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PubMed1984

Unstable DNA amplifications in methotrexate-resistant Leishmania consist of extrachromosomal circles which relocalize during stabilization.

Methotrexate-resistant Leishmania tropica contain two separate regions of DNA amplification, one encoding the bifunctional thymidylate synthetase-dihydrofolate reductase (TS-DHFR) characteristic of protozoans and the other of yet unknown function. The amplified DNAs are initially found as extrachromosomal closed circular forms, which are unstable in the absence of selection. After prolonged culture in methotrexate the amplified DNAs are found as repetitive arrays associated with the chromosomal DNA fraction after CsCl-ethidium bromide density gradient centrifugation, and are stable once selection is removed. The molecular description of gene amplification in Leishmania thus closely parallels the cytological features of gene amplification in cultured mammalian cells.

Animals↗

PubMed1991

Tunicamycin-resistant variants from five species of Leishmania contain amplified DNA in extrachromosomal circles of different sizes with a transcriptionally active homologous region.

Twelve independent variants were selected from five species of Leishmania for resistance to tunicamycin by exposure of cultured promastigotes to increasing concentrations of this antibiotic, an inhibitor of the microsomal N-acetylglucosamine-1-phosphate transferase in the dolichol pathway of N-glycosylation. All variants obtained from all species, as found previously with Leishmania amazonensis, contain amplified chromosomal DNA exclusively as extrachromosomal circles. These circular amplicons hybridize with amplified DNAs cloned previously from tunicamycin-resistant Leishmania amazonensis, but not with those from Leishmania resistant to other drugs. The amplicons from tunicamycin-resistant cells vary with different species in size from 30 to 70 kb, but all share a homologous region of 20 kb. Multiple independent transcripts are overexpressed from this region. Elevation of the microsomal glycosyltransferase activity is demonstrated in these variants from representative species. The results thus provide further evidence that this enzyme is overexpressed due to amplification of the gene in these cells. The consistent observation of this event in all cases studied also suggests that this is the predominant, if not the only mechanism of tunicamycin resistance in Leishmania.

Animals↗

PubMed1992

Homologies between the contiguous and fragmented rRNAs of the two Plasmodium falciparum extrachromosomal DNAs are limited to core sequences.

Plasmodium falciparum contains two extrachromosomal DNAs, a 6 kb linear element and a 35 kb circular DNA; both encode rDNA sequences. The 6 kb element rDNAs comprise fragments of both large and small subunit rRNAs. Comparison of these with corresponding rDNA sequences from the 35 kb DNA and E. coli show that sequences conserved between the three are largely confined to highly conserved core regions; in fact, most of the 6 kb rDNA sequences correspond to core regions. Both the 6 kb element and 35 kb rDNAs show less conservation to each other than to E. coli sequences, suggesting that the two extrachromosomal DNAs of P. falciparum are not closely related. The characteristics of the fragmented rRNAs from the 6 kb element suggest they are functional, possibly in mitochondrial ribosomes.

Animals↗

PubMed1995

Co-existence of circular and multiple linear amplicons in methotrexate-resistant Leishmania.

Circular and linear amplicons were analyzed in detail in Leishmania tropica cells resistant to methotrexate (MTX). Both types of elements presented sequences related to the H locus and coexisted in resistant cells. The linear amplicons appeared first during the selection process (at 10 microM MTX) and varied with regard to size and structure in cells exposed to increasing concentrations of drug. The circular element was evident at higher concentrations (50 microMs) but was the major amplified DNA in cells resistant to 1000 microM MTX while the level of amplification of the linear elements remained low. The extrachromosomal DNAs were unstable in the absence of drug and their disappearance coincided with an increase in sensitivity to MTX. Mapping of the minichromosomes and the circular element showed that they were all constituted by inverted duplications. The circular amplicon contained an inverted repeat derived from the H locus that encompassed the pteridine reductase gene (PTR1) responsible for MTX resistance. The amplified segment in the linear amplicons was longer and included the pgpB and pgpC genes that encode P-glycoproteins of unknown function previously characterized in different Leishmania species.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1994

The evolutionary origin of the 35 kb circular DNA of Plasmodium falciparum: new evidence supports a possible rhodophyte ancestry.

In common with other Apicomplexan parasites, Plasmodium falciparum carries two extrachromosomal DNAs, one of which, the 6 kb element, is undoubtedly mitochondrial. The second, generally referred to as the 35 kb circle, is of unknown provenance, but the nature and organization of its genetic content makes a mitochondrial association unlikely and the molecule has features reminiscent of plastid genomes. We now report the occurrence on the circle of an open reading frame specifying a predicted 470 amino acid protein that shares more than 50% identity with a gene currently known only on the plastome of red algae. This high degree of conservation confirms the 35 kb circle's plastid ancestry, and we speculate that it may have originated from the rhodoplast of an ancient red algal endosymbiont in the progenitor of the Apicomplexa.

