomes in the oocyte nucleus, and that the repaired DNA molecules preferentially follow the faster pathway.

Synthesis and processing of kinetoplast DNA minicircles in Trypanosoma equiperdum

Kinetoplast DNA, the mitochondrial DNA in trypanosomes, is a giant network containing topologically interlocked minicircles. Replication occurs on free minicircles that have been detached from the network. In this paper, we report studies on the synthesis and processing of the minicircle L and H strands. Analysis of free minicircles from Trypanosoma equiperdum by two-dimensional agarose gel electrophoresis indicated that elongating L strands are present on theta structures. Hybridization studies indicated that L-strand elongation is continuous and unidirectional, starting near nucleotide 805 and proceeding around the entire minicircle. The theta structures segregate into monomeric progeny minicircles, and those with a newly synthesized L strand have a 8-nucleotide gap between nucleotides 805 and 814 (J. M. Ntambi, T. A. Shapiro, K. A. Ryan, and P. T. Englund, J. Biol. Chem. 261:11890-11895, 1986). These molecules are reattached to the network, where repair of the gap takes place. Of the molecules labeled during a 10-min pulse with [3H]thymidine, gap filling occurred on half within about 15 min and on virtually all by 60 min; however, there was no detectable covalent closure of the newly synthesized L strand by 60 min.