Rearrangement of mitochondrial DNA molecules during the differentiation of mitochondria in yeast. I.-Electron microscopic studies of size and shape

Reaching for the ring: the study of mitochondrial genome structure

The linear molecules that comprise most of the mitochondrial DNA (mtDNA) isolated from most organisms result from the artifactual degradation of circular genomes that exist within mitochondria. This view has been adopted by most investigators and is based on DNA fragment mapping data as well as analogy to the genome-sized circular mtDNA molecules obtained in high yield from animals. The alternative view that linear molecules actually represent the major form of DNA within mitochondria is supported by two observations; (1) over a 1000-fold range of genome size among fungi and plants we find the same size distribution of linear mtDNA molecules, and (2) linear mtDNA molecules much larger than genome size can be found for some fungi and plants. The circles that represent only a small fraction of the mtDNA obtained from most eukaryotes could be optional sequence forms unimportant for mitochondrial function; they may also participate in mtDNA replication. The circles might result from incidental recombination events between directly repeated sequences within or between tandemly arrayed genome units on linear mtDNA molecules.

Mitochondrial DNA from Podospora anserina. II. Properties of mutant DNA and multimeric circular DNA from senescent cultures

Mitochondrial (Mt) DNA from mitochondrial mutants of race s Podospora anserina and from senescent cultures of races s and A was examined. In mutants, we observed that fewer full length circles (31 mu) were present; instead, smaller circles characteristic for each mutant studied were found. Eco R1 digestion of these mutant MtDNAs indicated that in certain mutants, although specific fragments were absent, the total molecular weight of the fragments was not much different than wild-type. The properties of senescent MtDNA was strikingly different from either wild-type or mutant Mt DNA. First, a multimeric set of circular DNA was observed for both race s and A, with a monomeric repeat size of 0.89 mu. These circles ranged in size from 0.89 mu to greater than 20 mu; only one molecule out of some 200 molecules was thought to be of full length (31 mu). Density gradient analysis showed that there were two density species: a majority were at the same density as wild-type (1.694 g/cm3) and a second at 1.699 g/cm3. Most of the circular molecules from MtDNA isolated by either total DNA extraction or by extraction of DNA from isolated mitochondria were contained in the heavy DNA fraction. Eco R1 enzymatic digestion indicated that the light DNA had several fragments (amounting to about 23 x 10(6) daltons) missing, compared with young, wild-type MtDNA. Heavy senescent MtDNA was not cleaved by Eco R1. Analysis with Hae III restriction endonuclease showed also that light senescent MtDNA was missing certain fragments. Heavy MtDNA of average size 20 x 10(6) daltons, yielded only one fragment, 2,500 bp long, by digestion with Hae III restriction endonuclease. Digestion of heavy DNA with Alu I enzyme yielded 10 fragments totalling 2,570 bp. By three criteria, electron-microscopy, Eco R1 and Hae digestion, we conclude that the heavy MtDNA isolated from senescent cultures of Podospora anserina consisted of a monomeric tandemly repeating subunit of about 2,600 bp length. These results on the properties of senescent MtDNA are discussed with regard to the published properties of the rho- mutation in the yeast, S. cerevisiae.

Circular molecules of heterogeneous size from mitochondrial fractions of the petite-negative yeast Schizosaccharomyces pombe

Size and shape of mitochondrial DNA molecules of Schizosaccharomyces pombe were analyzed by electron microscopy. Besides numerous linear molecules, circular molecules ranging from 0.83 micron to 12.81 micron were found. Depending on the method of preparation, both closed and open circular molecules were found. Most of the circular molecules could be assigned to five major size classes of 0.83 +/- 0.05 micron, 1.7 +/- 0.05 micron, 4.74 +/- 0.04 micron, 5.74 +/- 0.04 micron, and 8.32 +/- 0.07 micron. Possible explanations for the different size classes of mitochondrial DNA molecules are discussed.

Electron microscopy of analysis of circular repetitive mitochondrial DNA molecules from genetically characterized rho- mutants of Saccharomyces cerevisiae

1. We have studied mtDNA purified from nine p- petite mutants in which most of the wild type sequence has been deleted but the genetic markers conferring resistance to erythromycin of oligomycin or paromomycin have been retained. 2. All mtDNA contained numerous circular molecules. The size distribution of the circles conformed to a multimeric series which was characteristic for each mutant. We conclude that any one region of the wild type mtDNA molecule, when maintained in a p- clone, while other regions are deleted, can give rise to a multimeric series of circles. 3. In tandem straight repetitive mtDNAs the circles contain odd and even number of unit sequence repeats. In palindrome repetitive mtDNAs the circles contain mostly even number of unit sequence repeats. Thus, one straight or two inverted repeats constitute the monomeric unit of circularization. 4. We found that the frequency distribution of circles follows on a number basis a simple rule: frequency of numeric circles = 1/n frequency of monomeric circles, for n = 2, 3 and 4. Thus, on a mass basis each class represents the same fraction of total mtDNA and the mitochondrial genome has the same probability to constitute one monomeric circle or to be a part of n-meric circle. We interpret this finding that in vivo all molecules are circular. 5. Four mutants displayed a single multimeric series of circles ranging from 0.3 mum to 2.4 mum monomer circle length. Five mutants displayed multiple different multimeric series. In the latter case, the longest unit sequence repeat length was equal to the sum of the two shorter unit sequence repeat lengths. Sorting out, recombination and internal deletions of circular repetitive p- mtDNA molecules are discussed.

Rearrangement of mitochondrial DNA molecules during the differentiation of mitochondria in yeast. II. - Labelling studies of the precursor product relationship

The length distribution in sucrose sedimentation gradient of the newly-synthesized pulse-labelled mitochondrial DNA has been established at an early stage of depression in wild type yeast (Saccharomyces cerevisiae). This stage corresponded to the beginning of mitochondrial differentiation. The radioactive DNA was longer (mean lengths 5, 10 and 22-25 mu) than the preexisting cold DNA (mean length 6.5 mu with two shoulders at 4 mum and 10 mum and one minor peak at 2-2.5 mum). These date confirm that the mean size of the different length populations of linear yeast mitochondrial DNA are under physiological control. Chase experiments were undertaken as follows. The yeast cells were uniformly prelabelled under anaerobiosis. Therefore the mitochondrial DNA molecules were short. Respiratory adaptation was performed in a cold medium and the lengthening process was induced. The specific activities of the long molecules made up during the respiratory adaptation did mot markedly differ from that of prelabelled DNA (decrease of specific activity less than 18 per cent). Molecules as long as 40 mum were also recorded. This lengthening seems to proceed through a non reciprocal exchange of polynucleotide stretches between preexisting molecules. We call it rearrangement. It occurs during the differentiation of mitochondria. Much of the mitochondrial DNA is maintained whereas a small amount of DNA is synthesized. This hypothesis is favoured by recent genetical and physical studies on mitochondrial recombination in yeast.