In vitro DNA fragmentation of mitochondrial DNA caused by single-stranded breakage related to macroplasmodial senescence of the true slime mold, Physarum polycephalum

We found that mitochondrial DNA (mtDNA) isolated from Physarum polycephalum fragmented itself in weak ionic solutions. The mtDNA was dissolved in STE (saline Tris-EDTA: 150 mM NaCl, 10 mM Tris-HCl, 1 mM EDTA), TE (10 mM Tris-HCl, 1 mM EDTA) and DW, and then electrophoresed in an agarose gel. The intact 86-kbp mtDNA band was seen in STE, but several novel bands appeared in TE and DW. In TE, two discrete bands appeared at 6.7-kbp (α-band) and 5.0-kbp (β-band), whereas at least 17 discrete bands were observed in distilled water (DW). These fragmentation patterns were not stoichiometric, as seen when using restriction endonucleases, but were clearly different from the degradation of DNA caused by a physical shearing force or a contaminating nuclease. In this paper, we characterize this in vitro fragmentation of mtDNA from P. polycephalum. We located 19 fragments, including the α and β fragments, on a mtDNA restriction map, and demonstrated that these cleavage sites were S1 nuclease-sensitive regions, which are single-stranded DNA regions such as nicks and gaps in the mtDNA. The α and β fragments are derived from the region encoding ribosomal RNAs (rRNAs) and the ATP synthase (atpA) gene, while the other 17 fragments are not derived from any specific region, but the cleavage sites are located throughout the mtDNA molecule. In P. polycephalum, it is well known that the growth rate of macroplasmodia decreases with aging. Equal amounts of mtDNA from juvenile and aged macroplasmodia were electrophoresed and the frequency of the β fragment in each sample was measured. The ratio of the β band to the total signal including background was estimated to be 3.3–4.0% in juvenile macroplasmodia, whereas it increased to 8.3–28.2% in aged macroplasmodia. This result suggests that the in vitro fragmentation of mtDNA is associated with macroplasmodial senescence. The single-stranded breakage of mtDNA of P. polycephalum may accumulate with age. Received: 16 April / 2 September 1999     

The mitochondrial plasmid of the true slime mold <Emphasis Type="Italic">Physarum polycephalum</Emphasis> bypasses uniparental inheritance by promoting mitochondrial fusion

Mitochondrial DNA (mtDNA) is inherited maternally in most eukaryotes. Linear mitochondrial plasmids in higher plants and fungi are also transmitted from the maternal parent to the progeny. However, mF, which is a mitochondrial linear plasmid of Physarum polycephalum, evades uniparental mitochondrial inheritance. We examined 36 myxamoebal strains of Physarum and isolated three novel mF⁺ strains (JE8, TU111, NG111) that harbored free mF plasmids. These strains were mated with the mF^– strain KM88. Of the three mF^– × mF⁺ crosses, only KM88 × JE8 displayed complete uniparental inheritance. However, in KM88 × TU111 and KM88 × NG111, the mtDNA of KM88 and mF of TU111 and NG111 were inherited by the plasmodia and showed recombination. For example, although the mtDNA of TU111 was eliminated, the mF of TU111 persisted and became inserted into the mtDNA of KM88, such that recombinant mtDNA represented 80% of the total mtDNA. The parental mitochondria fused to yield giant mitochondria with two or more mitochondrial nucleoids. The mF appears to exchange mitochondria from the recipient (paternal) to the donor (maternal) by promoting mitochondrial fusion.The first two authors have equally contributed to this work     

A pair of invertedly repeated genes in Chlamydomonas reinhardtii encodes a zygote-specific protein whose expression is UV-sensitive

Uniparental inheritance of the chloroplast genome has been observed in a wide variety of green plants. In Chlamydomonas this phenomenon, which can be selectively inhibited by UV irradiation of mt ⁺ gametes, has been shown cytologically to be due to the preferential degradation of mt ⁻-derived chloroplast nucleoids in young zygotes. The zygote-specific pair of zys1 genes, zys1A and zys1B, is expressed earliest among five genes isolated from a “10-min” zygote library. We report here that the ZYS1 protein, which is encoded by the invertedly duplicated zys1 gene, accumulates in zygotes and is localized in nuclei. In addition, when mt ⁺ gametes (but not mt ⁻ gametes) are UV-irradiated before mating, only very limited accumulation of ZYS1 protein can be detected in the resulting zygotes. Received: 29 July 1998 / 30 April 1999     

Uniparental inheritance of the mitochondrial gene cytochrome b in Plasmodium falciparum

The inheritance of an extrachromosomal 6-kb element has been examined in the human malaria parasite Plasmodium falciparum. A single base pair difference in the cytochrome b gene from the 6-kb element of two different cloned lines of the parasite was identified, and used as a marker in a cross in the mosquito stage of the life cycle. Analysis of 59 individual hybrid oocysts resulting from this cross clearly demonstrated that inheritance of the cytochrome b gene was uniparental. This observation makes it possible to investigate the inheritance and evolution of cytoplasmic traits, including certain forms of drug resistance, in natural populations of this parasite.     

