Seven unidentified reading frames of human mitochondrial DNA encode subunits of the respiratory chain NADH dehydrogenase

A century of mitochondrial research, 1922-2022

Although recognized earlier as subcellular entities by microscopists, mitochondria have been the subject of functional studies since 1922, when their biochemical similarities with bacteria were first noted. In this overview I trace the history of research on mitochondria from that time up to the present day, focussing on the major milestones of the overlapping eras of mitochondrial biochemistry, genetics, pathology and cell biology, and its explosion into new areas in the past 25 years. Nowadays, mitochondria are considered to be fully integrated into cell physiology, rather than serving specific functions in isolation.

Getting mitochondria to center stage

The question of how eukaryotic cells assemble their mitochondria was long considered to be inaccessible to biochemical investigation. This attitude changed about fifty years ago when the powerful tools of yeast genetics, electron microscopy and molecular biology were brought to bear on this problem. The rising interest in mitochondrial biogenesis thus paralleled and assisted in the birth of modern biology. This brief recollection recounts the days when research on mitochondrial biogenesis was an exotic effort limited to a small group of outsiders.

The fires of life

This retrospective recounts the hunt for the mechanism of mitochondrial ATP synthesis, the early days of research on mitochondrial formation, and some of the colorful personalities dominating these often dramatic and emotional efforts. The narrative is set against the backdrop of postwar Austria and Germany and the stream of young scientists who had to leave their countries to receive postdoctoral training abroad. Many of them--including the author--chose the laboratory of a scientist their country had expelled a few decades before. The article concludes with some thoughts on the uniqueness of U.S. research universities and a brief account of the struggles to revive science in Europe.

mRNA differential display identification of vascular smooth muscle early response genes regulated by PDGF

The modulation of vascular smooth muscle cells (VSMCs) from the quiescent phenotype to the proliferative and migratory phenotype is a critical event in the pathogenesis of atherosclerosis. To-date several growth factors, including platelet-derived growth factor, PDGF, have been shown to induce VSMC proliferation and migration. To further understand the mechanism of PDGF-induced VSMC activation, quiescent human coronary artery SMC were treated with PDGF, and the genes that displayed transcriptional changes within 3 and 8 h were identified using differential display RT-PCR, real-time PCR, nucleotide sequencing and bioinformatics. Eleven genes that were highly upregulated or down-regulated at 3 and/or 8 h by PDGF, designated growth-factor regulated VSMC genes (GRSG1-11), were analyzed. GRSG5 and GRSG9-1 were identified as cortactin and cytochrome c oxidase subunit II, respectively. The remaining nine GRSGs were novel. GRSG3, 4, 5 and 9-2 showed wide tissue distribution whereas GRSG10-1, 10-2, and 11 were tissue specific. Cortactin was localized by immunohistochemical staining to the neointima and fibrous cap of human coronary artery atherosclerotic plaques. Domain analysis of open reading frames suggest that the novel GRSGs may participate in signaling, metabolic, translational or migrational processes during PDGF-induced VSMC activation.

The mitochondrial genome in embryo technologies

The mammalian mitochondrial genome encodes for 37 genes which are involved in a broad range of cellular functions. The mitochondrial DNA (mtDNA) molecule is commonly assumed to be inherited through oocyte cytoplasm in a clonal manner, and apparently species-specific mechanisms have evolved to eliminate the contribution of sperm mitochondria after natural fertilization. However, recent evidence for paternal mtDNA inheritance in embryos and offspring questions the general validity of this model, particularly in the context of assisted reproduction and embryo biotechnology. In addition to normal mt DNA haplotype variation, oocytes and spermatozoa show remarkable differences in mtDNA content and may be affected by inherited or acquired mtDNA aberrations. All these parameters have been correlated with gamete quality and reproductive success rates. Nuclear transfer (NT) technology provides experimental models for studying interactions between nuclear and mitochondrial genomes. Recent studies demonstrated (i) a significant effect of mtDNA haplotype or other maternal cytoplasmic factors on the efficiency of NT; (ii) phenotypic differences between transmitochondrial clones pointing to functionally relevant nuclear-cytoplasmic interactions; and (iii) neutral or non-neutral selection of mtDNA haplotypes in heteroplasmic conditions. Mitochondria form a dynamic reticulum, enabling complementation of mitochondrial components and possibly mixing of different mtDNA populations in heteroplasmic individuals. Future directions of research on mtDNA in the context of reproductive biotechnology range from the elimination of adverse effects of artificial heteroplasmy, e.g. created by ooplasm transfer, to engineering of optimized constellations of nuclear and cytoplasmic genes for the production of superior livestock.

