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PubMed1987

Structure of the extrachromosomal ribosomal RNA chromatin of Physarum polycephalum.

Isolated nucleoli from exponentially growing microplasmodia of Physarum polycephalum were digested with micrococcal nuclease or DNAase I, or were photoreacted with trimethyl psoralen. In the coding region for the precursor of the ribosomal RNA, micrococcal nuclease and DNAase I digestions show predominantly a smear, and treatment with psoralen leads to a fairly continuous crosslinking of the DNA. All three assays are compatible with the absence of a typical nucleosomal array in most of the gene copies. In contrast, in the central non-transcribed spacer, except in the immediate 5'-flanking region, micrococcal nuclease and DNAase I digestions yield fragments that are multiples of a basic repeat, compatible with a nucleosomal packing of this region. The crosslinking pattern with psoralen confirms this conclusion. In addition, there are three sites over 400 base-pairs long that are inaccessible for psoralen crosslinking. Two of these sites have been mapped to the putative origins of replication. In the terminal non-transcribed spacer, except in the immediate 3'-flanking region, digestions with micrococcal nuclease and DNAase I give a smeared repeat. The crosslinking pattern after treatment with psoralen suggests that this region is packed in nucleosomes, except for about 900 base-pairs constituting the telomere regions of the linear extrachromosomal palindromic rDNA. Micrococcal nuclease digestion of the immediate 5'-flanking region shows a complete absence of any nucleosomal repeat, but digestion with DNAase I leads to a faint ten base-pair repeat. In contrast, in the 3'-flanking regions both nuclease assays indicate a chromatin structure similar to the coding region. Both flanking regions are unusual with respect to psoralen crosslinking, in that crosslinking is reduced both in chromatin and deproteinized DNA. On the basis of the known sequence-dependent psoralen crosslinking and the established sequences in these regions, crosslinking should be expected to occur. However, it does not and we therefore propose the presence of an unusual DNA conformation in these regions.

Chromatin↗
PubMed1987

Expression of chimeric genes in Caenorhabditis elegans.

We have shown the expression of transformed genes in the nematode Caenorhabditis elegans using a new gene fusion system. Vectors consisting of the flanking regions of a collagen gene (col-1) or a major sperm protein gene of C. elegans fused to the Escherichia coli uidA gene, encoding beta-glucuronidase, were microinjected into worms and found to be propagated as high-copy extrachromosomal tandem arrays. We have detected beta-glucuronidase activity in transformed lines, and have shown that the activity is dependent upon the correct reading frame of the construction and on the presence of the worm sequences. The enzyme activity was shown to be encoded by the chimeric beta-glucuronidase gene by co-segregation analysis and by inactivation with specific antisera. Expression is at a very low level, and seems to be constitutive. We have used histochemical techniques to visualize the enzyme activity in embryos.

Animals↗
PubMed1987

Some extrachromosomal circular DNAs from Drosophila embryos are homologous to tandemly repeated genes.

In Drosophila melanogaster embryos we have identified three classes of extrachromosomal circular DNA molecules homologous to the three main families of tandemly repeated genes, 5 S, rDNA and histone. 5 S genes are present in circular multimeric molecules containing up to 16 copies of the 375(+/- 7) base-pair repeated unit. Circular molecules homologous to rDNA are also multimeric molecules, which contain up to ten copies of the 240 base-pair tandemly repeated sequence of the non-transcribed spacer. The two major genomic classes of histone units (4800 and 5000 bases) are found only as monomeric circular molecules. No circular intermediate of the I transposable element was detected in embryos laid by F1 dysgenic females produced by the I-R system of hybrid dysgenesis. As far as we know, it is the first time that genes have been identified among extrachromosomal circular molecules independently of any specific amplification phenomenon.

Animals↗
PubMed1987

Cloned extrachromosomal circular DNA copies of the human transposable element THE-1 are related predominantly to a single type of family member.

The 2300 base-pair transposon-like human element, THE-1, has been identified in the extrachromosomal circular DNA of the established human cell line HeLa as a relatively homogeneous population of covalently closed 1900 base-pair molecules. THE-1, which has been classified tentatively as a retroviral-like transposable element (a retrotransposon), is present in the extrachromosomal circular DNA of African green monkey (BSC-1) and human lymphoblastoid (Jurkat) cell lines. The 1900 base-pair extrachromosomal elements isolated and cloned from HeLa cells (1) appear to contain only THE-1-specific nucleotide sequences, (2) are circularized versions of the linear chromosomal sequence, and (3) are related predominantly to a single, or single type of, family member.

Autoradiography↗
PubMed1988

Structure of extrachromosomal circular DNAs excised from T-cell antigen receptor alpha and delta-chain loci.

