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PubMed1993

Analysis of human extrachromosomal DNA elements originating from different beta-satellite subfamilies.

By screening total human DNA with probes derived from the small polydisperse circular (spc) DNA fraction of cultured human cells, we identified three clones that carry long stretches of beta-satellite DNA. Further experiments have shown that the three sequences belong to at least two different beta-satellite subfamilies, which are characterized by different higher order subunits. Members of one of these subfamilies are located in the cytological satellites of all acrocentric chromosomes, whereas members of another are located on the short arms of the acrocentrics on both sides of the stalk regions and also in the centromeric regions of chromosomes 1 and 9. This is the first time that beta-satellite sequences obtained from the spcDNA of human cells have been assigned to beta-satellite subfamilies that are organized as long arrays of tandemly arranged higher order monomers. This indicates that beta-satellite sequences can be excised from their chromosomal loci via intrastrand-recombination processes.

Base Sequence↗
PubMed1985

DNA-protein interactions during replication of genetic elements of bacteria.

Specific interactions of DNA with proteins are required for both the replication of deoxyribonucleic acid proper and its regulation. Genetic elements of bacteria, their extrachromosomal elements in particular, represent a suitable model system for studies of these processes at the molecular level. In addition to replication enzymes (DNA polymerases), a series of other protein factors (e.g. topoisomerases, DNA unwinding enzymes, and DNA binding proteins) are involved in the replication of the chromosomal, phage and plasmid DNA. Specific interactions of proteins with DNA are particularly important in the regulation of initiation of DNA synthesis. Association of DNAs with the cell membrane also plays an important role in their replication in bacteria.

Bacterial Proteins↗
PubMed1993

Localization of a bidirectional DNA replication origin in the native locus and in episomally amplified murine adenosine deaminase loci.

Gene amplification is frequently mediated by the initial production of acentric, autonomously replicating extrachromosomal elements. The 4,000 extrachromosomal copies of the mouse adenosine deaminase (ADA) amplicon in B-1/50 cells initiate their replication remarkably synchronously in early S phase and at approximately the same time as the single-copy chromosomal locus from which they were derived. The abundance of ADA sequences and favorable replication timing characteristics in this system led us to determine whether DNA replication initiates in ADA episomes within a preferred region and whether this region is the same as that used at the corresponding chromosomal locus prior to amplification. This study reports the detection and localization of a discrete set of DNA fragments in the ADA amplicon which label soon after release of synchronized B-1/50 cells into S phase. A switch in template strand complementarity of Okazaki fragments, indicative of the initiation of bidirectional DNA replication, was found to lie within the same region. This putative replication origin is located approximately 28.5 kbp upstream of the 5' end of the ADA gene. The same region initiated DNA replication in the single-copy ADA locus of the parental cells. These analyses provide the first evidence that the replication of episomal intermediates involved in gene amplification initiates within a preferred region and that the same region is used to initiate DNA synthesis within the native locus.

Adenosine Deaminase↗
PubMedDate not supplied

[Genome instability].

The paper deals with the various manifestations and the role of genome changes, mainly in eukaryotes. I. Hereditary changes: 1) multiplication of genes in animals; 2) multiplication of genes in prokaryotes; 3) microsymbionts, mobile elements and supermutability; 4) extrachromosomal element delta in Drosophila; 5) hybrid dysgenesis in Drosophila; 6) mobile and unstable genes in drosophila; 7) controlling elements in planrs. II. Genome changes as a regulatory factor of genetic activity: 1) immunoglobulin genes; 2) mating types in yeast; 3) the inversion mechanism of switching gene activity in prokaryotes; 4) ribosomal and histone genes; 5) changes of DNA fractions in ontogenesis; 6) regulation of genome changes.

Animals↗
PubMedDate not supplied

[Phage-plasmid interactions in bacteria].

A review is devoted to consideration of the basic types of interaction of moderate and virulent bacteriophages and extrachromosomal elements in bacterial cells. Various experimental data confirm diversity of such interactions as well as resistance of bacteria to productive phage infection. Role of plasmids in such processes as abortion infection, lysogenic state, reparation of phage DNA as well as the effect of plasmids on the basic stages of phage development in the cells are analyzed. Possible mechanisms for limiting development of phages as a result of plasmids' presence in bacterial cells are considered.

Bacteria↗
PubMed2006

Trypanosoma brucei: composition, organisation, plasticity, and differential transcription of NlaIII repeat elements in drug-resistant and sensitive isolates.

A Trypanosoma brucei brucei DNA repeat sequence termed NlaIII repeat (NR) was originally isolated from a multidrug-resistant field isolate CP547 [Jamnadass, R., 1995. Identification and characterisation of an extrachromosomal element from a multidrug-resistant isolate of T. brucei brucei, Ph.D. thesis, Brunel University, UK]. Subsequently studied in a laboratory strain (Tb427) [Alsford, N.S., Navarro, M., Jamnadass, H.R., Dunbar, H., Ackroyd, M., Murphy, N.B., Gull, K., Ersfeld,K., 2003. The identification of circular extrachromosomal DNA in the nuclear genome of T. brucei. Molecular Microbiology 47, 277-288], NRs were exclusively episomal. Here we show that NR sequences in CP547 are present on linear chromosomes as well as on episomal circular elements. Sequence analysis shows that NRs are composed of three classes of sub-repeat arranged in a specific order. Heterogeneity in size and sequence of an episomal 6.6kbp element was shown in successive passages of the original CP547 isolate and derived clones in mice. Its copy number was unstable and was affected by selective pressure with the trypanocide diminazene aceturate. Some of the extrachromosomal elements appear to be composed of RNA-DNA hybrids. NR sequences were transcribed in a developmentally regulated manner but transcripts did not contain the spliced-leader sequence found on all trypanosome mRNAs.

