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In part of the patients with a disturbance in the mitochondrial energy metabolism, the defect can not be ascribed to a default in the respiratory chain, citric acid cycle or pyruvate dehydrogenase complex. Incubations of muscle mitochondria with various substrates under different conditions render it likely that defects in transport systems in the mitochondrial membranes, besides the known enzyme deficiencies, can be the cause of the biochemical abnormalities in human mitochondriopathies. This approach has resulted in the detection of two rare deficiencies: one in the ATP/ADP-translocator and another in the voltage-dependent anion channel (VDAC) protein.

The sea urchin mitochondrial D-loop binding protein (mtDBP) is a transcription termination factor that is able to arrest bidirectionally mitochondrial RNA chain elongation. The observation that the mtDBP binding site in the main non-coding region is located in correspondence of the 30 end of the triplex structure, where the synthesis of heavy strand mitochondrial (mt) DNA is either prematurely terminated or allowed to continue, raised the question whether mtDBP could also regulate mtDNA replication. By using a helicase assay in the presence of the replicative helicase of SV40, we show that mtDBP is able to inhibit the enzyme thus acting as a contrahelicase. The impairing activity of mtDBP is bidirectional as it is independent of the orientation of the protein binding site. The inhibition is increased by the presence of the guanosine-rich sequence that flanks mtDBP binding site. Finally, a mechanism of abrogation of mtDBP contrahelicase activity is suggested that is based on the dissociation of mtDBP from DNA caused by the passage of the RNA polymerase through the protein–DNA complex. All these findings favour the view that mtDBP, besides serving as transcription termination factor, could also act as a negative regulator of mtDNA synthesis at the level of D-loop expansion.

To obtain information on the mechanisms responsible of the generation of ragged red fibers (RRF) during aging, we analyzed the mitochondrial genotype of single skeletal muscle fibers of healthy individuals having an age comprised between 45 and 92 years. The sequencing of the D-loop region showed many sequence changes with respect to the Cambridge reference sequence (CRS), in both RRF and normal fibers. These changes were more abundant in RRF and their number increased between 50 and 60, and 61 and 70 years and then remained approximately constant. The analysis of the sequence changes showed that each subject contained one or more changes associated to RRF in positions of D-loop region that either do not change or that change very rarely. In general the same type of RRF-associated change was not found in more than one individual; exceptions were changes in positions 189, 295, 374 and 514, detected in 20–50% of analyzed subjects. In particular the A189G age-associated mutation was found only in old individuals and prevalently in RRF. Sequencing of other two mtDNA regions showed no relevant changes in the 16S/ND1 region and two RRF-associated original mutations, G5847A and A5884C, in two very conserved positions of tRNATyr. These results indicate that each subject has its own pattern of RRF-associated mutations in both coding and non-coding region of human mtDNA.

Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that DmTTF is synthesised as a precursor of 410 amino acids and is imported into mitochondria, giving rise to a mature product of 366 residues. Band-shift and DNase I protection experiments show that DmTTF binds two homologous, short, non-coding sequences of Drosophila mitochondrial DNA, located at the 3' end of blocks of genes transcribed on opposite strands. The location of the target sequences coincides with that of two of the putative transcription termination sites previously hypothesised. These results indicate that DmTTF is the termination factor of mitochondrial transcription in Drosophila. The existence of two DmTTF binding sites might serve not only to stop transcription but also to control the overlapping of a large number of transcripts generated by the peculiar transcription mechanism operating in this organism.

To gain further information on the role of mitochondrial transcription factor A (TFAM) in mitochondrial biogenesis, we studied the post-translational modifications of the protein in 6- and 28-month-old rat liver. Mass spectrometry and immunoblot analysis revealed that TFAM was acetylated at a single lysine residue and that the level of acetylation did not change with age. The measurement of the content of TFAM and of mitochondrial DNA (mtDNA) in several organs (cerebellum, heart, kidney, and liver) of young and old rats showed an age-related increase of mtDNA and TFAM in all the organs analyzed, except in heart. These data are discussed in the light of the multiple roles of TFAM in mitochondrial biogenesis and of the age-related change of the mitochondrial transcription.

