A transgenic model to study the pathogenesis of somatic mtDNA mutation accumulation in beta-cells.

Low levels of somatic mutations accumulate in mitochondrial DNA (mtDNA) as we age; however, the pathogenic nature of these mutations is unknown. In contrast, mutational loads of >30% of mtDNA are associated with electron transport chain defects that result in mitochondrial diseases such as mitochondrial encephalopathy lactic acidosis and stroke-like episodes. Pancreatic beta-cells may be extremely sensitive to the accumulation of mtDNA mutations, as insulin secretion requires the mitochondrial oxidation of glucose to CO(2). Type 2 diabetes arises when beta-cells fail to compensate for the increased demand for insulin, and many type 2 diabetics progress to insulin dependence because of a loss of beta-cell function or beta-cell death. This loss of beta-cell function/beta-cell death has been attributed to the toxic effects of elevated levels of lipids and glucose resulting in the enhanced production of free radicals in beta-cells. mtDNA, localized in close proximity to one of the major cellular sites of free radical production, comprises more than 95% coding sequences such that mutations result in changes in the coding sequence. It has long been known that mtDNA mutations accumulate with age; however, only recently have studies examined the influence of somatic mtDNA mutation accumulation on disease pathogenesis. This article will focus on the effects of low-level somatic mtDNA mutation accumulation on ageing, cardiovascular disease and diabetes.

Cardiac disease due to random mitochondrial DNA mutations is prevented by cyclosporin A.

Mice expressing an error-prone mitochondrial DNA polymerase rapidly accumulate random mutations in mitochondrial DNA. Expression of the transgene in the heart leads to dilated cardiomyopathy accompanied by a wave of apoptosis in cardiomyocytes, and a vigorous and persistent protective response, including upregulation of the anti-apoptotic protein, Bcl-2. To investigate the role of the mitochondrial permeability transition pore in the development of disease, we treated mice with cyclosporin A (CsA), an inhibitor of pore opening. Drug treatment prevented cardiac dilatation, transgene-specific apoptosis, and upregulation of Bcl-2. It also rescued hearts from the profound decrease in connexin 43, which characterizes the dilatated heart. Treatment with FK506, which like CsA inhibits cytoplasmic calcineurin but not the mitochondrial pore, did not affect disease development, suggesting that the relevant target of CsA was the mitochondrial pore. These data implicate breakdowns in the mitochondrial permeability barrier in pathogenesis of elevated frequencies of mtDNA mutations.

Oxidative stress is not an obligate mediator of disease provoked by mitochondrial DNA mutations.

With age, mitochondrial DNA mutations and oxidative stress increase, leading to the hypothesis that the production of reactive oxygen species causes the pathogenic effects of mitochondrial DNA mutations. We tested this hypothesis using transgenic mice that develop cardiomyopathy due to the accumulation of mitochondrial DNA mutations specifically in the heart. Surprisingly, the mechanism of pathogenesis does not involve increased oxidative stress. The amounts of DNA and protein oxidative adducts are not elevated in the transgenic heart. Neither are signs of increased oxidative stress detected by measurements of enzyme function or oxidative defense systems. Rather, we find that the mitochondrial DNA mutations induce a cytoprotective response including increases in the levels of Bcl-2 and Bfl-1, pro-survival proteins that inhibit apoptosis, and atrial natriuretic factor. Bcl-2 is elevated in nearly all cardiomyocytes before the onset of dilated cardiomyopathy. These results raise the possibility that a signaling pathway between the mitochondrion and the nucleus mediates the pathogenic effect of mitochondrial DNA mutations.

Genomic structure of murine mitochondrial DNA polymerase-gamma.

