Decrease of D-loop frequency in heart and cerebral hemispheres mitochondrial DNA of aged rat

A quantitative analysis of the frequency of the supercoiled mitochondrial DNA molecules containing the D-loop in rat heart and cerebral hemispheres, at different ages, is presented. Both tissues of aged animals exhibit a remarkable reduction in the content of super-coiled D-loop containing molecules compared to the adults. This alteration could be responsible for the age-dependent reduction of mitochondrial DNA transcription previously observed in rat brain and heart.

Evolutionary analysis of cytochrome b sequences in some Perciformes: evidence for a slower rate of evolution than in mammals

To obtain information relative to the phylogenesis and microevolutionary rate of fish mitochondrial DNA, the nucleotide sequence of cytochrome b gene in seven fish species belonging to the order of Perciformes was determined. Sequence analysis showed that fish mitochondrial DNA has a nucleotide compositional bias similar to that of sharks but lower compared to mammals and birds. Quantitative evolutionary analysis, carried out by using a markovian stochastic model, clarifies some phylogenetic relationships within the Perciformes order, particularly in the Scombridae family, and between Perciformes, Gadiformes, Cypriniformes, and Acipenseriformes. The molecular clock of mitochondrial DNA was calibrated with the nucleotide substitution rate of cytochrome b gene in five shark species having divergence times inferred from paleontological estimates. The results of such analysis showed that Acipenseriformes diverged from Perciformes by about 200 MY, that the Perciformes common ancestor dates back to 150 MY, and that fish mitochondrial DNA has a nucleotide substitution rate three to five times lower than that of mammals.

Correlation between mitochondrial DNA 4977-bp deletion and respiratory chain enzyme activities in aging human skeletal muscles

The content of the mitochondrial DNA 4977-bp deletion and the respiratory chain enzyme activities were determined in the same human skeletal muscle specimens. A direct correlation between damage to mtDNA and bioenergetic deficiency was observed. The time-course of the appearance of the mtDNA deletion was followed. The highest percentage of mtDNA-deleted molecules was 0.26% and it was found in the eighties which corresponds to the age of the major reduction in the respiratory chain enzyme activities. Two samples with very low mitochondrial respiratory enzyme activities exhibited much higher levels of deletion compared to the similar age counterparts. Given, however, the low absolute level of the deletion also in these samples, we suggest that damage to the respiratory chain complexes, especially complex IV, might be the cause more than the effect of the increased number of mtDNA molecules bearing deletions in aged human skeletal muscle.

Effect of aging and acetyl-L-carnitine on the activity of cytochrome oxidase and adenine nucleotide translocase in rat heart mitochondria

The effect of aging and treatment with acetyl-L-carnitine on the activity of cytochrome oxidase and adenine nucleotide translocase in rat heart mitochondria was studied. It was found that the activity of both these mitochondrial protein systems was reduced (by around 30%) in aged animals. Treatment of aged rats with acetyl-L-carnitine almost completely reversed this effect. Changes in the mitochondrial cardiolipin content appear to be responsible for these effects of acetyl-L-carnitine.

Purification and characterization of a mitochondrial DNA-binding protein that binds to double-stranded and single-stranded sequences of Paracentrotus lividus mitochondrial DNA

A mitochondrial protein, able to specifically bind two double-stranded homologous sequences of sea-urchin mitochondrial DNA, has been partially purified from Paracentrotus lividus eggs. This protein, present at a low concentration, is a polypeptide of 40 kDa. One of the binding sequences, located in the main non-coding region, contains the replication origin of the mitochondrial DNA H-strand. By a combination of band-shift, DNase footprinting, and modification interference analyses with homologous and heterologous probes we identified YCYYATCAN(A/T)RC as the minimum sequence required for the binding. The protein also shows a single-stranded DNA-binding activity, as it is able to specifically interact with one of the strands of the binding sites. These features are consistent with a function of the protein in the modulation of sea-urchin mitochondrial DNA replication during the development stages.

