Physicochemical characterization of mitochondrial DNA from pea leaves

Isolation and physicochemical characterization of mitochondrial DNA from cultured cells ofPetunia hybrida

Mitochondrial DNA ofPetunia hybrida was purified from cell suspension cultures. Up to 50% of the DNA could be isolated as supercoiled DNA molecules by CsCl-ethidium bromide density gradient centrifugation. The DNA purified from DNase-treated mitochondria bands at a single buoyant density of 1.760 gcm(-3) in neutral density gradients and runs on agarose gels as a single band with an apparent molecular weight exceeding 30 megadaltons (Md). Summing of the restriction endonuclease fragment lengths indicates a mitochondrial genome size of at least 190 Md. Electron microscopic analysis reveals the presence of a heterogeneous population of circular DNA molecules, up to 60 Md in size. Small circular DNA molecules, ranging in size from 2-30 Md are present, but unlike in cultured cells of other plant species they do not form discrete size classes and furthermore, they constitute less than 5% of the total DNA content of the mitochondria. The restriction endonuclease patterns of mitochondrial DNA do not qualitatively alter upon prolonged culture periods (up to at least two years).

Mitochondrial gene expression in Cucurbitaceae: conserved and variable features

We have examined mitochondrial DNA (mtDNA) sequence conservation, transcriptional patterns of mitochondrial genes, and mitochondrial translation products in four species of the plant family Cucurbitaceae, in which there is a seven-fold range in mitochondrial genome size. A set of conserved mtDNA sequences which we term "core" DNA is present in all cucurbit genomes examined. In watermelon, only those mtDNA restriction fragments which contain "core" DNA hybridize with mtRNA. Similar numbers of polypeptides are synthesized by isolated mitochondria from all species examined, but an extra set of mtDNA sequences is transcribed in the largest genome (muskmelon). Taken together, these results suggest that some mtRNA is untranslated in muskmelon. Cloned mitochondrial genes of known function, from maize, identified mitochondrial transcripts that varied in both size and number among cucurbit species.

Homology between the ribosomal DNA of Escherichia coli and mitochondrial DNA preparations of maize is principally to sequences other than mitochondrial rRNA genes

E. coli ribosomal DNA has been used to probe maize mitochondrial DNA. It hybridizes primarily with chloroplast ribosomal DNA sequences and with fungal and bacterial sequences which may contaminate the mtDNA preparations. It also hybridizes to the chloroplast 16S ribosomal RNA gene sequence present in the mitochondrial genome (1) as well as to the mitochondrial 18S ribosomal RNA gene sequence. Weak sequence homology was detected between E. coli rDNA and the mitochondrial 26S ribosomal RNA gene.

Recombination sequences in plant mitochondrial genomes: diversity and homologies to known mitochondrial genes

Several plant mitochondrial genomes contain repeated sequences that are postulated to be sites of homologous intragenomic recombination (1-3). In this report, we have used filter hybridizations to investigate sequence relationships between the cloned mitochondrial DNA (mtDNA) recombination repeats from turnip, spinach and maize and total mtDNA isolated from thirteen species of angiosperms. We find that strong sequence homologies exist between the spinach and turnip recombination repeats and essentially all other mitochondrial genomes tested, whereas a major maize recombination repeat does not hybridize to any other mtDNA. The sequences homologous to the turnip repeat do not appear to function in recombination in any other genome, whereas the spinach repeat hybridizes to reiterated sequences within the mitochondrial genomes of wheat and two species of pokeweed that do appear to be sites of recombination. Thus, although intragenomic recombination is a widespread phenomenon in plant mitochondria, it appears that different sequences either serve as substrates for this function in different species, or else surround a relatively short common recombination site which does not cross-hybridize under our experimental conditions. Identified gene sequences from maize mtDNA were used in heterologous hybridizations to show that the repeated sequences implicated in recombination in turnip and spinach/pokeweed/wheat mitochondria include, or are closely linked to genes for subunit II of cytochrome c oxidase and 26S rRNA, respectively. Together with previous studies indicating that the 18S rRNA gene in wheat mtDNA is contained within a recombination repeat (3), these results imply an unexpectedly frequent association between recombination repeats and plant mitochondrial genes.

A review of the structure and organization of the mitochondrial genome of higher plants

The structure, organisation and functions of the mitochondrial genome of most groups of eukaryotic organisms are known to varying degrees with the notable exception of higher plants. With the recent completion of physical mapping studies on the Brassica campestris (Chinese cabbage, turnip) and Zea mays (maize) mitochondrial genomes, many of the apparent problems of plant mitochondrial genome structure can now be answered. In this manuscript I review the literature relating to the physical observations on plant mitochondrial DNA (mtDNA) and assess the data in relation to our current understanding of mitochondrial genome structure.