We have sequenced a genomic clone of the gene encoding the mouse mitochondrial DNA polymerase. The gene consists of 23 exons, which span approximately 13.2 kb, with exons ranging in size from 53 to 768 bp. All intron-exon boundaries conform to the GT-AG rule. By comparison with the human genomic sequence, we found remarkable conservation of the gene structure; the intron-exon borders are in almost identical locations for the 22 introns. The 5' upstream region contains approximately 300 bp of homology between the mouse and human sequences that presumably contain the promoter element. This region lacks any obvious TATA domain and is relatively GC rich, consistent with the housekeeping function of the mitochondrial DNA polymerase. Finally, within the 5' flanking region, both mouse and human genes have a region of 73 bp with high homology to the tRNA-Arg gene.

Construction of transgenic mice with tissue-specific acceleration of mitochondrial DNA mutagenesis.

Transgenic mice having rapid accumulation of mitochondrial DNA (mtDNA) mutations specifically in the heart were created. These mice contained a transgene encoding a proofreading-deficient, mouse mitochondrial DNA polymerase (pol gamma) driven by the promoter for the cardiac-specific alpha-myosin heavy chain. Starting shortly after birth greater than 95% of all pol gamma mRNA in the heart was transgene derived; expression in other tissues was low or absent. Mutations in cardiac mtDNA began to accumulate by 7 days after birth. At 1 month of age the frequency of point mutations was 0.014% as determined by DNA sequencing of cloned mtDNA. By long-extension PCR multiple different deletion mutations that had removed several thousand basepairs of genomic sequence were also detected. Sequencing of two deletion molecules showed that one was flanked at the breakpoint by direct repeat sequences. The expression of proofreading-deficient pol gamma had no apparent deleterious effect on mitochondrial DNA and protein content, gene expression, or respiratory function. However, associated with the rise in mtDNA mutation levels was the development of cardiomyopathy as evidenced by enlarged hearts in the transgenic mice. These mice may prove to be useful models to study the pathogenic effects of elevated levels of mitochondrial DNA mutations in specific tissues.

Phosphorylation is required for high-affinity binding of DBP, a yeast mitochondrial site-specific RNA binding protein.

All yeast mitochondrial mRNAs terminate at their 3' ends with a conserved dodecamer sequence, a site for high-affinity binding by DBP (dodecamer binding protein). Using purified DBP, we show that binding requires an intact dodecamer site and is enhanced by the presence in an oligonucleotide of the immediate 4-5 upstream nucleotides. Binding affinity varied from 0.25 to 0.85 nM towards a set of RNA oligonucleotides containing messenger specific upstream sequences in addition to the dodecamer site. Furthermore, we show that phosphatase treatment of DBP abolishes its specific binding, indicating the involvement of reversible phosphorylation in the regulation of its binding activities. This finding will further our understanding of the mechanism of DBP in the regulation of RNA metabolism in yeast mitochondria.

The frequency of point mutations in mitochondrial DNA is elevated in the Alzheimer's brain.

Using a PCR-based strategy, we found that point mutation frequencies in mitochondrial DNA (mtDNA) were 2- to 3-fold higher in the parietal gyrus, hippocampus, and cerebellum from subjects with Alzheimer's disease (AD) compared to normal controls. In contrast, levels of a commonly studied deletion mutation, mtDNA(4977), were not elevated in AD. The frequency of point mutations did not vary significantly among the three brain areas, whereas the frequency of mtDNA(4977) was 15- to 25-fold lower in the cerebellum in comparison to the cortex; this regional variation was seen in both the normal and Alzheimer's brain. In blood mtDNA, point mutation frequencies were not elevated in AD patients. The elevated frequency of point mutations in all three brain regions is consistent with the idea that increased oxidant stress is associated with AD.

Purification and characterization of an RNA dodecamer sequence binding protein from mitochondria of Saccharomyces cerevisiae.