Restriction map of the mitochondrial DNA of the true slime mould,Physarum polycephalum: linear form and long tandem duplication

Summary The mitochondrial DNA (mtDNA) of the true slime mould, Physarum polycephalum strain CH934xCH938, was isolated and characterized by restriction mapping. Cloned fragments of the mtDNA were assembled and used to construct the restriction map. This map showed that the mtDNA was a linear molecule of 86.0 kb with a tandem duplication of 19.6 kb. The terminal fragments were identified by sensitivity to Bal31 exonuclease. One of the duplications was located at the right end and the other was located 5 kb from the left end. Each duplicated segment contained 26 restriction sites for ten enzymes and these restriction sites were completely conserved in each duplication. Genes for the large and small rRNAs were mapped to positions about 30 kb from the right end of the mtDNA by hybridization with its own rRNAs. With the exception of a probe for the gene for the large rRNA in Tetrahymena pyriformis mtDNA, various probes from the mtDNAs of Saccharomyces cerevisiae and T. pyriformis showed no significant hybridization to any of the restriction fragments of the mtDNA from P. polycephalum.     

Mitochondrial DNA rearrangements associated with mF plasmid integration and plasmodial longevity in Physarum polycephalum

Plasmodial cultures of Physarum polycephalum have defined life spans and undergo a reproducible decline (senescence) before losing the ability to be subcultured. Studies of the mtDNA of a long-lived Physarum strain, which does not undergo senescence, revealed a 7.9-kb insertion in its mtDNA. This insertion is derived from a mitochondrial plasmid which enhances mitochondrial fusion and mtDNA recombination. Four different recombination events are required to convert the parental mtDNA to the form found in the long-lived strain. An additional recombination event, which deletes a 2.4-kb region of the insert from the long-lived strain, has been identified in the mtDNA of a normally senescing strain. These observations imply a mitochondrial involvement in the process of plasmodial senescence and implicate a region of the DNA derived from the mitochondrial plasmid as being necessary for plasmodial longevity. Received: 11 August / 18 November 1997     

Smart behavior of true slime mold in a labyrinth.

Even for humans it is not easy to solve a maze. But the plasmodium of true slime mold, an amoeba-like unicellular organism, has shown an amazing ability to do so. This implies that an algorithm and a high computing capacity are included in the unicellular organism. In this report, we discuss information processing in the microorganism to focus on the issue as to whether the maze-solving behavior is akin to primitive intelligence.     

Telomeric structures in a linear mitochondrial plasmid from Physarum polycephalum

Summary A mitochondrial plasmid was isolated from Physarum polycephalum and characterized by restriction mapping. Cloned fragments of the plasmid were assembled and used to construct a restriction map. This plasmid was a linear molecule with telomeric structures at each end. Southern hybridization with the ends of the plasmid as probes revealed that the plasmid included repeating units at both ends, with each unit being approximately 125 bp in length. The most extensive array of repeats consisted of at least 17 repetitions of the 125-bp unit. The sensitivity of these repeats to Bal31 exonuclease confirmed that they were at, or very near to, the ends of the plasmid. From the extent of the repetitions, the size of the plasmid was estimated to vary from 13.3 kbp to more than 18.3 kbp.     

Rapid disappearance of one parental mitochondrial genotype after isogamous mating in the myxomycete Physarum polycephalum

Summary Five haploid amoebal strains of the myxomycete Physarum polycephalum, each with a distinct mitochondrial genotype, were crossed in all pairwise combinations. The mitochondrial genotype in the diploid plasmodia resulting from these isogamous matings were found to be transmitted uniparentally. This uniparental inheritance could be arranged in a dominant hierarchical order. Time-course analysis of the presence of mitochondrial genotypes in the zygotes and young developing plasmodial genotypes is virtually completed during the first two nuclear cycles in the zygote/differentiating plasmodium. To our knowledge this is the first report indicating an active mechanism involving the degradation of mitochondrial genomes in sexual crosses.     