Mitochondrial DNA heteroplasmy in Drosophila mauritiana

Mitochondrial DNA extracted from an isofemale strain of Drosophila mauritiana (subgroup melanogaster) appeared to be heterogeneous in size. A short genome [S; 18,500 base pairs (bp)] and a longer one (L; 19,000 bp) coexist in the preparation. The additional 500 bp have been located within the A+T-rich region. Hpa I digest patterns suggest that the S genome may carry a duplication of a 500-bp sequence including an Hpa I site and that the L genome may carry a triplication of the same sequence. At the 30th generation of the isofemale strain, 60 female genotypes were examined individually. Half of the files were pure either for the S or the L DNA. The remaining 50% exhibited various degrees of heteroplasmy for the two DNA types. Among metazoan animals, this D. mauritiana strain offers an exceptional situation with regard to the number of individuals heterogeneous for mtDNA and the relative stability of heteroplasmy through generations.

Comparative electrophoretical analysis of plasmid-like mitochondrial DNAs in Vicia faba and in some other legumes

Minicircular DNAs found in mitochondria of 6-d-old etiolated seedlings of Vicia faba L. were also present in mitochondria isolated from cell suspension cultures and from green leaves of this plant. These results support the suggestion that the plasmid-like molecules found in mitochondria of V. faba are an essential component of the mitochondrial genome. The minicircular DNAs were, apparently, peculiar for the species V. faba since they were found in all three cultivars of this species which were studied. The distribution pattern of plasmid-like DNAs in Vicia villosa L. was completely different and mitochondria from Medicago sativa L. also contained specific minicircular DNAs. Thus, minicircular DNAs are typical for the mitochondrial genomes of several legumes and different plant species have their specific mitochondrial plasmid-like DNAs.

Excision and replication of extrachromosomal DNA of pea (Pisum sativum)

Experiments with cultured pea roots were conducted to determine (i) whether extrachromosomal DNA was produced by cells in the late S phase or in the G2 phase of the cell cycle, (ii) whether the maturation of nascent DNA replicated by these cells achieved chromosomal size, (iii) when extrachromosomal DNA was removed from the chromosomal duplex, and (iv) the replication of nascent chains by the extrachromosomal DNA after its release from the chromosomal duplex. Autoradiography and cytophotometry of cells of carbohydrate-starved root tips revealed that extrachromosomal DNA was produced by a small fraction of cells accumulated in the late S phase after they had replicated about 80% of their DNA. Velocity sedimentation of nascent chromosomal DNA in alkaline sucrose gradients indicated that the DNA of cells in the late S phase failed to achieve chromosomal size. After reaching sizes of 70 X 10(6) to 140 X 10(6) daltons, some of the nascent chromosomal molecules were broken, presumably releasing extrachromosomal DNA several hours later. Sedimentation of selectively extracted extrachromosomal DNA either from dividing cells or from those in the late S phase showed that it replicated two nascent chains, one of 3 X 10(6) daltons and another of 7 X 10(6) daltons. Larger molecules of extrachromosomal DNA were detectable after cells were labeled for 24 h. These two observations were compatible with the idea that the extrachromosomal DNA was first replicated as an integral part of the chromosomal duplex, was cut from the duplex, and then, once free of the chromosome, replicated two smaller chains of 3 X 10(6) and 7 X 10(6) daltons.

Characterization of mitochondrial DNA in citrus

Characterization of mitochondrial DNA from leaves of four species of the genus Citrus by electron microscopy shows the presence of circular molecules with a great size dispersion and absence of discrete size classes. Restriction endonuclease patterns confirm the heterogeneity of the molecules.

Cells of pea (Pisum sativum) that differentiate from G2 phase have extrachromosomal DNA

Velocity sedimentation in an alkaline sucrose gradient of newly replicated chromosomal DNA revealed the presence of extrachromosomal DNA that was not replicated by differentiating cells in the elongation zone. The extrachromosomal DNA had a number average molecular weight of 12 X 10(6) to 15 X 10(6) and a weight average molecular weight of 25 X 10(6), corresponding to about 26 X 10(6) and 50 X 10(6) daltons, respectively, of double-stranded DNA. The molecules were stable, lasting at least 72 h after being formed. Concurrent measurements by velocity sedimentation, autoradiography, and cytophotometry of isolated nuclei indicated that the extrachromosomal molecules were associated with root-tip cells that stopped dividing and differentiated from G2 phase but not with those that stopped dividing and differentiated from G1 phase.

