Mitochondrial DNA from sheep heart

Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline

Mitochondria are unusual organelles in that they contain their own genomes, which are kept apart from the rest of the DNA in the cell. While mitochondrial DNA (mtDNA) is essential for respiration and most multicellular life, maintaining a genome outside the nucleus brings with it a number of challenges. Chief among these is preserving mtDNA genomic integrity from one generation to the next. In this review, we discuss what is known about negative (purifying) selection mechanisms that prevent deleterious mutations from accumulating in mtDNA in the germline. Throughout, we focus on the female germline, as it is the tissue through which mtDNA is inherited in most organisms and, therefore, the tissue that most profoundly shapes the genome. We discuss recent progress in uncovering the mechanisms of germline mtDNA selection, from humans to invertebrates.

Estimating evolutionary distance from restriction maps of mitochondrial DNA with arbitrary G+C content

We develop a mathematical model for estimating evolutionary distance from restriction enzyme maps, which incorporate non-uniformity of the rate of base substitution into the theory and allows for an arbitrary G+C content at equilibrium. When the G+C content differs significantly from 1/2, the traditional model of base changes can introduce a systematic bias which depends upon the base composition of the restriction site. In addition, the accuracy of estimated evolutionary distance depends heavily upon the choice of restriction enzyme in that the expected number of sites is also affected. Monte Carlo experiments are conducted to check the validity of the present theoretical treatment and from which we draw several cautionary notes on estimation. An application is made to the available data on restriction enzyme maps of human mitochondrial DNA where the G+C content is approximately 1/3.

Uniqueness of sperm mtDNA as compared to somatic mtDNA in ram

Sperm mtDNA exhibits unique physicochemical properties compared with mtDNA from somatic tissues in the ram. The buoyant density of sperm mtDNA was 1,6983 g/cm3 while the brain, heart and liver mtDNAs was about 1.7005 g/cm3. The Tm of the liver and sperm mtDNA was 71.0 degrees C and 69.5 degrees C, respectively. The G + C content of sperm mtDNA was 3.0 moles % lower than the liver mtDNA. The contour length of the circular sperm mtDNA was 5.01 micrometers compared with the liver mtDNA with contour length of 5.33 micrometers.

A partial map of the circular mitochondrial genome of Drosophila melanogaster. Location of EcoRI-sensitive sites and the adenine-thymine-rich region

The mitochondrial genome of Drosophila melanogaster is a circular DNA molecule of mol wt 12.35 X 10(6) daltons. A single region accounting for approx. 25% of this molecule can be reproducibly differentially denatured presumably because it is rich in adenine and thymine. We have mapped on the circular mitochondrial genome of D. melanogaster the relative positions of this adenine-thymine (A-T) rich region and the sites sensitive to cleavage by the restriction endonuclease EcoRI, using agarose gel electrophoresis and electron microscopy. Digestion of mitochondrial DNA (mtDNA) molecules to completion with EcoRI resulted in the production of four fragments, A, B, C, and D which represent (+/- SD) 58.9 +/- 1.1%, 27.5 +/- 0.8%, 8.9 +/- 0.5%, and 4.5 +/- 0.3%, of the circular genome length, respectively. Fragments produced by EcoRI digestion and circularized by incubation at 2 degrees C also fell into four distinct length groups with means (+/- SD) of 59.1 +/- 0.5%, 27.5 +/- 0.5%, 9.2 +/- 0.3%, and 4.6 +/- 0.2% of the circular genome length. From a consideration of the lengths of fragments resulting from incomplete EcoRI digestion, it was determined that the arrangement of the fragments in the circular genome was A-C-B-D. By electron microscope examination of partially denatured EcoRI fragments, the A-T-rich region was shown to be located in the A fragment closer to one end than to the other. By similar partial-denaturation studies of fragments resulting from incomplete EcoRI digestion, it was determined that, in the circular genome, of the two EcoRI sites which define the limits of the A fragment, the site between the A and D fragment lies nearest to the A-T-rich region.

An electron microscope study of mitochondrial DNA in spontaneous human tumours and chemically induced animal tumours

MtDNA was extracted by a phenol method from transplanted and primary DAB induced hepatomata in male Wistar rats, normal rat liver, spontaneous human tumours (2 Wilm's tumours, one neuroblastoma and one adrenal carcinoma), as well as 2 specimens of normal human kidney, BNU induced "leukaemias" in mice and CHO fibroblasts in monolayer culture. The proportion of monomers, catenated dimers and oligomers, open dimers and small circles was determined by electron microscopy of the fractions comprising lower and middle DNA bands in a CsCl-EthBr gradient. Tumours were compared where possible with their normal tissue of origin. Open dimers were found in 2 Wilm's tumours and their attached "normal-looking" kidney tissue but not in normal, non-malignant kidney or any other tissue studied. In Wilm's tumours, the occurrence of open dimers is far from being an all-or-none phenomenon. Malignancy produced little change in the relative proportions of catenated dimers and oligomers in the tissues studied. Small circles were found associated with mtDNA from every tissue. Tumour mtDNA was not more heterogeneous in length than monomers from the corresponding normal tissue, neither was the mean length of tumour mtDNA significantly different from its corresponding normal mtDNA.