Transmitochondrial differences and varying levels of heteroplasmy in nuclear transfer cloned cattle

To assess the extent of cytoplasmic genetic variability in cloned cattle produced by nuclear transplantation procedures, we investigated 29 individuals of seven male cattle clones (sizes 2-6) from two different commercial sources. Restriction enzyme and direct sequence analysis of mitochondrial DNA (mtDNA) detected a total of 12 different haplotypes. Transmitochondrial individuals (i.e., animals which share identical nuclei but have different mitochondrial DNA) were detected in all but one of the clones, demonstrating that mtDNA variation among cloned cattle is a very common phenomenon which prevents true genetic identity. The analyses also showed that the cytoplasmic genetic status of some investigated individuals and clones is further complicated by heteroplasmy (more than one mtDNA type in an individual). The relative proportions of different mtDNA-types in two animals with mild heteroplasmy were estimated at 2:98% and 4:96% in DNA samples derived from blood. This is in agreement with values expected from karyoplast-cytoplast volume ratios. In contrast, the mtDNA haplotype proportions observed in six other heteroplasmic animals of two different clones ranged from 21:79% to 57:43%, reflecting a marked increase in donor blastomere mtDNA contributions. These results suggest that mtDNA type of donor embryos and recipient oocytes used in nuclear transfer cattle cloning should be controlled to obtain true clones with identical nuclear and cytoplasmic genomes.

The complete mitochondrial DNA sequence of the white rhinoceros, Ceratotherium simum, and comparison with the mtDNA sequence of the Indian rhinoceros, Rhinoceros unicornis

The complete nucleotide sequence of the mitochondrial genome of the white rhinoceros, Ceratotherium simum, was determined. The length of the reported sequence is 16,832 nucleotides. This length can vary, however, due to pronounced heteroplasmy caused by differing numbers of a repetitive motif (5'-CG-CATATACA-3') in the control region. The 16,832 nucleotide sequence presented here is the longest version of the molecule and contains 35 copies of this motif. Comparison between the complete mitochondrial sequences of the white and the Indian (Rhinoceros unicornis) rhinoceroses allowed an estimate of the date of the basal evolutionary divergence among extant rhinoceroses. The calculation suggested that this divergence took place approximately 27 million years before present.

Mitochondrial NADH dehydrogenase and CYP2D6 genotypes in Lewy-body parkinsonism

The cause of nerve-cell death in sporadic Parkinson's disease remains unknown. Although environmental factors have been traditionally implicated in the etiology of Parkinson's disease, recent studies strongly suggest that there is a genetic contribution to this multifactorial disorder. We studied archival brain tissue from clinically and neuropathologically verified cases of Parkinson's disease, using nonradioactive cycle sequencing and restriction enzymatic analysis of polymerase chain reaction products. Twenty-one Parkinsonian brains with brain stem Lewy-bodies and 77 control brains were genotyped at two mitochondrial loci previously implicated in the etiology of neurodegenerative disease. In addition, genotyping was performed for two alleles of the debrisoquine 4-hydroxylase gene (CYP2D6). A heteroplasmic mtDNAG5460A missense mutation in the ND2 subunit gene of NADH dehydrogenase was three times more frequent in Parkinson cases (4/21) compared to controls (5/77). A homoplasmic mtDNAA4336G transition which alters the mitochondrial tRNAGln gene product was found in one Parkinson case. Frequencies of the CYP2D6G1934A and CYP2D6C2938T alleles were not significantly different between Parkinson cases and controls. Two Parkinsonian brains with high degrees of heteroplasmy for the ND2G5460A mutation and one CYP2D6C2938T homozygous case showed very high numbers of Lewy-bodies in the substantia nigra. The results of this study are in line with the concept that different genetic loci may be involved in Parkinson's disease susceptibility. They provide a hint that the ND2(5460) mutation, in combination with other factors, could play a role in disease pathogenesis in a subset of patients.

Screening for the two most frequent mutations in Leber's hereditary optic neuropathy by duplex PCR based on allele-specific amplification

This report describes a rapid and inexpensive assay, which allows detection, in whole blood and by PCR alone, of the two most frequent mitochondrial DNA mutations causing Leber's hereditary optic neuropathy. The assay is based on allele-specific amplification, using primers with the mutation-specific base in the 3' position, and a deliberately introduced G-->C substitution of base no. four from the 3' end, which prevents amplification of the wild-type allele.

The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina

The nucleotide sequence of the mitochondrial DNA (mtDNA) of the harbor seal, Phoca vitulina, was determined. The total length of the molecule was 16,826 bp. The organization of the coding regions of the molecule conforms with that of other mammals, but the control region is unusually long. A considerable portion of the control region is made up of short repeats with the motif GTACAC particularly frequent. The two rRNA genes and the 13 peptide-coding genes of the harbor seal, fin whale, cow, human, mouse, and rat were compared and the relationships between the different species assessed. At ordinal level the 12S rRNA gene and 7 out of the 13 peptide-coding genes yielded a congruent topological tree of the mtDNA relationship between the seal, cow, whale, human, and the rodents. In this tree the whale and the cow join first, and this clade is most closely related to the seal.