Mitochondrial modifications associated with the cytoplasmic male sterility in faba beans

Isolated mitochondria of faba beans carrying two different determinisms of the cytoplasmic male sterility (cytoplasms 447 and 350) have been compared to fertile lines. 1. In addition to the major mitochondrial DNA, five small DNA species (in the range of 1000-2000 base pairs) were detected by agarose gel electrophoresis in the four cytoplasms. An additional small DNA species was found specifically in the cytoplasm 350. After endonuclease restriction of the mitochondrial DNA, the patterns obtained for both male-sterile cytoplasms were identical to each other but distinct by two to four fragments from the patterns obtained for male-fertile cytoplasms. 2. [35S]Methionine labeling in situ of the mitochondrial protein synthesis revealed an additional polypeptide (Mr = 25000) detected only in the two male-sterile cytoplasms. 3. The male-sterile cytoplasm 350 showed a decrease of the respiratory state 3 of oxygen uptake during oxidation of NADH or malate + pyruvate. This decrease is thought to reflect a smaller capacity of the respiratory chain. These specific mitochondrial modifications support the hypothesis of a mitochondrial localization of the cytoplasmic male sterility determinant in faba beans.

Extranuclear DNA of a Marine Chromophytic Alga : RESTRICTION ENDONUCLEASE ANALYSIS

Two extranuclear DNA species have been isolated from the marine alga Olisthodiscus luteus. Rapid lysis of cells followed by the immediate addition of CsCl to the lysate was critical to the preservation of these satellite DNA species. Restriction endonuclease analysis demonstrates a molecular weight of 99 x 10(6) for chloroplast DNA and 23 x 10(6) for a second satellite species. The origin of the second satellite is not known. However, this smaller satellite DNA which originates from a nonnuclear, DNAse insensitive cellular component, displays no sequence homology with ctDNA by hybridization experiments. Constancy of restriction endonuclease fragment patterns of chloroplast and second satellite species during all phases of the growth cycle, whether cultures were maintained synchronously or asynchronously, was demonstrated.

Cells of pea (Pisum sativum) that differentiate from G2 phase have extrachromosomal DNA

Velocity sedimentation in an alkaline sucrose gradient of newly replicated chromosomal DNA revealed the presence of extrachromosomal DNA that was not replicated by differentiating cells in the elongation zone. The extrachromosomal DNA had a number average molecular weight of 12 X 10(6) to 15 X 10(6) and a weight average molecular weight of 25 X 10(6), corresponding to about 26 X 10(6) and 50 X 10(6) daltons, respectively, of double-stranded DNA. The molecules were stable, lasting at least 72 h after being formed. Concurrent measurements by velocity sedimentation, autoradiography, and cytophotometry of isolated nuclei indicated that the extrachromosomal molecules were associated with root-tip cells that stopped dividing and differentiated from G2 phase but not with those that stopped dividing and differentiated from G1 phase.

Mitochondrial genes at Cold Spring Harbor

The flowering dogwood trees and green lawns of Cold Spring Harbor provided the setting for a meeting devoted to Mitochondrial Genes from May 13-17th, 1981. Dedicated to the memory of Boris Ephrussi, who pioneered mitochondrial genetics at a time when the only kinds of genetics were nuclear or unclear, the meeting showed that the study of mtDNA has had impact on many areas of molecular biology including the genetic code and decoding, tRNA function, mechanisms of splicing and molecular evolution. Curiously, as Herschel Roman pointed out in his opening address, Ephrussi took great pains to avoid any mention of mitochondrial DNA in connection with his observations on cytoplasmic inheritance, preferring instead to refer to 'cytoplasmic particles, endowed with genetic continuity' (Ephrussi 1953). This reticence was not shared by participants at the meeting, as the following, brief report will show.

The integrated forms of the S1 and S2 DNA elements of maize male sterile mitochondrial DNA are flanked by a large repeated sequence

The mitochondrial DNA of maize was cloned using the cosmid, Homer I. Recombinants carrying sequences homologous to the S1 and S2 DNA elements of male sterile maize have been analysed. Restriction endonuclease maps for Sac II, Sma I and Bam HI have been constructed. The S1 and S2 sequences are single copy sequences occurring at unique sites; each is flanked by a 26 kb repeated sequence. The repeated sequence has been shown not to contain the mitochondrial ribosomal RNA genes.