Mitochondrial DNA copy number and mitochondrial DNA deletion in adult and senescent rats

In order to understand the cause of the reduced mitochondrial DNA transcription in heart and brain of senescent rat previously reported, we focused our attention on the content and structure of rat mitochondrial DNA in adult and senescent rats. The estimate of the mtDNA copy number in liver, heart and brain of adult and senescent rats showed that in all organs examined the senescent individuals have a mtDNA content higher than the adult counterparts. The analysis of mtDNA structural changes involved the search for point mutations and large deletions. As for the first case, the determination of the nucleotide sequence of many independent clones containing two mtDNA restriction fragments isolated from rat cerebral hemispheres did not show any sequence difference between adult and senescent individuals. However, analysis of mtDNA deletions by the polymerase chain reaction in liver and brain of adult and senescent rats identified a small population of mtDNA molecules harboring a deletion of 4834 bp. The estimate of the proportion of deleted molecules in the liver showed that they represent 0.02% and 0.0005% of total mtDNA in senescent and adult rat liver respectively. Therefore, a mtDNA deletion also accumulates in the rat during aging. This result supports the hypothesis of the accumulation of deleted mtDNA molecules in aging. However, the low percentage of deleted mtDNA molecules already found and the reversibility of the reduced mitochondrial DNA transcription in senescent rat raise doubts on the primary role of the irreversibly damaged mtDNA molecules in aging. Deleted mtDNA molecules along with changes caused by lipid peroxidation of mitochondrial membranes might contribute to the overall decline of mitochondrial function.

Lipid composition in synaptic and nonsynaptic mitochondria from rat brains and effect of aging

The cholesterol, phospholipid, and fatty acid compositions in synaptic and nonsynaptic mitochondria from rat brains and the effect of aging were studied. Both cholesterol and phospholipid contents were found to be significantly different in synaptic compared to nonsynaptic mitochondria. In both types of brain mitochondria, aging decreases the cholesterol content by 27% and the phospholipid content by approximately 12%. The difference between these decreases observed in the organelles causes decreases in the cholesterol/phospholipid molar ratios for synaptic and nonsynaptic mitochondria of 17 and 19%, respectively. Also, the phospholipid composition is significantly different in synaptic compared to nonsynaptic mitochondria. Among phospholipids, only the cardiolipin fraction showed a significant decrease (26%) in nonsynaptic mitochondria from the brains of aged rats. Instead, the fatty acid composition was not significantly different in synaptic compared to nonsynaptic mitochondria. The 21% aging decrease in linoleic acid (18:2), observed only in nonsynaptic mitochondria, may be related to a decrease in cardiolipin, which contains a large amount of this fatty acid.

The effect of aging and acetyl-L-carnitine on the activity of the phosphate carrier and on the phospholipid composition in rat heart mitochondria

The effect of aging and treatment with acetyl-L-carnitine on the activity of the phosphate carrier and on the phospholipid composition in rat heart mitochondria was studied. It was found that the activity of the phosphate carrier was reduced by aging. Treatment of aged rats with acetyl-L-carnitine reversed this effect. The mitochondrial level of cardiolipin was decreased with aging. Treatment of aged rats with acetyl-L-carnitine restored the level of cardiolipin to that of young rats. It is proposed that acetyl-L-carnitine may restore the correct phospholipid composition (cardiolipin level) of the mitochondrial membrane, altered by aging, thereby restoring the activity of the phosphate carrier.

Identification of two homologous mitochondrial DNA sequences, which bind strongly and specifically to a mitochondrial protein of Paracentrotus lividus

Using a combination of band shift and DNasel protection experiments, two Paracentrotus lividus mitochondrial sequences, able to bind tightly and selectively to a mitochondrial protein from sea urchin embryos, have been found. The two sequences, which compete with each other for binding to the protein, are located in two genome regions which are thought to contain regulatory signals for mitochondrial replication and transcription. A computer analysis suggests that the sequence TTTTRTANNTCYYATCAYA, common to the two binding regions, is the minimal recognition signal for the binding to the protein. We discuss the hypothesis that the protein binding capacity of these two sequences is involved in the control of sea urchin mtDNA replication during developmental stages.