Animals↗
PubMed2005

Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements.

Prokaryotes contain short DN repeats known as CRISPR, recognizable by the regular spacing existing between the recurring units. They represent the most widely distributed family of repeats among prokaryotic genomes suggesting a biological function. The origin of the intervening sequences, at present unknown, could provide clues about their biological activities. Here we show that CRISPR spacers derive from preexisting sequences, either chromosomal or within transmissible genetic elements such as bacteriophages and conjugative plasmids. Remarkably, these extrachromosomal elements fail to infect the specific spacer-carrier strain, implying a relationship between CRISPR and immunity against targeted DNA. Bacteriophages and conjugative plasmids are involved in prokaryotic population control, evolution, and pathogenicity. All these biological traits could be influenced by the presence of specific spacers. CRISPR loci can be visualized as mosaics of a repeated unit, separated by sequences at some time present elsewhere in the cell.

Base Sequence↗
PubMed1988

High-affinity SV40 T-antigen binding sites in the human genome.

We describe two different approaches to isolate human genomic sequences possessing high-affinity binding sites for the simian virus 40 (SV40) large T antigen. First, SV40 T antigen was added to Sau3A-restricted human DNA; the resulting T-antigen-DNA complexes were collected after repeated passages through nitrocellulose filters. The second approach involves the specific immunoprecipitation of chromatin fragments, generated by Sau3A treatment of nuclear chromatin from SV40-transformed human cells. The DNA fragments obtained were cloned in plasmid vectors for further investigation. Using the filter binding approach we isolated four different fragments with high-affinity binding sites. The binding site in one fragment was related to the strong T-antigen binding site I in the SV40 genome. The other three fragments contained multiple recognition pentamers, GA(G)GGC. Only one fragment with a high-affinity binding site was identified among the immunoprecipitable chromatin fragments. This DNA fragment belongs to the L1 family of human repetitive DNA. We present evidence suggesting that a significant fraction of human L1 elements possesses T-antigen binding sites. L1-related sequences appear as extrachromosomal elements in an SV40-transformed human cell line, and the amount of extrachromosomal L1 DNA was found to increase after fusion of transformed cells to permissive monkey cells.

Antigens, Polyomavirus Transforming↗
PubMed1992

Replication of bovine papillomavirus vectors in murine cells.

Varying capacities for autonomous replication have been obtained with bovine papillomavirus type 1 (BPV-1)-based expression vectors in mouse C127 cells. Both integration of the vector DNA into the genome of the host cell and replication as monomeric extrachromosomal elements have been observed. In this study, we have examined what features of BPV-1 vectors influence their replication potential. Transfection of the entire BPV-1 genome into C127 cells resulted in the replication of extrachromosomal monomeric BPV-1 elements. The same result was obtained when a plasmid sequence was inserted into the BPV-1 DNA. However, introduction of foreign, transcriptionally active units resulted in chromosomal integration of the expression vectors. This result was obtained with clones isolated by co-transfection followed by neomycin selection, as well as with clones isolated from neoplastic foci. Supertransfection of a BPV-1-based expression vector into cells harbouring unintegrated replicating BPV-1 genomes resulted in integration of the vector DNA, whereas replication of the resident BPV-1 genomes was unaffected. Extrachromosomal replication of such a vector was achieved when the enhancer and promoter region of the foreign gene were deleted.

Animals↗
PubMed1988

Typing of Salmonella species.

Epidemiological markers of strains of Salmonella are classified as major or minor. Major epidemiological markers are determined by chromosomal genes and are not affected by extrachromosomal elements. They are subspecies and serovars. Minor epidemiological markers are either affected by extrachromosomal replicons or have an insufficiently proven genetic stability and are used to subdivide serovars in detailed epidemiological investigations. These minor markers are biovars, phagovars, bacteriocinovars, patterns of resistance to antimicrobial agents, and restriction patterns of chromosomal and plasmid DNA.

Animals↗
PubMed1988

pUB307 mobilizes resistance plasmids from Escherichia coli into Neisseria gonorrhoeae.

The plasmid pUB307, a derivative of RP1, is a conjugative, broad-host-range plasmid. We have shown that this element mobilizes gonococcal resistance plasmids from Escherichia coli to Neisseria gonorrhoeae, thus providing evidence that extrachromosomal elements can efficiently enter gonococci by conjugation. Furthermore, pUB307 can also be used as a helper element to mobilize the cloning vector pLES2 into N. gonorrhoeae. This finding significantly increases the usefulness of pLES2 as a shuttle vector between E. coli and gonococcus.

Cloning, Molecular↗