Mitochondrial DNA from Oenothera berteriana: PURIFICATION AND PROPERTIES

Mitochondrial DNA (mt-DNA) from Oenothera berteriana tissue culture cells was isolated and characterized with respect to buoyant density in CsCl, melting point, contour length, and restriction fragments.Because of the rather long purification procedure very few molecules retained their circularity. Only one distinct size class of molecules with a length of 100 kilobases was found. Restriction fragments were obtained with the enzymes, restrictionendonuclease I from Serratia marcescens, restrictionendonuclease III from Haemophilus influenzae, restrictionendonuclease I from Bacillus amyloliquefaciens H, and restrictionendonuclease I from Escherichia coli (Bohnert 1977 Exp Cell Res 106: 426-430); the added lengths of these fragments amounted to 180 to 190 kilobases. As in other higher plants, an intermolecular heterogeneity has to be postulated to explain the large number of restriction fragments. Unique to the mt-DNA from Oenothera berteriana, as compared to other higher plants, is the unusual high guanosine + cytosine content with 51% as determined by the buoyant density in CsCl of 1.710 grams/cubic centimeter and the melting point of 90 C.

Organization and expression of the mitochondrial genome of plants I. The genes for wheat mitochondrial ribosomal and transfer RNA: evidence for an unusual arrangement

We show here that mitochondrial-specific ribosomal and transfer RNAs of wheat (Triticum vulgare Vill. [Triticum aestivum L.] var. Thatcher) are encoded by the mitochondrial DNA (mtDNA). Individual wheat mitochondrial rRNA species (26S, 18S, 5S) each hybridized with several mtDNA fragments in a particular restriction digest (Eco RI, Xho I, or Sal I). In each case, the DNA fragments to which 18S and 5S rRNAs hybridized were the same, but different from those to which 26S rRNA hybridized. From these results, we conclude that the structural genes for wheat mitochondrial 18S and 5S rRNAs are closely linked, but are physically distant from the genes for wheat mitochondrial 26S rRNA. This arrangement of rRNA genes is clearly different from that in prokaryotes and chloroplasts, where 23S, 16S and 5S rRNA genes are closely linked, even though wheat mitochondrial 18S rRNA has previously been shown to be prokaryotic in nature. The mixed population of wheat mitochondrial 4S RNAs (tRNAs) hybridized with many large restriction fragments, indicating that the tRNA genes are broadly distributed throughout the mitochondrial genome, with some apparent clustering in regions containing 18S and 5S rRNA genes.

Characterisation of mycobacteriophage ATCC 11759. Unusual physiocochemical properties of its DNA

Growth conditions and a purification procedure for mycobacteriophage ATCC 11759, a lytic phage for Mycobacterium smegmatis, are described. The phage is a large DNA phage with a very long tail (240 nm). A study of its DNA revealed three interesting features. 1. After denaturation the DNA molecule yields two strands of different buoyant densities. 2. The native DNA has unusual physical properties: its buoyant density in CsC1 is very low (1.654 g/cm3), its sedimentation rate is lower than expected for the molecular weight, its thermal stability at low ionic strength is high. 3. The DNA (in its native form or after reannealing) is resistant to various restriction endonucleases.

Isolation and characterization of mitochondrial DNA from Chlamydomonas reinhardtii

Mitochondrial DNA (mtDNA) has been isolated from a mitochondrial pellet of Chlamydomonas reinhardtii. The mtDNA has a buoyant density of 1.706 g/ml in CsCl, a melting temperature of 87.9 degrees in standard saline citrate, and a nucleoside composition of 47.5% deoxyguanidine plus deoxycytidine with no odd nucleosides. Thermal denaturation and renaturation studies have shown that (i) mtDNA contains no extensive intramolecular heterogeneity nor significant base bias between the complementary polynucleotide chains and (ii) mtDNA renatures as a single homogeneous class with a kinetic complexity of 9.78 X 10(6) daltons. Although rare (less than or equal to 1%), both open and supercoiled circular mtDNA molecules have been observed in the electron microscope. Contour lengths of linear and open and closed circular molecules are all within the range of 4.0-5.4 micron with a mean of 4.67 +/- 0.30 micron. This size is similar to that of animal mtDNA but approximately 1/8 that of the higher plant mtDNAs. The magnitude of mtDNA reiteration in C. reinhardtii is estimated to be of the same order as that of chloroplast DNA.