Reduced synthesis of mtRNA in isolated mitochondria of senescent rat brain

A system for studying RNA synthesis in isolated mitochondria from rat brain was set up to investigate the mechanisms responsible for the age-dependent reduction of mtRNA content. In the presence of an appropriate incubation buffer both synaptic and non-synaptic mitochondria from cerebral hemispheres were able to synthesize and process mtRNA in a way quantitatively and qualitatively similar to the in vivo transcription. The comparison of the electrophoretic pattern of mtRNAs synthesized by adult and senescent rat showed, in the senescent rat, a 50% reduction in the mtRNA synthesis rate relative to the adult value. This indicates that the age-dependent decrease of the mtRNA content is linked to a lower efficiency of the mt transcription.

Acetyl-L-carnitine increases cytochrome oxidase subunit I mRNA content in hypothyroid rat liver

The effect of acetyl-L-carnitine on the quantity of the messenger RNA for the subunit I of cytochrome oxidase in the liver mitochondria of hypothyroid rat was measured by Northern blot and solution hybridization. Three hours after pre-treatment of hypothyroid rat with acetyl-L-carnitine, the level of the transcript increased strongly. This effect was also obtained when acetyl-L-carnitine was administered to T3 pre-treated hypothyroid rats. These results add further evidence to the suggestion that acetyl-L-carnitine is able to stimulate mitochondrial transcription under altered metabolic conditions.

Effect of aging and acetyl-L-carnitine on the lipid composition of rat plasma and erythrocytes

The effect of aging and treatment with acetyl-L-carnitine on the lipid composition of rat plasma and erythrocytes was studied. It was found that aging increases the levels of free and esterified cholesterol. Fatty acid patterns in the plasma of aged rats show remarkable alterations when compared with control rats. These changes reverted to normal after three hours of acetyl-L-carnitine treatment. No significant differences in the erythrocyte lipid pattern of young and aged rats were observed. This study provides the first proof that acetyl-L-carnitine probably acts by lowering free and esterified cholesterol and arachidonic acid (20:4) levels in the plasma.

Mapping and characterization of Paracentrotus lividus mitochondrial transcripts: multiple and overlapping transcription units

This paper reports the mapping of both mature and precursor Paracentrotus lividus mitochondrial transcripts. Several mtRNAs were found to have 5' and 3' termini which differ from those inferred through DNA sequencing (Cantatore et al. 1989). The 3' ends of the two rRNAs (12S and 16S) overlap with the downstream transcripts (tRNAGlu and CoI mRNA) by 5 and 10 nt respectively. The 132 nt non-coding region is extensively transcribed: in particular it contains a 124 nt RNA and the 5' end of a possible precursor of 13 clustered tRNAs. This latter overlaps by 7 nt with the 3' end of the 124 nt RNA. In addition to the mature RNAs, 32 high molecular weight RNAs, which are probably the precursors of the smaller more abundant mature species, were detected by Northern blotting. The mapping of these transcripts indicates that they are processed at the level of tRNA or tRNA-like sequences and suggests the existence of two transcription initiation sites upstream of the ND1 and the cytochrome b genes respectively. In the light of these results it appears that P. lividus mitochondrial DNA transcription takes place via multiple and probably overlapping transcription units. Moreover, the wide variation in the steady-state levels of the mature mRNAs indicates that sea urchin mitochondrial DNA expression is also regulated at the level of RNA decay.