Amino Acid Sequence↗

PubMed1994

Maternal inheritance of extrachromosomal DNA in malaria parasites.

Plasmodium falciparum has two extrachromosomal genomes, the mitochondrial 6-kb DNA element and the 35-kb circular DNA. The mitochondrial gene cytochrome b on the 6-kb element has been shown to be inherited uniparentally. In order to ascertain whether the route is maternal or paternal we have examined preparations of male and female gametes of the closely related Plasmodium gallinaceum for the presence of extrachromosomal DNA. DNA from purified preparations of gametes was hybridised to probes for both the 6-kb and 35-kb extrachromosomal genomes. Both probes hybridised to the preparation of Plasmodium gallinaceum female gametes but not to that of the males. We conclude that the extrachromosomal DNAs of malaria parasites are transmitted maternally.

Animals↗

PubMed1995

Plasmodium falciparum: alterations in organelle transcript abundance during the erythrocytic cycle.

The malaria parasite Plasmodium falciparum has two extrachromosomal DNAs, a 6 kb reiterated element which appears to be the mitochondrial DNA and a 35 kb circular DNA of unknown function. Examination of relative steady-state transcript abundance during parasite development in the erythrocyte shows that transcripts of 6 kb element protein-coding genes are least abundant in the ring and early trophozoite stages and most abundant in late trophozoites and schizonts, while transcripts from the RNA polymerase subunits of the 35 kb DNA, also least abundant in ring stage, are relatively similar in abundance in succeeding stages. The fragmented rRNAs of the 6 kb element appear to be constitutively abundant except for an increase in the schizont stage, while rRNAs from the 35 kb DNA are least abundant in early trophozoites and most abundant in schizonts. Thus the relative abundance of organelle transcripts alters during the erythrocytic portion of the P. falciparum developmental cycle. These alterations may reflect the relative importance of the roles played by organelle gene products in different life cycle stages.

Animals↗

PubMed1992

Circular extrachromosomal DNA codes for a surface protein in the (+) mating type of the zygomycete Absidia glauca.

A small protein with a molecular mass of 15 kDa, which is specifically found on the hyphal surface of a (+) mating-type strain of the model zygomycete Absidia glauca, was purified to electrophoretic homogeneity and partially sequenced. The corresponding gene was cloned by means of an oligonucleotide probe deduced from the protein sequence. It could be localized on an extrachromosomal circular DNA element with a total length of 1250 bp. Electron microscopic analysis of A. glauca DNA showed that small extrachromosomal DNAs with varying length are a common feature of this zygomycete. There are no indications of additional chromosomal copies of the gene for this surface protein, and the plasmid is absent from DNA preparations of the (-) mating type. The copy number ranges around three per haploid genome, and a single transcript with a length of 400 bp, coding for the surface protein, could be found by employing a hybridization probe which spans the complete fungal plasmid. This is the first report of naturally occurring extrachromosomal DNA in a Mucor-like fungus, and the only example where an integral protein of the cell wall is encoded by a plasmid.

Amino Acid Sequence↗

PubMed1976

Extrachromosomal deoxyribonucleic acid in R factor-harboring Enterobacteriaceae.

Extrachromosomal deoxyribonucleic acid (DNA) from 24 different R factor-harboring Enterobacteriaceae was isolated and characterized by analytical ultracentrifugation and electron microscopy. The R factors represented 15 different patterns of transferable drug resistance found in enterobacteria from an enclosed geographic area. All of the strains contained extrachromosomal, circular DNA molecules within the range of 0.4 to 52 mum. More than one size class of circular DNA molecules was observed in the majority of the extrachromosomal DNA preparations. The buoyant density of the extrachromosomal DNA ranged from 1.700 to 1.720 g/cm3. The majority of the bacteria contained extrachromosomal DNAs of various densities. Three-fourths of the R factors were classified as fi+. The investigation illustrates the extensive variability in the physical characteristics of plasmid DNA from R factor-harboring strains.

DNA, Bacterial↗

PubMed1993

Extrachromosomal maintenance and amplification of yeast artificial chromosome DNA in mouse cells.