Isolation and characterization of mitochondrial DNA from Drosophila melanogaster

Mitochondrial DNA (MtDNA) with a neutral buoyant density of 1.681 g/cm(3) has been isolated from unfertilized eggs of Drosophila melanogaster. This DNA is a circular molecule with an average length of 5.3 microm; it reassociates with a low C(0)t(1/2) after denaturation, and in alkaline isopycnic centrifugation it separates into strands differing in density by 0.005 g/cm(3). MtDNA isolated from purified mitochondria of unfertilized eggs or from total larval DNA melts with three distinct thermal transitions. The three melting temperature values suggest that the molecule may have three regions differing in average base composition. DNA isolated from unfertilized eggs of D. melanogaster contains approximately equal amounts of MtDNA and another DNA with a buoyant density of 1.697 g/cm(3), slightly less dense than main peak DNA. The possibility that the heavier DNA fraction consists of amplified ribosomal DNA was excluded by hybridization experiments, but otherwise nothing is known of its origin or function.

Studies on mitochondria. II. Mitochondrial DNA of thoracic muscles of Schistocerca gregaria

The buoyant densities of the nuclear and mitochondrial DNA from the thoracic muscles of Schistocerca gregaria were found to be 1 702 and 1.689 g/cm(3), respectively, corresponding to guanine plus cytosine (G + C) content of 42.2 and 30% A preliminary treatment of the mitochondrial pellet with DNase (25 degrees C, 20 min) is necessary to eliminate the contaminating nuclear DNA. The mitochondrial DNA renatures readily after heat denaturation and incubation at 65 degrees C. The DNA released from the mitochondrial pellet by osmotic shock consists of circular open and closed molecules with a contour length around 5 micro The instability of insect mitochondria in in vitro preparations is discussed.

Studies with cholroplast and mitochondrial DNA. I. Evidence of sequence homology between chloroplast and nuclear DNA (Broad Bean) and between mitochondrial and nuclear DNA (rat liver)

A mixture of broad bean chloroplast and nuclear DNA or rat liver mitochondrial and nuclear DNA was taken through a heating and annealing cycle, and examined by CsCl density gradient centrifugation. The formation of intermediates between the two DNAs during joint annealing was used as a method of detecting sequence homology in different DNA samples. Homology was found between chloroplast and nuclear DNA from broad bean and between mitochondrial and nuclear DNA from rat liver. Since this method produces only qualitative data no implication for possible nucleocytoplasmic relationship can be assessed.

Heart denaturation studies of rat liver mitrochondrial DNA. A denaturation map and changes in molecular configurations

The effect of progressive denaturation of open circular molecules (component II) and supercoiled covalently closed circular molecules (component I) of rat liver mitochondrial DNA has been followed by heating in the presence of formaldehyde and examination in the electron microscope. After heating at 49 degrees C, two, three, or four regions of strand separation were visible in 25% of the component II molecules. Comparisons of the patterns of distribution of these regions in individual molecules indicated that they occurred at at least three specific positions around the molecule. Also, these regions, which were assumed to be rich in adenine and thymine, were within a segment which was less than 50% of the length of the molecule. After heating at 50 degrees C, up to 14 regions of strand separation were observed, but when comparisons were made no clear groupings were found. At 51 degrees C, component II molecules were completely separated into a single-stranded circle and a single-stranded linear piece of similar length. Strand separation was accompanied by shortening of the molecule. At 70 degrees C, single-stranded circles had a mean length of 2.7 micro, compared with 5.0 micro for native molecules. Progressive heating of component I molecules resulted first in conversion to an open circle (I') and then to a second supercoiled form (I''). Visualization of further denaturation products of component I was prevented by crosslinking of the molecule by formaldehyde at high temperatures.