Reduced transcription of mitochondrial DNA in the senescent rat. Tissue dependence and effect of L-carnitine

A quantitative study on the effect of senescence on mitochondrial DNA expression has been carried out by measuring the levels of the 12S rRNA and of the mRNA for the subunit I of cytochrome oxidase in several tissues of adult and senescent rats. The concentration of both RNA species/mitochondrial DNA molecule is significantly reduced in senescent brain and heart, as opposed to the respective adult tissues. No appreciable variation occurs in the liver. A 1-h pretreatment with acetyl-L-carnitine brings back the level of senescent brain and heart transcripts to that of adult tissues. The same treatment of adult rats does not cause significant changes in mitochondrial RNA content. These results suggest that the age-dependent impairment of both heavy-strand mitochondrial DNA transcription units is related to altered environmental conditions which acetyl-L-carnitine, a substance which acts by stimulating, directly or indirectly, the energy metabolism, is able to remove.

The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus

The 15,697-nucleotide sequence of Paracentrotus lividus mitochondrial DNA is reported. This genome codes for 2 rRNAs, 22 tRNAs, and 12 mRNAs which specify 13 subunits of the mitochondrial inner membrane respiratory complexes. The gene arrangement differs from that of other animal species. The two ribosomal genes 16 S and 12 S are separated by a stretch of about 3.3 kilobase pairs which contains the ND1 and ND2 genes and a cluster of 15 tRNA genes. The ND4L coding sequence is not contained in the ND4 mRNA but has its own mRNA which maps between the tRNA(Arg) and the Co II genes. The main noncoding region, located in the tRNA gene cluster, is only 132 nucleotides long, but contains sequences homologous to the mammalian displacement loop. Other short noncoding sequences are interspersed in the genome: they contain a conserved AT consensus which probably has a role in transcription or RNA processing. As regards the mitochondrial genetic code, the codons AGA and AGG specify serine and are recognized by a tRNA with a GCU anticodon, whereas AUA and AAA code for isoleucine and asparagine rather than for methionine and lysine. Except for ND4L which starts with AUC and ATPase 8 which starts with GUG, AUG is used as the initiation codon. In 11 out of 13 cases the genes terminate with the canonical stop codons UAA or UAG. These observations suggest that during invertebrate evolution each lineage developed its own mechanism of mitochondrial DNA replication and transcription and of RNA processing and translation.

Content of mitochondrial DNA and of three mitochondrial RNAs in developing and adult rat cerebellum

The content of DNA and of 16S rRNA and of two mRNAs, i.e., the mRNA for the cytochrome c oxidase subunit I and the mRNA for one subunit of the NADH dehydrogenase (ND4), in free (nonsynaptic) mitochondria of developing and adult rat cerebellum has been determined. During postnatal development, DNA content of free (nonsynaptic) mitochondria increases 10 times from 1 to 30 days of age whereas, in adult rats, it is about 60% compared to that found in 30-day-old rats. The total content of each RNA species studied also increases during development. However, when the content of each RNA is expressed per mtDNA molecule, rRNAs and mRNAs behave differently: 16S rRNA level does not change during development and it is not significantly different from that of the adult rat, whereas the level of mRNAs is higher during development than in the adult rat and changes with age. These results are discussed in light of mitochondrial biogenesis in rat cerebellum during development and of the regulation of the mitochondrial DNA transcription process.

Faithful and highly efficient RNA synthesis in isolated mitochondria from rat liver

Isolated rat liver mitochondria in the presence of an appropriate incubation buffer are able to support DNA transcription and RNA processing in a way qualitatively and quantitatively similar to that used by intact cells. This system is also able to synthesize an RNA species of 155-175 nucleotides which probably corresponds to the 7S RNA, a type of RNA found so far only in growing cells. The role of this RNA in the mitochondrial replication and transcription processes, in relation to the cell metabolism, is discussed.

Clustering of tRNA genes in Paracentrotus lividus mitochondrial DNA

We have determined the base sequence of the restriction fragment Bam1-2 (3,593) of Paracentrotus lividus (sea urchin) mtDNA. This fragment contains, in addition to genes previously identified (part of the 12S rRNA, ND1 and part of the ND2 mRNA), a cluster of 15 tRNA genes located between the 12S and ND1 genes. Also to be found in the tRNA gene cluster, between the tRNA(Thr) and tRNA(Pro) genes, is a sequence of 134 bp which constitutes the only non-coding region of this DNA so far identified. The distinctive organization of the tRNA genes and the extreme size reduction of the non-coding region suggest the existence of unique mechanisms for the regulation of gene expression in this organism.

Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes

During the evolution of sea urchins, a transfer RNA gene lost its tRNA function and became part of a protein-coding gene. This functional loss of a tRNA with specificity for one group of leucine codons (CUN, where N is any base) was accompanied by the gain of a new tRNA with that specificity. The new tRNA gene for CUN codons appears to have evolved by duplication and divergence from a tRNA gene specific for another group of leucine codons (UUR, where R is a purine). These proposals account for (1) the strong sequence resemblance between the modern tRNA genes for CUN and UUR codons in Paracentrotus, (2) the altered location of the CUN gene in mitochondrial DNA of this urchin, and (3) the persistence of a 72-base pair sequence containing a trace of the old CUN gene at its original location. The old CUN gene now codes for an extra 24 amino acids at the amino end of subunit 5 in NADH dehydrogenase. Besides giving clues about the mechanisms by which tRNA genes move during mitochondrial DNA evolution, this finding leads us to propose a pathway relating the arrangements of other genes in mitochondrial DNAs from four animal phyla.

Synthesis and turnover rates of four rat liver mitochondrial RNA species

The synthesis and turnover rates of the two 12 S and 16 S mt rRNAs and of the mt mRNAs for subunits I and III of cytochrome oxidase have been determined by measuring the kinetics of incorporation of [3H]uridine in the mtRNA of rat hepatocytes. All the RNA species examined have approximately the same turnover (t1/2 approximately 100 min) and therefore the rate of synthesis, which is about 10-times higher for the rRNAs, seems to be the factor responsible for the different mt rRNA and mRNA steady-state levels.

A novel gene order in the Paracentrotus lividus mitochondrial genome

The mitochondrial DNA (mtDNA) from Paracentrotus lividus (sea urchin) eggs, a circular molecule of about 15,500 bp, has been cloned in plasmid vectors after cleavage with various restriction enzymes. By a combination of Northern blot hybridization and nucleotide sequence analysis we have characterized most of the P. lividus mitochondrial transcripts and determined the basic gene organization of the mtDNA. The nucleotide sequence of a gene for one NADH dehydrogenase (ND) subunit, ND4L, has also been determined. Our results show the existence of a novel gene order. The 12S and 16S rRNA genes are not contiguous but are separated from each other by ND1 and ND2 genes. The ND4L gene is not adjacent to ND4 but is located between the tRNAArg gene and the gene for subunit II of cytochrome oxidase (CoII). The tRNA genes are reshuffled and contrary to all vertebrate mitochondrial genomes studied so far, there are no intergenic regions between the tRNAPhe and the cytochrome b genes. These characteristics suggest a peculiar mechanism for the regulation of gene expression in this organism and provide information on the evolution of the mitochondrial genetic system in animal cells.

Quantitation of mitochondrial RNA species during rat liver development: the concentration of cytochrome oxidase subunit I (CoI) mRNA increases at birth

A quantitative study on the concentration of mitochondrial DNA and two species of mtRNA, the ribosomal (16S rRNA) and messenger (CoI mRNA) has been carried out in rat liver between -3 and 14 days of age. The cellular content of mitochondrial DNA begins to increase at one day of life and goes up linearly until 14 days of age. The cellular level of 16S rRNA and CoI mRNA changes during development: the 16S rRNA increases linearly after birth, whereas CoI mRNA shows a peak at birth and thereafter remains more or less constant. The concentration of 16S rRNA per mitochondrial DNA molecule remains substantially unchanged during development, whereas that of CoI mRNA increases before birth and, at birth, reaches values higher than in adults. These results support an independent regulation of mitochondrial rRNA and mRNA level in rat liver mitochondria during development.