Saccharomyces cerevisiae mitochondrial mRNAs terminate at their 3' ends with a conserved dodecamer sequence, 5'-AAUAA(U/C)AUUCUU-3'. We have identified a nuclear-encoded protein (DBP) which specifically binds to the dodecamer sequence and have purified it to apparent homogeneity by RNA affinity chromatography. DBP consists of a single polypeptide of 55 kDa and binds to its RNA substrate with a 1:1 stoichiometry. Scatchard analysis determines that K(d) is 0.93 nM for the canonical dodecamer sequence (5'-AAUAAUAUUCUU-3') and 0.46 nM for the only naturally occurring variant (5'-AAUAACAUUCUU-3') unique to oli1 gene. Based on the studies using mutant oligonucleotides, DBP appears to recognize primarily the nucleotide sequence of an RNA rather than its potential secondary structure.

The DExH box protein Suv3p is a component of a yeast mitochondrial 3'-to-5' exoribonuclease that suppresses group I intron toxicity.

The yeast mitochondrial protein Suv3p is a putative NTP-dependent RNA helicase. Here we report that in cells lacking Suv3p, there is an approximately 50-fold increase in the excised form of the group I intron omega of the mitochondrial 31S rRNA gene. Surprisingly, little mature 21S rRNA accumulates in those cells; instead, unligated 21S rRNA exons appear. Intron overaccumulation could lead to spliced exon reopening via a reaction known to be catalyzed by group I introns in vitro. We also show that Suv3p is a functional component of a novel mitochondrial NTP-dependent 3'-to-5' exoribonuclease activity that can degrade group I intron RNAs. These findings account for group I intron overaccumulation in cells lacking Suv3p and define a novel function for putative RNA helicases in direct RNA degradation.

Evidence for a nucleotide-dependent topoisomerase activity from yeast mitochondria.

Yeast mitochondria were found to contain a novel topoisomerase-like activity which required nucleoside di- or tri-phosphates as a cofactor. ADP supported activity as effectively as ATP and the optimal concentration for each was approximately 20 microM. None of the other standard ribo- or deoxyrib-onucleotides could fully substitute for either ADP or ATP. The non-hydrolyzable ATP analogs, adenosine-5'-0-(3-thiotriphosphate) (ATP-gamma-S), adenylyl (beta,gamma-methylene) (AMP-PCP), and andenyl-imidodiphosphate (AMP-PNP) also supported activity suggesting that the nucleotide cofactor regulated topoisomerase activity rather than serving as an energy donor in the reaction. The mitochondrial topoisomerase activity relaxed both positively and negatively supercoiled DNA. It was not inhibited by concentrations of ethidium bromide up to 2 micrograms/ml nor by either nalidixic or oxolinic acids; novobiocin, coumermycin, and berenil inhibited the activity. Genetic and biochemical analysis of the mitochondrial topoisomerase activity indicated that it was not encoded by the nuclear TOP1, TOP2, and TOP3 genes.

Evidence for a site-specific endonuclease in yeast mitochondria which recognizes the sequence 5'GCCGGC.

We have discovered a mitochondrial, site-specific DNase in Saccharomyces cerevisiae with properties like that of a Type II restriction endonuclease. The enzyme, termed SceIII, cleaves the palindromic sequence 5'GCCGGC, to give 3' ends recessed by 4 bases. SceIII is the first restriction-like endonuclease to be described in yeast mitochondria.

Analysis of the role of the NUC1 endo/exonuclease in yeast mitochondrial DNA recombination.

Mitochondrial DNA recombination was reduced in an yeast mutant lacking the NUC1 endo/exonuclease. Between linked markers in either the omega or cob region the frequency of recombination decreased nearly 50% compared to wild-type. Gene conversion frequencies in the var1 gene and in the omega region were also lower in the mutant strain. In particular, the gradient of gene conversion at omega was most affected by the absence of the NUC1 nuclease. In crosses between nuclease-deficient and wild-type strains, gene conversion frequencies at omega were reduced only when the omega+ allele was contributed to the zygote by the nuclease-deficient parent. We propose that the 5' exonuclease activity of the NUC1 nuclease functions during recombination to enlarge heteroduplex tracts following a double-strand break in DNA. In crosses between nuclease-deficient and wild-type strains, the anisotropy in gene conversion frequencies at omega is hypothesized to be due to the slow mixing of parental mitochondrial membranes as they fuse in the zygote.