Evidence for a relationship between equine abortion (herpes) virus deoxyribonucleic acid synthesis and the S phase of the KB cell mitotic cycle

Autoradiographic analyses of deoxyribonucleic acid (DNA) synthesis in randomly growing KB cell cultures infected with equine abortion virus (EAV) suggested that viral DNA synthesis was initiated only at times that coincided with the entry of noninfected control cells into the S phase of the cell cycle. Synchronized cultures of KB cells were infected at different stages of the cell cycle, and rates of synthesis of cellular and viral DNA were measured. When cells were infected at different times within the S phase, viral DNA synthesis was initiated 2 to 3 hr after infection. However, when cells in G1 and G2 were infected, the initiation of viral DNA synthesis was delayed and occurred only at times corresponding to the S phase. The times when viral DNA synthesis began were independent of the time of infection and differed by as much as 5 hr, depending on the stage of the cell cycle at which cells were infected. Viral one-step growth curves were also related to the S phase in a manner which indicated a relationship between the initiation of viral DNA synthesis and the S phase. These data support the concept that initiation of EAV DNA synthesis is dependent upon some cellular function(s) which is related to the S phase of the cell cycle.

Electron microscopy of kinetoplastic DNA from Trypanosoma mega

The electron microscopical aspect of kinetoplast DNA has been studied in preparations obtained by osmotic disruption of isolated organelles. A large amount of this DNA appears to be of large molecular size. This is apparently at variance with the observations, made by others using a different technical approach, of kinetoplast DNA consisting mainly of small circular molecules of constant size. As a homogeneous population of small circles (0.74 mum in contour length) could also be seen in our samples, the possibility that at least two different kinds of DNA exist in the kinetoplast is discussed.

Induction of cytochromes in human cells by oxygen

The mechanism of cytochrome induction in human cells was investigated. Cultured fibroblasts grown in low oxygen had markedly reduced contents of cytochromes A + A(3), B, and C + C(1) as measured by absorption spectra. Chloramphenicol but not cycloheximide or actinomycin blocked the initial increase in cytochrome oxidase activity in cells shifted from low to ambient oxygen, suggesting that initiation of enzyme induction requires mitochondrial but not cytoplasmic protein synthesis or transcription of nuclear genes. Turnover of cytochrome oxidase was demonstrated in cells in stationary phase.

Mitochondrial deoxyribonucleic acid from Tetrahymena pyriformis and its kinetic complexity

1. Mitochondrial DNA from Tetrahymena pyriformis strain T has a buoyant density (rho) of 1.685 compared with rho1.688 for whole cell DNA. Mitochondrial preparations from T. pyriformis strain W show an enrichment of a light satellite (rho1.686), although this is not obtained free from nuclear DNA (rho1.692). 2. T. pyriformis mitochondrial DNA renatures rapidly and the kinetics of this process indicate a complexity of approx. 3x10(7) daltons. 3. The base-pairing in the renaturation product is of a precise nature, since the ;melting' temperature (80.5 degrees C) is indistinguishable from that of the native DNA (80.5 degrees C). 4. Centrifugation of mitochondrial DNA in an alkaline caesium chloride density gradient gives two bands, implying the separation of the complementary strands.

The form and size of mitochondrial DNA of the red bean, Phaseolus vulgaris

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Replicating molecules of circular mitochondrial DNA

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Renaturation and hybridization studies of mitochondrial DNA

The products of the renaturation reaction of mitochondrial DNA from oocytes of Xenopus laevis have been studied by electron microscopy and CsCl equilibrium density gradient centrifugation. The reaction leads to the formation of intermediates containing single-stranded and double-stranded regions. Further reactions of these intermediates result in large complexes of interlinking double-stranded filaments. The formation of circular molecules of the same length as native circles of mitochondrial DNA was also observed. The formation of common high molecular weight complexes during joint reannealing of two DNA's with complementary sequences was used as a method to detect sequence homology in different DNA samples. Although this method does not produce quantitative data it offers several advantages in the present study. No homologies could be detected between the nuclear DNA and the mitochondrial DNA of X. laevis or of Rana pipiens. In interspecies comparisons homologies were found between the nuclear DNA's of X. laevis and the mouse and between the mitochondrial DNA's of X. laevis and the chick, but none between the mitochondrial DNA's of X. laevis and yeast. These results are interpreted as indicating the continuity of mitochondrial DNA during evolution.

Studies on circular deoxyribonucleic acid. I. Isolation of bovine papilloma virus and characterization of its deoxyribonucleic acid

A simple method is described for the isolation of bovine papilloma virus and its deoxyribonucleic acid (DNA). As found with other representatives of this virus group, this DNA preparation contains two components, I and II, as shown by sedimentation and electron microscopic studies. Component I is a fast-sedimenting, twisted, circular DNA molecule and represents usually 70 to 90% of the DNA in the mixture. The direction of the twist in the superstructure is right-handed. Component II originates from I by one or more single-strand breaks and is the "relaxed" circular from of the viral DNA.

Circular DNA forms of a bacterial sex factor

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Heterogeneous length distribution of circular DNA filaments from yeast mitochondria

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Evidence for circular DNA forms of a bacterial plasmid

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A dye-buoyant-density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells

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