The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus

The composition of the mitochondrial DNA (mtDNA) of the fin whale, Balaenoptera physalus, was determined. The length of the molecule is 16,398 bp, and its organization conforms with that of other mammals. The general similarity between the mtDNA of the fin whale and the cow is greater than the similarity between the fin whale and other species (human, mouse, rat) in which the composition of the entire molecule has been described. The D-loop region of the mtDNA of the fin whale is 81% identical to the D-loop of dolphin DNA, and the central portion of the D-loop is similar to the bovine D-loop. The accumulation of transversions and gaps in the 12S and 16S rRNA genes was assessed by comparing the fin whale, cow, and human. The sequence difference between human and the whale and human and the cow was at the same level, indicating that the rate of evolution of the mtDNA rRNA genes is about the same in artiodactyls and cetaceans. In the 12S rRNA gene an accumulation rate of 0.05% per million years places the separation of cetaceans and artiodactyls at about 55 million years ago. The corresponding figure for human and either the whale or the cow is about 80 million years. In the 16S rRNA gene a 0.08% accumulation rate of transversions and gaps per million years yields concurring figures. A comparison between the cytochrome b gene of the fin whale and cytochrome b sequences in the literature, including dolphin (Stenella) sequences, identified the cetaceans as monophyletic and the artiodactyls as their closest relatives. The comparison between the cytochrome b sequences of the fin whale and Stenella showed that differences in codon positions one or two were frequently associated with a change in another codon position.

Codon usage is imposed by the gene location in the transcription unit

A characteristic profile of the fluctuations of codon usage is observed in bacteriophages and mitochondria. By following the DNA in the direction of transcription, one moves slowly from a region where selective pressure favours codons ending with C to a region where the bias is in favour of codons ending with T; then, abruptly, one again enters a region of codons ending in C. The transcription end point takes place in the area of abrupt change in codon usage. By comparing Drosophila yakuba and mouse mitochondrial genomes, it is possible to show that the strategy of codon usage for a given gene depends on its location along the transcription unit and not on the encoded protein. The choice of codons ending in T or C allows large scale variations of DNA stability which could regulate the speed of propagation of the RNA polymerase.

Evidence for the frequent use of TTG as the translation initiation codon of mitochondrial protein genes in the nematodes, Ascaris suum and Caenorhabditis elegans

Data obtained from alignments of nucleotide sequences of mitochondrial (mt) DNA molecules of the nematode worms Ascaris suum and Caenorhabditis elegans indicate that in six of the mt-protein genes of A. suum and three of the mt-protein genes of C. elegans TTG is used as the translation initiation codon. Also, GTT seems to be the translation initiation codon of the A. suum COIII gene. All of the five remaining A. suum mt-protein genes appear to begin with ATT and the remaining nine C. elegans mt-protein genes appear to begin with either ATT or ATA. Therefore, in contrast to all other metazoan mtDNAs sequenced so far, it is likely that none of the nematode mt-protein genes use the standard ATG translation initiation codon. Some A. suum and C. elegans mt-protein genes end in T or TA, suggesting that, as found in other metazoan mitochondria, 3'-terminal polyadenylation is occasionally necessary to generate complete translation termination codons in transcripts of nematode mt-protein genes.

Mitoskelin: a mitochondrial protein found in cytoskeletal preparations

A 70 kD protein, which we have named mitoskelin, is highly enriched in cytoskeletal preparations from bovine cardiac muscle. Mitoskelin has three main variants with isoelectric points between 5.6 and 5.8. Immunoblotting with polyclonal antibodies directed against mitoskelin shows that, like intermediate filament proteins, the majority of mitoskelin resists solubilization from a myocardial homogenate by a series of extraction solutions ranging from very low salt to 0.6 M KI buffers and by 0.1-1% Nonidet P-40 detergent. By double-label immunofluorescence on cells and tissues, mitoskelin is colocalized with the mitochondrial marker cytochrome c oxidase. Mitoskelin is associated with the inner membranes of mitochondria as shown by immunoelectron microscopy and immunoblotting. Immunological cross-reactivity and similarities of molecular weight, pI, distribution, and chromatographic properties indicate that mitoskelin is the 70 kD component of complex I (NADH: ubiquinone oxidoreductase), a portion of the mitochondrial oxidative phosphorylation system. No function or activity has yet been demonstrated for the 70 kD component of the 25-polypeptide complex I. Dialysis against physiological buffers allows purified, urea-solubilized mitoskelin to form 10 nm wide filamentous structures that do not closely resemble intermediate filaments. These results suggest the exciting possibility that mitochondria may contain a membrane-associated filamentous skeleton.

Photolabelling of a mitochondrially encoded subunit of NADH dehydrogenase with [3H]dihydrorotenone

Mitochondrial NADH dehydrogenase from bovine heart was photolabelled with the inhibitor [3H]dihydrorotenone. A constituent of the hydrophobic domain of the enzyme of Mr 33,000 was the major site of labelling. The identity of this protein with the mitochondrially encoded ND-1 gene product was established by immunoblotting and immunoprecipitation with an antiserum raised to the expected C-terminal sequence of the human ND-1 gene product.