The ATPase subunit 6 gene of tobacco mitochondria contains an unusual sequence

Summary We have isolated and characterized the F₀-ATPase subunit 6 gene (atp6) from tobacco mitochondria. The tobacco sequence exists as a single copy, is transcribed and contains an open reading frame (ORF) capable of encoding a peptide of 395 amino acids. The first 130 amino acids of the tobacco putative polypeptide show limited homology with the N terminus predicted for the maize ATPase subunit 6. Although poorly conserved at the sequence level, the tobacco and maize amino termini are hydrophilic and have a high percentage of charged amino acids. This portion of the predicted peptide may represent a presequence that is common to the ATPase subunit 6 of plants. Significant homology between tobacco and maize begins with amino acid 131, in a region that is highly conserved among fungal ATPase 6 subunits. In the remainder of the predicted protein, tobacco and maize share approximately 81% homology. A 41 by sequence and a 175 by conserved region found upstream from the tobacco atp6 coding region are homologous with sequence elements found in the 5 flanking regions of other plant mitochondrial genes and may be important for regulation and expression of the atp6 gene.     

tRNA genes in rat liver mitochondrial DNA

Summary Continuing the analysis of rat liver mitochondria) DNA, we have determined the sequences of two segments containing several tRNA genes. One of these segments also comprises the L-strand origin of replication. The characteristics of the 15 rat liver mitochondrial tRNA structures known at present are compared with those from other mammalian mitochondria.Abbreviations mtDNA mitochondrial DNA - U.R.F. unidentified reading frame (Anderson et al. 1981) - bp and Kbp base pairs and Kilobase pairs - Pu and Py purine and pyrimidine residues     

Conserved tRNA gene cluster in starfish mitochondrial DNA

Summary Partial sequencing of mtDNA from four long-diverged species of starfish reveals the existence of a conserved cluster of 13 tRNA genes, organized in a manner similar to that of the tRNA cluster of sea urchin mtDNA, but located at a position distant from the presumed replication origin. These findings suggest that a clustered organization of tRNA genes may have been present in the ancestral mitochondrial genome, and raise the possibility that tRNAs may have catalyzed the dispersal rather than the accumulation of the genes which encode them.     

The maxicircle of Trypanosoma brucei kinetoplast DNA hybridizes with a mitochondrial gene encoding cytochrome oxidase subunit II

A restriction endonuclease fragment of the maxicircle of Trypanosoma brucei brucei kinetoplast DNA hybridizes with a cloned mitochondrial DNA sequence which encodes cytochrome oxidase subunit II of Zea mays. A cloned mitochondrial DNA sequence encoding cytochrome oxidase subunit II of Saccharomyces cerevisiae also hybridizes with kDNA, but exhibits less homology with the maxicircle than does the maize gene. The hybridizing maxicircle DNA was localized to a 2.8 kbp segment which is bounded by TaqI restriction endonuclease sites and nearby HindIII and EcoRI restriction sites. The TaqI restriction fragment is conserved between T. brucei brucei, T. brucei rhodesiense and T. brucei gambiense and hybridizes with the Zea mays probe in each case.     

Nucleotide sequence of the cytochrome B gene and adjacent regions from rat liver mitochondrial DNA

Summary The nucleotide sequence of a 1.76 Kbp segment from rat liver mitochondrial DNA has been determined. It contains the gene for the cytochrome b apoprotein and the tRNA genes for threonine, glutamic acid, and proline. The arrangement of these genes in rat liver mitochondria is the same as in human (Anderson et al. 1981) or mouse (Bibb et al. 1981) mitochondria. The comparison of the cytochrome b sequences so far determined, reveals that several regions in these proteins are highly conserved. Abbreviations: Cyt b, cytochrome b apoprotein; U.R.F., unidentified reading frame (Anderson et al. 1981). Other abbreviations follow IUB-IUPAC conventions     

Cytochrome oxidase subunit II mRNAs in Oenothera mitochondria are edited at 24 sites

Summary Analysis of cDNA clones covering the entire coding region of cytochrome oxidase subunit II in Oenothera mitochondria reveals 24 potential editing sites: 23 C to U transitions and one U to C conversion. One editing event is observed outside the open reading frame in the 3 non-coding region. Thirteen editing sites are found altered in all cDNA clones, whereas the other eleven sites are only edited in some of the cDNA clones. These differentially edited sites occur most frequently at silent codon positions or in triplets at non-conserved amino acids.     