Linear and circular forms of a 660-kb yeast artificial chromosome (YAC) containing the human hypoxanthine phosphoribosyltransferase gene were introduced into mouse L A-9 cells by fusion with yeast spheroplasts, and in situ hybridization was used to determine the location and fate of the yeast- and YAC-derived DNA in 25 fusion cell lines. Human and yeast DNAs were observed as extrachromosomal DNA molecules, present at least 27 cell divisions after fusion, in half the cell lines. The extrachromosomal molecules replicate extrachromosomally but segregate poorly like plasmids that contain an autonomously replicating sequence element in yeast. This system may allow analysis of DNA requirements for replication and segregation in mammalian cells. The extrachromosomal elements resemble double minutes (DMs), and in five cell lines human and yeast DNAs were present as very large integrated blocks of DNA resembling homogeneously staining regions (HSRs). Thus, the fusion cell lines contain the two characteristic forms of amplified DNA observed in cancer cell lines, DMs and HSRs, indicating that these can be formed from fragments of DNA introduced by cell fusion.

Animals↗

PubMed1992

Subcellular fractionation of the two organelle DNAs of malaria parasites.

Malaria parasites contain two extrachromosomal DNAs, a 6 kb repetitive linear molecule which is assigned on the basis of its genetic content to the mitochondria, and a 35 kb transcriptionally active circular molecule whose intracellular location is not known. We used the polymerase chain reaction to detect and estimate the numbers of both molecules in sub-cellular fractions derived from the rodent parasite Plasmodium yoelii. The two DNA molecules were not coordinately partitioned by the fractionation process, the 6 kb molecule being more abundant, relative to the 35 kb circle, in a fraction enriched for mitochondria, the converse being true for a less dense fraction of unknown identity. This implies that the two molecules are located in different cellular compartments, and is consistent with other evidence suggesting they have different evolutionary origins.

Animals↗

PubMed1992

Unstable amplification of two extrachromosomal elements in alpha-difluoromethylornithine-resistant Leishmania donovani.

We describe the first example of unstable gene amplification consisting of linear extrachromosomal DNAs in drug-resistant eukaryotic cells. alpha-Difluoromethylornithine (DFMO)-resistant Leishmania donovani with an amplified ornithine decarboxylase (ODC) gene copy number contained two new extrachromosomal DNAs, both present in 10 to 20 copies. One of these was a 140-kb linear DNA (ODC140-L) on which all of the amplified copies of the odc gene were located. The second was a 70-kb circular DNA (ODC70-C) containing an inverted repeat but lacking the odc gene. Both ODC140-L and ODC70-C were derived from a preexisting wild-type chromosome, probably by a conservative amplification mechanism. Both elements were unstable in the absence of DFMO, and their disappearance coincided with a decrease in ODC activity and an increase in DFMO growth sensitivity. These results suggest the possibility that ODC70-C may play a role in DFMO resistance. These data expand the diversity of known amplification mechanisms in eukaryotes to include the simultaneous unstable amplification of both linear and circular DNAs. Further characterization of these molecules will provide insights into the molecular mechanisms underlying gene amplification, including the ability of linear amplified DNAs to acquire telomeres and the determinants of chromosomal stability.

Animals↗

PubMed1987

Pulse-labeled, small closed circular DNA in cultured mouse and human cells.

Mouse (erythroleukemia, TSA8, and FM3A) cells and human (HeLa and HL-60) cells were pulse-labeled with [3H]thymidine and covalently closed circular DNA in the extrachromosomal fraction was analyzed by fluorography following polyacrylamide gel electrophoresis. Two discrete bands for mouse and at least one, different, band for human cells emerged in the position to which small circular DNA (less than 1 kb) migrate, suggesting there to be species-specific, preferentially labeled, small circular DNA in mammalian cells. The incorporation of [3H]thymidine into the DNA was inhibited by cycloheximide but unaffected by aphidicolin. Restriction enzyme (AluI) digestion of the DNA fraction from MEL cells produced approximately 120-, 100-, and 50-bp labeled DNA fragments. The origin of the pulse-labeled DNAs is discussed.

Animals↗

PubMed1986

[DNA metabolism during maturation of male germ cells. II. Amplification structures in the nuclei of rat germ and somatic cells].

Amplification structures have been found in preparations of histone-depleted somatic (liver) and sex (spermatogonia, spermatocytes 1) rat cells. Multi-forked chromosomal (2-4 replicative forks originating from a single strand of DNA) and extrachromosomal circular amplification structures have been detected in the nuclei of sex cells. All the circular molecules of DNA detected belong, according to size, to the class of small nuclear polydispersed circular DNAs. Chromosomal amplification structures (eye-in-eye or several replicative forks originating from one DNA strand) have been only detected in the nuclei of somatic cells.

Animals↗

PubMed2002

Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue.