Qualitative and quantitative alterations of mitochondrial DNA (mtDNA) in the skeletal muscle from two patients with cirrhosis and severe asthenia have been studied. The 4977 bp (mtDNA4977) and the 7436 bp (mtDNA7436) mtDNA deletions, as well as other mtDNA deletions, revealed by long extension PCR (LX-PCR), were found in the two patients, whereas the 10,422 bp (mtDNA10,422) mtDNA deletion was absent. Altogether, the qualitative alterations of mtDNA in cirrhotic patients with severe asthenia were comparable to those of age-matched healthy individuals. The mtDNA content, on the contrary, was substantially decreased in both patients with respect to control. Such mtDNA depletion might be explained by an increased, disease-related, oxidative damage to mtDNA, which probably affects the replication of the mitochondrial genome as already suggested in other oxidative stress-associated diseases.

The cloning of the cDNA for two mitochondrial proteins involved in sea urchin mtDNA replication and transcription is reported here. The cDNA for the mitochondrial D-loop binding protein (mtDBP) from the sea urchin Strongylocentrotus purpuratus has been cloned by a PCR-based approach. The protein displays a very high similarity with the Paracentrotus lividus homologue as it contains also the two leucine zipper-like domains which are thought to be involved in intramolecular interactions needed to expose the two DNA binding domains in the correct position for contacting DNA. The cDNA for the mitochondrial single-stranded DNA-binding protein (mtSSB) from P. lividus has been also cloned by a similar approach. The precursor protein is 146 amino acid long with a presequence of 16 residues. The deduced amino acid sequence shows the highest homology with the Xenopus laevis protein and the lowest with the Drosophila mtSSB. The computer modelling of the tertiary structure of P.lividus mtSSB shows a structure very similar to that experimentally determined for human mtSSB, with the conservation of the main residues involved in protein tetramerization and in DNA binding.

Mitochondrial DNA (mtDNA) sequence variation in the segment of the D-loop region encompassing the initiation sites for replication and transcription was analyzed in the blood of 277 Italian type 2 diabetes patients and 277 Italian healthy subjects. Compared with the Cambridge Reference Sequence, diabetic patients show a slightly higher propensity to accumulate base changes in this region, with respect to controls, although no significant association can be established between any of the detected changes and the diabetic condition. Subjects, patients and controls, harbouring base changes at the replication origins (positions 57 and 151) and at position 58 were analyzed for mtDNA content. The mtDNA content increased three–four times only in the diabetic patients bearing the m.151C>T transition, whereas in those bearing the m.58T>C change the mtDNA content doubled, independently of the affiliation haplogroup. This result suggests that the m.151C>T transition and, to a lower extent, the m.58T>C might confer to the blood cells of diabetic patients the capability of increasing their mtDNA content, whereas the same transitions have no effect on control subjects.

Mitochondrial dysfunction has been implicated in rare and common forms of type 2 diabetes (T2DM). Additionally, rare mitochondrial DNA (mtDNA) mutations have been shown to be causal for T2DM pathogenesis. So far, many studies have investigated the possibility that mtDNA variation might affect the risk of T2DM, however, when found, haplogroup association has been rarely replicated, even in related populations, possibly due to an inadequate level of haplogroup resolution. Effects of mtDNA variation on diabetes complications have also been proposed. However, additional studies evaluating the mitochondrial role on both T2DM and related complications are badly needed. To test the hypothesis of a mitochondrial genome effect on diabetes and its complications, we genotyped the mtDNAs of 466 T2DM patients and 438 controls from a regional population of central Italy (Marche). Based on the most updated mtDNA phylogeny, all 904 samples were classified into 57 different mitochondrial sub-haplogroups, thus reaching an unprecedented level of resolution. We then evaluated whether the susceptibility of developing T2DM or its complications differed among the identified haplogroups, considering also the potential effects of phenotypical and clinical variables. MtDNA backgrounds, even when based on a refined haplogroup classification, do not appear to play a role in developing T2DM despite a possible protective effect for the common European haplogroup H1, which harbors the G3010A transition in the MTRNR2 gene. In contrast, our data indicate that different mitochondrial haplogroups are significantly associated with an increased risk of specific diabetes complications: H (the most frequent European haplogroup) with retinopathy, H3 with neuropathy, U3 with nephropathy, and V with renal failure.