Isolation of a membrane-DNA-RNA complex from rat liver mitochondria

DNA-binding proteins of mammalian mitochondria

Acid-soluble proteins were isolated from liver and spleen mitochondria and their ability to form complexes with DNA was investigated. According to electrophoresis data, acid-soluble proteins include about 20 polypeptides ranging in the molecular mass from 10 to 120 kDa. It was found that acid-soluble proteins form stable DNA-protein complexes at a physiological NaCl concentration. Different polypeptides possess different degrees of DNA affinity. There is no significant difference between DNA-binding proteins of mitochondria from liver and those from spleen as to their ability to form complexes with mtDNA and nDNA. In the presence of 5 microg of DNA most polypeptides were bound to DNA, and further increase in DNA amount affected little the binding of proteins to DNA. There was no distinct difference in DNA-protein complex formation of liver mitochondrial acid-soluble proteins with nDNA or mtDNA. Also, it was detected that with these mitochondrial acid-soluble proteins, proteases that specifically cleave these proteins are associated. It was shown for the first time that these proteases are activated by DNA. DNA-binding proteins including DNA-activated mitochondrial proteases are likely to participate in the regulation of the structural organization and functional activity of mitochondrial DNA.

Protein Components of Mitochondrial DNA Nucleoids in Higher Eukaryotes

Mitochondrial DNA (mtDNA) is not packaged in nucleosomal particles, but has been reported to associate with the mitochondrial inner membrane. Gentle lysis of Xenopus oocyte mitochondria with nonionic detergent liberates a nucleoprotein complex containing mtDNA associated with a previously characterized DNA binding partner, mitochondrial transcription factor A (mtTFA), as well as a series of inner membrane proteins identified by sequencing. More extensive detergent treatment stripped most of these proteins from the DNA, leaving a limited number of proteins in a nucleoid core. Sequencing of the major proteins retained in association with mtDNA revealed the expected mtDNA binding proteins, mtTFA and mitochondrial single-stranded DNA binding protein (mtSSB), as well as four proteins not previously reported to associate with mtDNA. These include adenine nucleotide translocator 1, the lipoyl-containing E2 subunits of pyruvate dehydrogenase and branched chain alpha-ketoacid dehydrogenase and prohibitin 2. The association of several of these proteins with mtTFA-containing mtDNA nucleoids was confirmed by immunoprecipitation.

Isolation and characterization of a membrane-DNA complex in the mitochondria of Physarum polycephalum

A membrane-DNA complex was isolated by centrifugation of sheared lysate of isolated mitochondria in 20-60% sucrose step solution. Analyses using Hoechst 33258/CsCl density gradient centrifugation and restriction endonuclease treatment showed that DNA in the membrane-DNA complex was AT-rich compared with total mitochondrial DNA (mt DNA) and contained Eco RI fragments of E-4, 5 and 8, which were localized on the right hand of Physarum mitochondrial genome. Phenethyl alcohol (PEA) and ethidium bromide (EB) could disrupt the membrane-DNA complex to release DNA fragments from their complex in vitro. Addition of 0.5% or more PEA, which released 80-90% of the DNA from the membrane-DNA complex in vitro, inhibited not only mitochondrial nuclear division but also mitochondrial division in vivo. EB treatment at more than 1 mg/ml disrupted the membrane-DNA complex in vitro to release 77% of the total DNA in the complex. Addition of 10 micrograms/ml EB induced unequal mitochondrial nuclear division in the microplasmodia, e.g., a dividing dumbbell-shaped mitochondrion had the mt-nucleus in one side and as a result formed then one nucleated and one enucleated mitochondrion. From the EB-pretreated mitochondria, a lesser amount of the membrane-DNA complex was isolated than from the control. These findings mean than the unequal mt-nuclear division is due to dissociation of DNA and the membrane system in the membrane-DNA complex. They strongly suggested that the DNA region (E-4, 5 and 8), where the mitochondrial nucleus is associated with the mitochondrial membrane system plays an important role in mitochondrial nuclear division.