Formation of the 3' end of yeast mitochondrial mRNAs occurs by site-specific cleavage two bases downstream of a conserved dodecamer sequence.

Mitochondrial mRNAs in yeast arise by processing of polygenic primary transcripts at a conserved dodecamer sequence (5'-AAUAAPyAUUCUU-3'). Previous results indicated that processing at dodecamer sites interrupted the sequence implying that it functioned primarily as a signal for 3' end formation of mRNAs. We have determined the precise cleavage site for RNAs processed at the dodecamer sequences associated with the oli1 gene and the omega intron of the 21S rRNA gene. In both cases cleavage occurred two bases downstream of the site. Hydrolysis left the PO4 group attached to the 3' terminus of the cleavage products. These results demonstrate for the first time that mature mitochondrial mRNAs terminate with an intact dodecamer sequence. In light of the recent identification of a protein complex within mitochondria that binds to RNAs terminating with an intact dodecamer sequence, these results support the idea that the dodecamer sequence functions not only within pre-mRNAs as a processing site, but within mature mRNAs as well, possibly for the stabilization and/or translation.

A nucleoside triphosphate-regulated, 3' exonucleolytic mechanism is involved in turnover of yeast mitochondrial RNAs.

We have employed cell-free transcription reactions with mitochondria isolated from Saccharomyces cerevisiae to study the mechanism of RNA turnover. The specificity of RNA turnover was preserved in these preparations, as were other RNA-processing reactions, including splicing, 3' end formation of mRNAs, and maturation of rRNAs. Turnover of nascent RNAs was found to occur exonucleolytically; endonucleolytic cleavage products were not detected during turnover of the omega intron RNA, which was studied in detail. However, these experiments still leave open the possibility that endonucleolytic cleavage products with very short half-lives are kinetic intermediates in the decay of omega RNA. Exonucleolytic turnover was regulated by nucleotide triphosphates and required their hydrolysis. A unique signature of this regulation was that any one of the eight standard ribo- or deoxyribonucleotide triphosphates supported RNA turnover. A novel hybrid selection protocol was used to determine the turnover rates of the 5', middle, and 3' portions of one mitochondrial transcript, the omega intron RNA. The results suggested that degradation along that transcript occurred with a 3'-->5' polarity. The similarity between features of mitochondrial RNA turnover and the properties of a nucleotide triphosphate-dependent 3' exoribonuclease that has been purified from yeast mitochondria suggests that this single enzyme is a key activity whose regulation is involved in the specificity of mitochondrial RNA turnover.

Localization of a cruciform cutting endonuclease to yeast mitochondria.

We have found a cruciform cutting endonuclease in the yeast, Saccharomyces cerevisiae, which localizes to the mitochondria. This activity apparently is associated with the mitochondrial inner membrane since the activity is not released into solution by osmolysis, in contrast to the matrix enzyme, isocitrate dehydrogenase. The cruciform cutting activity appears to be encoded by CCE1. This gene has been shown to encode one of the major cruciform cutting endonucleases present in yeast cell. In cce1 strains, which lack CCE1 endonuclease activity, the mitochondrial cruciform cutting endonucleolytic activity is also absent. Since CCE1 is allelic to MGT1, a gene required for the highly biased transmission of petite mitochondrial DNA in crosses between rho+ and hypersuppressive rho- cells, it seems likely that the CCE1 endonuclease functions within mitochondria.

Identification of a protein complex that binds to a dodecamer sequence found at the 3' ends of yeast mitochondrial mRNAs.