Rearrangements in the Physarum polycephalum mitochondrial genome associated with a transition from linear mF-mtDNA recombinants to circular molecules

Although mitochondrial DNA (mtDNA) is transmitted to progeny from one parent only in Physarum polycephalum, the mtDNAs of progeny of mF⁺ plasmodia vary in structure. To clarify the mechanisms associated with the mitochondrial plasmid mF that generate mtDNA polymorphisms, 91 progeny of four strains (KM88 × JE8, KM88 × TU111, KM88 × NG111, Je90) were investigated using RFLP analysis, PCR, and pulse-field gel electrophoresis (PFGE). Nine mtDNA rearrangement types were found, with rearrangements occurring exclusively in the mF regions. PFGE revealed that, in the groups containing rearranged mtDNA, the linear mF–mtDNA recombinants had recircularized. Sequencing the rearranged region of one of the progeny suggested that the mF plasmid and the mtDNA recombine primarily at the ID sequences, linearizing the circular mtDNA. Recombination between the terminal region of the mF plasmid and a region about 1 kbp upstream of the mitochondrial/plasmid ID sequence results in a rearranged circular mtDNA, with variations caused by differences in the secondary recombination region.     

Evaluation of the efficiency of sexual reproduction in restoring Podospora anserina mitochondrial DNA to wild-type

A Podospora anserina mitochondrial DNA (mtDNA) rearrangement mutant, Mn19, was crossed with a deletion mutant, αΔ5. Ascospores (212) from random asci were tested for viability, growth and life-span phenotypes, and mtDNA inheritance. Some spore inviability was detected along with early growth arrest (at the time of spore germination) from which some isolates recovered. However, the majority had wild-type growth and life-span phenotypes. All isolates tested at the DNA level (102) had wild-type mtDNA hybridization patterns with probes that detected defects in the parents. About 20% also inherited low levels of mtDNA molecules with the rearrangement characteristic of the Mn19 parent. These results demonstrate that P. anserina has a remarkable ability, through sexual reproduction, to restore its mtDNA to wild-type, even when the parents are predominately mutant. Received: 3 January / 25 July 1997     

The fate of mitochondrial DNAs of mt + and mt − origin in gametes and zygotes of Chlamydomonas

Summary In order to study the mechanism responsible for the uniparental transmission of the mitochondrial genome in crosses between Chlamydomonas reinhardtii and C. smithii, we have analyzed the fate of mitochondrial DNA during gametogenesis, zygospore differentiation and sporulation by hybridization experiments. Both mt ⁺ and mt ^– gametes contain the same amount of mitochondrial DNA and the two parental genomes persist for several days in the zygotes. The DNA of mt ⁺ origin is slowly eliminated during the period of zygote maturation. Light is required for total elimination of mt ⁺ mitochondrial DNA in the zygospores. Using appropriate restriction enzymes, we have been unable to detect methylation of the mitochondrial DNA during gametogenesis or zygospore formation. The possibility that the mt ⁺ mitochondria themselves are specifically eliminated in the course of zygote maturation is discussed.     

Detection and analysis of “CpG-rich” islands in the genome of Physarum polycephalum

Summary A small fraction (Physarum polycephalum contains a high-density of cleavage sites for the restriction endonuclease HpaII. This component can be distinguished from the bulk of the DNA by ³²P-end-labelling followed by size-fractionation using agarose-gel or polyacrylamide-gel electrophoresis. In contrast to the situation in mammalian-cell DNA, where the majority of such small HpaII DNA fragments are derived from CpG-rich islands within diverse single-copy sequences located in the proximity of housekeeping genes, most of the Physarum small HpaII DNA fragments form an array of distinct bands when analysed on polyacrylamide gels, indicating that they are repetitive DNA sequences. Direct sequence analysis shows that the majority of these sequences are derived from the Physarum rDNA minichromosome.     

Morphology of the mitochondria in heat shock protein 60 deficient fibroblasts from mitochondrial myopathy patients. Effects of stress conditions

We have described two mitochondrial (mt) myopathy patients with reduced activities of various mt enzymes associated with significantly decreased amounts of heat shock protein 60 (hsp60). Experimental evidence suggested that the lack of hsp60 was the primary defect. Since hsp60 is essential for the proper folding of enzyme subunits in the mt matrix a partial deficiency of this protein can explain the observed defects of the mitochondria. Here we report on morphological studies aimed at obtaining more insight into the relation between lack of hsp60 and pathological changes of the mitochondria. Under standard culture conditions mitochondria in the partially hsp60 deficient fibroblasts showed profound morphological aberrations. In contrast, the mitochondria in fibroblasts from a MELAS patient and a cytochrome c oxidase-deficient patient appeared normal. Under stress conditions the integrity of the hsp60 deficient mitochondria declined even further: heat shock induced a temporary collapse of the electrochemical potential across the inner mt membrane, but did not affect the ultrastructure of the mitochondria; prolonged growth in confluent cultures resulted in decrease in mt number. The altered mt morphology in the hsp60 deficient cells is probably indicative of the severely impaired mt metabolism whereas the decreased stress tolerance is likely to be a direct result of paucity of the heat shock protein. Both variables are potentially useful in the diagnosis and molecular characterization of mt disorders with systemic manifestation and multiple enzyme deficiency.     