Plasmids have been described in almost all bacterial species analysed and have proven to be essential genetic tools. In many bacteria these extrachromosomal DNAs are cryptic with no known markers or function, which makes their characterization and genetic exploitation extremely difficult. Here we describe a system that will allow the rescue of any circular DNA (plasmid or phage) using an in vitro transposition system to deliver both a selectable marker (kanamycin) and an Escherichia coli plasmid origin of replication. In this study, we demonstrate the rescue of four cryptic plasmids from the opportunistic pathogen Mycobacterium avium. To evaluate the host range of the rescued plasmids, we have examined their ability to be propagated in Mycobacterium smegmatis and Mycobacterium bovis BCG, and their compatibility with other mycobacterial plasmids. In addition, we use a library of transposon insertions to sequence one plasmid, pVT2, and to begin a genetic analysis of plasmid genes. Using this approach, we identified a putative conjugative relaxase, suggesting this myco-bacterial plasmid is transferable, and three genes required for plasmid establishment and replication.

Base Sequence↗

PubMed1994

Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum.

Malaria and other Apicomplexan parasites harbour two extrachromosomal DNAs. One is mitochondrial and the other is a 35-kb circle with some plastid-like features but whose provenance and function is unknown. In addition to genes for rRNAs, tRNAs and ribosomal proteins, the 35-kb circular DNA of Plasmodium falciparum carries an rpoBC operon which encodes subunits of a eubacteria-like RNA polymerase. The phylogenetic analysis of the complete rpoB sequence presented here supports our inference that the 35-kb circle is the remnant of a plastid genome.

Amino Acid Sequence↗

PubMed1992

Double minute chromosomes carrying the human multidrug resistance 1 and 2 genes are generated from the dimerization of submicroscopic circular DNAs in colchicine-selected KB carcinoma cells.

This study characterizes amplified structures carrying the human multidrug resistance (MDR) genes in colchicine-selected multidrug resistant KB cell lines and strongly supports a model of gene amplification in which small circular extrachromosomal DNA elements generated from contiguous chromosomal DNA regions multimerize to form cytologically detectable double minute chromosomes (DMs). The human MDR1 gene encodes the 170-kDa P-glycoprotein, which is a plasma membrane pump for many structurally unrelated chemotherapeutic drugs. MDR1 and its homolog, MDR2, undergo amplification when KB cells are subjected to stepwise selection in increasing concentrations of colchicine. The structure of the amplification unit at each step of drug selection was characterized using both high-voltage gel electrophoresis and pulsed-field gel electrophoresis (PFGE) techniques. An 890-kb submicroscopic extrachromosomal circular DNA element carrying the MDR1 and MDR2 genes was detected in cell line KB-ChR-8-5-11, the earliest step in drug selection in which conventional Southern/hybridization analyses detected MDR gene amplification. When KB-ChR-8-5-11 was subjected to stepwise increases in colchicine, this circular DNA element dimerized as detected by PFGE with and without digestion with Not 1, which linearizes the 890-kb amplicon. This dimerization process, which also occurred at the next step of colchicine selection, resulted in the formation of cytologically detectable DMs revealed by analysis of Giemsa-stained metaphase spreads.

Chromosomes, Human↗

PubMed1990

[Extrachromosomal DNA in mammalian cells].

Extrachromosomal DNA (eDNA) is mammalian cells is represented not only as mitochondrial DNA but also as circular DNA existing both in the nucleus and in the cytoplasm. According to its size eDNA could be divided into two major classes: small polydisperse circular DNAs and large circular DNAs. Small polydisperse circular DNAs sized from 150 to 20,000 base pair are found both in the nucleus and in the cytoplasm. Large circular DNAs from 150,000 to 900,000 base pair are found in the nucleus only. Small polydisperse circular DNAs contain mainly repetitive sequences but occasionally they may contain very low repetitive sequences or unique ones. Such sequences may result from intrachromosomal recombinations, replicon misfiring, reverse transcription or fragmentation of chromosomal DNA by endogenous nucleases. Large circular DNAs are known to consist mainly of amplified sequences of oncogenes or MDR genes, which result from the deletion of appropriate regions of chromosomes. The number of copies of eDNA is greater in the malignant cells and in cells at certain stages of differentiation. The increase in copy number of eDNA reflects the intensity of processes in the cells. Autonomous replication of small and large circular DNAs is evident in tumor cells, although not all eDNAs can replicate autonomously. The presence in tumor cells of self-replicating molecules of eDNA, which are distributed in daughter cells independently of chromosomal DNA, determines presumably the high rate of adaptability of these cells to environmental conditions (metastasis and resistance to chemotherapeutic agents). It is quite possible that the existence of amplified copies of oncogenes and some other genes in the form of eDNA can determine some phenotypic characteristics of the transformed cells.

Animals↗