Covalent binding of benzene and its metabolites to DNA in rabbit bone marrow mitochondria in vitro

Rabbit bone marrow mitochondria, stripped of their outer membrane (mitoplasts), have been shown to carry out the NADPH-dependent bioactivation of radiolabelled benzene in vitro to metabolites capable of covalently binding to mtDNA, thereby inhibiting transcription. The metabolites of benzene produced in bone marrow cells by the microsomal cytochrome P-450 are thought to be phenol, catechol, hydroquinone and p-benzoquinone (Andrews et al., Life Sci., 25 (1979) 567; Irons et al., Chem.-Biol. Interact., 30 (1980) 241). Incubation of mitoplasts from rabbit bone marrow cells in vitro with varying concentrations of the putative microsomal metabolites showed a concentration-dependent inhibition of RNA synthesis. The 50% inhibitory molar concentration (IC50) for each metabolite was determined to be: 1,2,4- benzenetriol , 6.3 X 10(-7); p-benzo-quinone, 2 X 10(-6); phenol, 2.5 X 10(-5); hydroquinone, 5 X 10(-5); catechol, 2 X 10(-3); benzene, 1.6 X 10(-2). DNA, isolated from rabbit bone marrow cell or rat liver mitoplasts prelabelled in DNA with [3H]dGTP and exposed to [14C]benzene in vitro, was enzymatically hydrolyzed to nucleosides which were chromatographed on a Sephadex LH-20 column to separate free nucleosides from nucleoside-adducts. The elution profiles indicated that rat liver mtDNA contained six guanine nucleoside-adducts and rabbit bone marrow cell mtDNA contained seven guanine nucleoside-adducts. Incubation of bone marrow mitoplasts in vitro in the presence of benzene and the hydroxyl radical scavenger, mannitol, resulted in the inhibition of formation of four of the guanosine-adducts. When [3H]dATP was substituted as the prelabelled precursor nucleotide, the LH-20 column profile indicated that two adenine nucleoside-adducts were also formed from benzene in vitro. Furthermore, a comparison of the Sephadex LH-20 column profiles of purine adducts derived from [14C]benzene- and [3H]dGMP-labelled mtDNA with profiles generated by individually incubating each of the putative unlabelled metabolites with bone marrow mitoplasts in vitro has indicated that p-benzoquinone, phenol, hydroquinone and 1,2,4- benzenetriol form adducts with guanine. One of the two adenosine-adducts may arise from hydroquinone; the compound forming the other adduct is unknown at the present time. Exposure of mitoplasts to catechol in vitro resulted in the formation of a guanine nucleoside-adduct that was present in rat liver mtDNA but absent from the DNA isolated from rabbit bone marrow cell mitoplasts exposed to [14C]benzene in vitro. This suggests that catechol is probably not a major metabolite of benzene formed in bone marrow cell mitochondria.

Membrane-bound mitochondrial DNA: isolation, transcription and protein composition

Mitochondrial membrane-bound DNA complex from bovine heart mitochondria lysed in the presence of Triton X-100 was isolated by differential centrifugation. The yield of "nucleoid" is about 30 microgram protein/mg mitochondrial protein. It contains about 3-5 microgram DNA/mg protein and varying amounts of RNA. The heart mitochondrial nucleoid actively synthesizes RNA. The nucleoid fraction contains about sixteen different proteins as evidenced by urea-SDS gel electrophoresis and about twenty-one proteins as evidenced by acid-urea gel electrophoresis. It appears that the nucleoid is attached to the inner membrane since it does contain cytochromes.