Small polydisperse circular (spc) DNA was isolated from mouse thymocytes, fragmented by HindIII digestion and cloned into the vector. Sixty DNA clones were randomly selected from the 10,400 phage library. The average size of insert was one-fifth of the original circular molecule. Twenty spc-DNA clones were homologous to DNA probes derived from T-cell antigen receptor (TCR) alpha-chain loci. We have characterized nine clones by DNA sequencing; they contain new germline sequences of the TCR alpha-chain variable (V alpha) and joining (J alpha) gene segments and the products out of the recombination of a V alpha with a J alpha gene segment. An additional four spc-DNA clones carried a new rearranging gene of the TCR delta-chain that is located between V alpha and J alpha genes. At least nine of 60 DNA clones carried the recombination junction of a heptamer-heptamer head-to-head structure expected from an excised product of V-J joining. This shows that most extrachromosomal circular DNAs in the thymus are formed by a sequence-dependent recombination mechanism. We suggest that a functional T-cell receptor V alpha gene can be constructed by somatic random rearrangements through successive looping-out, excision and deletion.

Animals↗
PubMed1991

Mitochondrial-like DNA sequences flanked by direct and inverted repeats in the nuclear genome of Toxoplasma gondii.

In the course of our genetic studies on Toxoplasma gondii, it was discovered that one cosmid hybridized to a repetitive element. The hybridization pattern observed for the enzyme BglII indicated that this cosmid hybridized to a large number of discrete, but related elements. Four BglII fragments were subcloned from the cosmid, and each was shown to hybridize with all the others, as well as to numerous dispersed sequences in genomic DNA. Three subclones were sequenced in their entirety, and shown to contain fragments of the genes for cytochrome oxidase subunit I and apocytochrome b, complete and functional copies of which have been found in only mitochondrial genomes. All the subcloned fragments were bounded at both ends by a 91 base-pair sequence, which contains a site for BglII. This 91 base-pair sequence could be found as either a direct or inverted repeat. It was determined that the BglII elements are arrayed downstream from a single copy nuclear gene. Comparison of genomic and cosmid DNAs confirmed that the cosmid faithfully reflects the nuclear genome. Although the mitochondrial genome of Toxoplasma has not been characterized, these nuclear mitochondrial-like sequences appear to be internally rearranged with respect to known, functional mitochondrial genomes, and with respect to each other. The finding of short repeated sequences flanking these elements may be a clue to the mechanism of their dissemination.

Amino Acid Sequence↗
PubMed1967

On the origin of mitosing cells

A theory of the origin of eukaryotic cells ("higher" cells which divide by classical mitosis) is presented. By hypothesis, three fundamental organelles: the mitochondria, the photosynthetic plastids and the (9+2) basal bodies of flagella were themselves once free-living (prokaryotic) cells. The evolution of photosynthesis under the anaerobic conditions of the early atmosphere to form anaerobic bacteria, photosynthetic bacteria and eventually blue-green algae (and protoplastids) is described. The subsequent evolution of aerobic metabolism in prokaryotes to form aerobic bacteria (protoflagella and protomitochondria) presumably occurred during the transition to the oxidizing atmosphere. Classical mitosis evolved in protozoan-type cells millions of years after the evolution of photosynthesis. A plausible scheme for the origin of classical mitosis in primitive amoeboflagellates is presented. During the course of the evolution of mitosis, photosynthetic plastids (themselves derived from prokaryotes) were symbiotically acquired by some of these protozoans to form the eukaryotic algae and the green plants. The cytological, biochemical and paleontological evidence for this theory is presented, along with suggestions for further possible experimental verification. The implications of this scheme for the systematics of the lower organisms is discussed.

Animals↗
PubMed1983

A preliminary model of double-minute-mediated gene amplification.

A mathematical model of double minute (dm) population dynamics has been developed based upon current concepts of the saltatory replication, random partitioning, nuclear exclusion and loss, and cellular growth inhibition of these extrachromosomal elements. A highly accurate approximate analytical solution has been obtained for the dm frequency distribution at steady state and preliminary analysis of transient states has been performed. The steady state solution has been fit to experimental frequency data of the SW527N carcinoma line, the excellent goodness of fit (X2 = 2.6, d.f. = 29) providing preliminary evidence for the consistency of this set of mechanisms. Two special cases are examined in which extrareplicative dms are produced on both the chromosome and existing dms at equal rates or on the chromosome alone. The model predicts that the population--average rate of extrareplicative dm production is 0.039 +/- S.E. 0.009 dms/hr/cell in the first case and is tenfold higher than when such replication occurs on the chromosome alone (0.0043 +/- S.E. 0.0004 dms/hr/cell). Allowable ranges of the extent of dm-related growth inhibition and dm loss are determined for the SW527N cell line. It is found that dm-related growth inhibition can be nearly as high as that observed for the S180 sarcoma lines (on the order of 0.5% per dm lengthening of the doubling time) or as low as zero.

Animals↗