Analysis of mitochondrial DNA and its inheritance in Populus

Summary The mitochondrial genome of several poplar clones has been characterized by restriction analysis and hybridization with gene probes from Oenothera. The mitochondrial (mt) DNA of Populus has a complex restriction fragment pattern and its genome size was estimated to be about 450 kilobase pairs (kb). Restriction fragment length polymorphisms (RFLPs) could be detected only between, and not within, species of Populus and were used as genetic markers to follow mitochondrial inheritance. Location of the apocytochrome b (cob) gene on different Eco RI or Hin dIII fragments in Muhle Larsen (P. trichocarpa) and Androscoggin (P. maximowiczii × P. trichocarpa) has been used for analysis of mitochondrial inheritance. All hybrids investigated exhibit a fragment pattern identical to that of the female parent. Hybridization with other gene probes (coxIII/HindIII, coxIII/SalI, coxIII/Xho I, atp6/Bgl1, atp6/Hco RI, atp6/Hin dIII, nad1/Hin dIII, nad1/Sal I, nad1/Xba I) showed the same results as given by cob hybridization. Thus, mtDNA seems to be inherited maternally in Populus.     

Occurrence of nuclear-encoded tRNAIle in mitochondria of the liverwort Marchantia polymorpha

 Although 29 tRNA genes have been deduced from the complete nucleotide sequence of the mitochondrial genome from the liverwort Marchantia polymorpha, a tRNA^Ile gene decoding AUU and AUC codons is conspicuously absent. In order to address the question of the possible involvement of nuclear-encoded tRNA, we isolated and identified three variant copies of the nuclear-encoded tRNA^Ile(AAU) gene from the liverwort. Northern analysis showed the presence of nuclear-encoded tRNA^Ile both in the mitochondrion and the cytosol, while both chloroplast DNA-encoded tRNA^Ile and nuclear-encoded tRNA^Tyr were absent in liverwort mitochondria. These results unequivocally establish that import of nuclear tRNA^Ile into mitochondria indeed occurs in one of the most primitive plants, M. polymorpha. Received: 11 January 1996/18 March 1996     

Loss of mt +-derived zygotic chloropiast DNA is associated with a lethal allele in Chlamydomonas monoica

Summary The Chlamydomonas monoica mutant allele mtl-1, is associated with the formation of nonviable zygospores following self-mating of the mutant strain. Furthermore, mtl-1 heterozygote populations show a 50% reduction in germination frequency and no transmission of a chloroplast antibiotic resistance marker carried by the mtl-1 parent. To determine whether the effects on zygospore viability and chloroplast gene transmission resulted from the direct involvement of the mtl-1 locus in the control of mt ⁺-directed uniparental inheritance of chloroplast DNA (cpDNA), we have used the DNA-specific fluorochrome DAPI to follow the fate of cpDNA during the maturation of zygotes. Throughout the first few hours after the initial fusion of gametes, the young zygotes show DAPI-fluorescent nucleoids distributed symmetrically around the region of nuclear fusion, and presumably located within both of the parental chloroplasts. Wild-type and mtl-1 mutant zygotes show similar early staining patterns. As the zygotes age, the staining patterns become asymmetric for the wildtype population, with all of the visible cytoplasmic nucleoids restricted to one side of the zygote. In contrast, mtl-1 homozygotes appear to lose cytoplasmic nucleoids from both sides of the zygote simultaneously and within 24 h are apparently devoid of cpDNA. By introducing a mutation which arrests cell fusion (and prevents plastid fusion), we can show that (1) the asymmetric nucleoid distribution in wildtype zygotes results from the loss of nucleoids from one gamete in each mating event, and (2) the additional loss of cpDNA in mtl-1 homozygotes does not require contact between parental plastids (thus the nuclease responsible for cpDNA degradation is not sequestered within the chloroplast of one gamete). We propose that the mtl-1 mutant strain is defective for a process which normally protects cpDNA of mt ⁺ origin.