Physicochemical characterization of mitochondrial DNA from soybean

Mitochondrial DNA (mtDNA) of soybean (Glycine max L.) was isolated and its buoyant density was contrasted with that of nuclear (nDNA) and chloroplast (ctDNA) DNA. Each of the three DNAs banded at a single, characteristic buoyant density when centrifuged to equilibrium in a CsCl gradient. Buoyant densities were 1.694 g/cm(3) for nDNA and 1.706 g/cm(3) for mtDNA. These values correspond to G-C contents of 34.7 and 46.9%, respectively. Covalently closed, circular mtDNA molecules were isolated from soybean hypocotyls by ethidium bromide-cesium chloride density gradient centrifugation. Considerable variation in mtDNA circle size was observed by electron microscopy. There were seven apparent size classes with mean lengths of 5.9 mum (class 1), 10 mum (class 2), 12.9 mum (class 3), 16.6 mum (class 4), 20.4 mum (class 5), 24.5 mum (class 6), and 29.9 mum (class 7). In addition, minicircles were observed in all preparations. Partially denatured, circular mtDNA molecules with at least one representative from six of the seven observed size classes were mapped. In class 4, there appear to be at least three distinct denaturation patterns, indicating heterogeneity within this class. It is proposed that the mitochondrial genome of soybean is distributed among the different size circular molecules, several copies of the genome are contained within these classes and that the majority of the various size molecules may be a result of recombination events between circular molecules.

Heterogeneous base distribution in mitochondrial DNA of Neurospora crassa

The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+C rich, part of the genome.

On the question of integration of Agrobacterium tumefaciens deoxyribonucleic acid by tomato plants

Treatment of tomato plants with Agrobacterium tumefaciens causes subsequently administered [3H]thymidine to be preferentially incorporated into a satellite deoxyribonucleic acid (DNA) whose buoyant density is between that of bacterial DNA (rho = 1.718 g/cm3) and plant main band DNA (rho = 1.692 g/cm3). Satellite DNA upon shearing or sonic treatment releases fragments of higher and lower buoyant density, as reported by earlier investigators. The satellite has no significant base sequence homology with A. tumefaciens DNA, for its rate of reassociation is not accelerated by the addition of high concentrations of the latter. Tomato DNA isolated from shoots or from leaf nuclei accelerates renaturation of labeled satellite DNA. We conclude that the intermediate density labeled DNA is a plant satellite and not the product of covalent joining of bacterial and plant DNA as suggested by earlier investigators.

The complexity of satellite deoxyribonucleic acid in a higher plant

Purified satellite DNA from melon (Cucumis melo) was shown to contain at least two components from thermal-denaturation and renaturation studies. Two components were separated after partial renaturation, a fast-renaturing fraction similar in complexity to mouse satellite DNA, and one with 6000 times greater complexity. Both components renatured very accurately, indicating a minimum of sequence divergence. Centrifugation of the purified satellite DNA in Ag+/Cs2SO4 gradients resolved two major and several minor fractions. The two major fractions were only slightly enriched for fast- or slow-renaturing sequences.

Purification and quantitative changes of mitochondrial DNA in etiolated cucumber seedlings

The mtDNA (mitochondrial DNA) extracted from etiolated seedlings of Cucumis sativus L. has been purified by a three-step procedure: RNase and pronase treatment, bio-gel filtration, analytical CsCl gradient centrifugation. This procedure appeared rapid, suitable for small quantities of DNA and gave highly reproducible results. It was used to follow the quantitative variation of the mtDNA in hypocotyls and cotyledons of dark-grown cucumber seedlings.The major feature occurring during the etiolation process appeared to be an important accumulation of the mtDNA in hypocotyls between 3 and 5 days of culture. The amount of the mtDNA per hypocotyl increased 5 times, the hypocotyl length and the total DNA increased 6 and 12 times respectively, between these two stages. It was demonstrated that at least during the first week of culture in the dark, endogeneous hormone-induced elongation in the cucumber hypocotyl (a non-dividing tissue) was associated to an important accumulation of mtDNA.

Conservation of 70S ribosomal RNA genes in the chloroplast DNAs of higher plants

Chloroplast DNAs of higher plants have been found to contain two chloroplast ribosomal RNA genes. The base sequences of these chloroplast ribosomal RNA genes in chloroplast DNAs have been studied by molecular hybridization. The results have shown that these genes have undergone little divergence in the evolution of either monocotyledonous or dicotyledonous plants.

Isolation and characterization of mitochondrial deoxyribonucleic acid of Acanthamoeba castellanii

DNA was prepared from isolated mitochondria of Acanthamoeba castellanii and was shown to behave as a single component in density gradients, on ;melting' and on renaturation. From measurements of renaturation kinetics, sedimentation coefficient and electron micrographs the genome size of the mitochondrial DNA was calculated to be about 3.4x10(7) daltons. A small proportion of the preparations could be isolated as relaxed circular molecules of mean contour length 16.2mum.