An activity from Saccharomyces cerevisiae mitochondria was identified that specifically bound to a 12-nucleotide sequence, AAUAA(U/C)AUUCUU, that is a site for processing of pre-mRNAs so as to generate the mature 3' ends of mRNAs. Because processing occurs 3' to the end of the dodecamer site, all mRNAs in yeast mitochondria terminate with that sequence. RNase T1 digestion fragments which terminated precisely at their 3' ends with the dodecamer sequence bound the activity, indicating that mRNAs in vivo would be capable of binding. Gel mobility shift analyses using RNA oligonucleotides showed that binding was reduced by a U-to-A substitution at position 3 of the dodecamer sequence; a C-to-A substitution at position 10 eliminated binding. UV cross-linking identified three polypeptides with approximate molecular masses of 19, 60, and 70 kDa as constituents of the binding activity. These estimates included the contribution of the 32P-labeled RNA oligonucleotide used to tag these polypeptides. An oligonucleotide with a UA-->AU substitution at positions 3 and 4 of the dodecamer site formed complexes deficient in the 19-kDa species, suggesting that binding specificity was inherent to the higher-molecular-weight polypeptides. Assembly of the complex at a dodecamer site on an RNA protected sequences located 5' to the dodecamer site from digestion by a nucleoside triphosphate-dependent 3' exoribonuclease found in yeast mitochondria. Since mitochondrial mRNAs terminate with an intact dodecamer sequence, the binding activity may function in the stabilization of mRNAs in addition to 3'-end formation of mRNAs.

Isolation and characterization of an NTP-dependent 3'-exoribonuclease from mitochondria of Saccharomyces cerevisiae.

RNA turnover in eukaryotes is thought to require 3'-exonuclease activity but so far no RNase with that specificity has been isolated from a eukaryote. We report here on the purification and characterization of a 3'-exoribonuclease isolated from the mitochondria of Saccharomyces cerevisiae. In vitro the purified enzyme displayed an absolute requirement of NTPs for activity. Each of the eight standard ribo- and deoxyribonucleotides supported activity with Km values ranging from 20 to 90 microM. The enzyme also displayed RNA-stimulated NTPase activity. The NTP-dependent enzyme cofractionated with three polypeptides of molecular masses 75,000, 90,000, and 110,000 daltons, although the native enzyme appears to have a molecular mass of 160,000 daltons predicted from the Stokes radius. The possible functions of this enzyme in vivo in the regulated decay of mitochondrial RNAs are discussed.

Quantitation of radioactively labeled RNA by hybrid selection using biotinylated oligonucleotides.

We describe a procedure to quantify specific, radioactively labeled RNA sequences. This procedure combines hybrid selection of an RNA using biotinylated oligonucleotides with gel electrophoretic analysis of the selected RNA. We show that the hybrid selection procedure is specific and quantitative. It enriches a specific RNA sequence at least 600-fold. Specificity and sensitivity are increased to at least 10,000-fold enrichment by a combination of RNase T1 digestion of the RNA:oligonucleotide hybrid prior to selection, followed by gel electrophoretic fractionation of the selected RNA fragment. Furthermore, this modification allows one to quantify specific regions of an RNA transcript, as well as to monitor several different RNA sequences in one experiment. It is estimated that the sensitivity of this procedure is high enough to detect specific RNA sequences present at 1 part in 100,000.

Characterization of a novel NTP-dependent 3' exoribonuclease from yeast mitochondria.

We have purified and characterized a novel exoribonuclease that was isolated from the mitochondria of Saccharomyces cerevisiae. The enzyme degraded RNA in a 3' to 5' direction and was dependent on nucleotide triphosphates for activity. All eight of the standard ribo- and deoxyribonucleotide triphosphates supported activity with an apparent Km ranging from 20 to 90 uM. The enzyme also exhibited an RNA-dependent ATPase activity. Evidence suggests that in vivo the enzyme may associate with mitochondrial factors which can alleviate the dependence on nucleotide triphosphates for enzymatic activity. A model is discussed for the role of the enzyme in regulating the turnover of mitochondrial RNAs.