Studies of mitochondria and mitochondrial DNA extracted from organelles harboring an intramitochondrial virus

(1) Two viper cells lines were investigated, one which harbors IMV in the mitochondria (VSW cells) and one without detectable IMV (VH3 cells). (2) The size of closed circular mtDNA molecules from both VSW and VH3 cells was found to be significantly greater (5.4 to 5.6 micron) than the contour lengths of typical mammalian cells (4.8 to 5.2 micron). (3) A small percentage of mini-circles ranging in size from 0.1 to 0.6 micron was observed to band with closed circular mtDNA from both cell lines. Minicircles were especially abundant in VH3 cells. (4) MtDNA from VSW cells contained 34.1% dimers plus oligomers (10.2% oligomers), whereas VH3 cells had only 14.8% dimeric and oligomeric forms (5.4% oligomers). (5) Treatment of VSW cells with 1 microng/ml ethidium bromide for 48 hours resulted in an increased incidence of IMV (IMV in 15% of mitochondrial sections) as compared with untreated VSW cells (IMV in 3% of mitochondrial sections).

On the synthesis of viral ribonucleic acids and ribonucleoproteins in the submitochondrial system completely free of interfering cytoplasmic contaminations

The synthesis of virus-specific macromolecules was studied in the reconstituted system containing inner membrane-matrix fraction from rat liver mitochondria and infectious RNA of Venezuelian equine encephalomyelitis (VEE) virus. In a series of preliminary experiments it was shown that isolated submitochondrial fraction was completely free of interfering cytoplasmic contaminations and particularly, of cytoplasmic 80S ribosomes. VEE RNA when added to submitochondrial system caused significant stimulation of RNA and protein synthesis. These processes were resistant to actinomycin D which inhibited profoundly the synthesis of proper mitochondrial macromolecules. The stimulating effect of VEE RNA in experiments with submitochondrial system was about three times higher than that with intact mitochondria. The stimulation of 14C-amino acid incorporation increased as a function of incubation time; a certain lag-period being observed. The newly formed virus-specific RNA's and ribonucleoproteins were identified with the aid of sedimentation analysis. In particular, radioactive RNA's with sedimentation coefficients 40S and 26-18S were isolated from the incubated system. These RNA's are similar respectively to VEE genome RNA and double-stranded VEE replicative RNA. In double labelling experiments with 3H-uridine and 14C-amino acids it was shown that VEE RNA induced synthesis of ribonucleoproteins containing newly formed RNA and protein. These RNP possessed sedimentation coefficients 60-80S, 140S and 300S in sucrose gradient and buoyant densities 1.32 and 1.50 g/cm3 in cesium chloride gradients. These properties of ribonucleoproteins synthesized de novo in submitochondrial system are close to those of RNP intermediates of VEE virus reproduction in the infected cells. We concluded that viral RNA could program virus-specific synthesis in the submitochondrial system under conditions that eliminated the contribution of cytoplasmic ribosomes.

Temperature-dependent formation of dimers and oligomers of mitochondrial DNA in cells transformed by a thermosensitive mutant of Rous sarcoma virus

In chick-embryo fibroblasts infected by T5, a temperature-sensitive mutant of Schmidt-Ruppin Rous sarcoma virus, the level of catenated dimeric and oligomeric mitochondrial DNA is temperature-dependent and correlates with the phenotypic manifestation of transformation. At the permissive temperature (36 degrees ), where transformation is expressed, the 2- to 3-fold elevated level characteristic of cells transformed by the wild-type Rous sarcoma virus was observed, but at the nonpermissive temperature (41 degrees ), at which cells appear normal and behave normally, the oligomer level was characteristic of uninfected cells. Temperature shifts from 41 to 36 degrees and vice versa resulted in phenotypic reversion and reversals of the respective levels of multiple-length DNA. Cellular growth rates were not altered. Treatment of control cells with cycloheximide resulted in a 5-fold increase of oligomeric DNA, whereas exposure to 9-beta-D-arabinofuranosyladenine had little effect. With both inhibitors, nuclear but not mitochondrial DNA synthesis was inhibited. The possible relation of formation of oligomeric mitochondrial DNA to alterations in the mitochondrial membranes of transformed cells and to inhibition of protein synthesis in the cytoplasm is discussed.