Analysis of a DNA segment from rat liver mitochondria containing the genes for the cytochrome oxidase subunits I,II and III,ATPase subunit 6, and several tRNA genes

Summary The sequence of a 6.24 kb DNA segment of the mitochondrial genome from rat liver has been determined. It comprises several genes coding for mitochondrial protein subunits and five tRNA genes in the following order: cytochrome oxidase subunit I — tRNA _(UCN) ^Ser —tRNA^Asp — cytochrome oxidase subunit II — tRNALys —ATPase subunit — cytochrome oxidase subunit III —tRNA^Gly — potential open reading frame — tRNA^Arg —two potential open reading frames. The tRNA genes were detected by a computer search programme. The assignments for the protein coding sequences were made through comparison with known sequences, mainly from the yeast mitochondrial proteins (e.g. Bonitz et al. 1980). Our data are discussed with regard to the features of gene arrangement, codon usage, and tRNA structure in mammalian mitochondria (Anderson et al. 1981).Abbreviations COX I, COX II, COX III mitochondrial cytochrome oxidase subunits I, II, and III - ATPase mitochondrial ATPase subunit 6 - U.R.F. unidentified reading frame (Anderson et al. 1981). Other abbreviations follow IUB-IUPAC conventions.     

Fine structure of OXI1, the mitochondrial gene coding for subunit II of yeast cytochrome c oxidase

Summary Genetic and biochemical studies have been performed with 110 mutants which are defective in cytochrome a·a₃ and map in the regions on mit DNA previously designated OXI1 and OXI2. With 88 mutations allocated to OXI1 fine structure mapping was achieved by the analysis of rho ^– deletions. The order of six groups of mutational sites (A 1, A2, B 1, B2, C 1, C2) thus determined was confirmed by oxi _i x oxi _j recombination analysis.Analysis of mitochondrially translated polypeptides of oxil mutants by SDS-polyacrylamide electrophoresis reveals three classes of mutant patterns: i) similar to wild-tpye (19 mutants); ii) lacking SU II of cytochrome c oxidase (53 mutants); iii) lacking this subunit and exhibiting a single new polypeptide of lower M_r (16 mutants). Mutations of each of these classes are scattered over the OXI1 region without any detectable clustering; this is consistent with the assumption that all oxil mutations studied are within the same gene.New polypeptides observed in oxil mutants of class iii) vary in Mr in the range from 10,500 to 33,000. Those of M_r 17,000 to 33,000 are shown to be antigenically related to subunit II of cytochrome c oxidase. Colinearity is established between the series of new polypeptides of M_r values increasing from 10,500 to 31,500 and the order of the respective mutational sites on the map, e.g. mutations mapping in A 1 generate the smallest and mutations mapping in C2 the largest mutant fragments.From these data we conclude that i) all mutations allocated to the OXI1 region are in the same gene; ii) this gene codes for subunit II of cytochrome c oxidase; iii) the direction of translation is from CAP to 0X12. Out of 19 mutants allocated to OXI2 three exhibit a new polypeptide; these and all the other oxi2 mutants lack subunit III of cytochrome oxidase. This result provides preliminary evidence that the OXI2 region harbours the structural gene for this subunit III.Abbreviations mitDNA mitochondrial DNA - SU I, SU II, SU III subunits of cytochrome c oxidase - SDS sodium dodecyl sulfate - M_r Molecular weight - d Dalton     

DNA sequence analysis of the 24.5 Kilobase pair cytochrome oxidase subunit I mitochondrial gene from Podospora anserina: a gene with sixteen introns

Summary The DNA sequence of a 26.7 Kilobase pair (10³ base pairs = 1 Kb) region of the mitochondrial genomes of races s and A from Podospora anserina was determined. Within this region, the 24.5 Kb cytochrome oxidase subunit I gene was located and its exon sequences determined by computer analysis comparisons with other fungal genes. The Podospora COI gene was interrupted by two group II introns (one in race s) and fourteen group I introns ranging in size from about 2.2 Kb to 404 bp. Earlier studies on secondary structure analysis, as well as comparison of their open reading frames (ORFs), showed that the two group II introns were closely related. The fourteen group I introns were representatives of three subgroupings (IB, C and a new category, subgroup ID). Two of these group I introns were separated by just a single exon codon. The analysis of all these introns is discussed in comparison with other fungal introns as well as with the known Podospora anserina introns.     

A gene for cytochrome c oxidase subunit III (COXIII) in broad bean mitochondrial DNA: structural features and sequence evolution

Summary A nucleotide sequence of broad bean mitochondrial DNA (mtDNA) that contains the coxIII gene is presented, and compared to corresponding sequences of Oenothera and corn mtDNAs. Upstream from the broad bean coxIII gene are three potential secondary structures: a single stem and loop (hairpin) that is conserved in the Oenothera and corn sequences; a second single stem and loop; and a double stem and loop. The rate of evolution of the coxIII gene has been slower in plants than in mammals. Constraints on the fixation of at least some kinds of mutations in silent (synonymous) third position nucleotides, as well as of mutations that cause amino acid replacements, seem to have contributed to this slower rate.     

A new pathologic mitochondrial DNA mutation in the cytochrome oxidase subunit I (MT-CO1)

A disorder of mitochondrial energy metabolism may be missed in children with a very mild phenotype. Here, we described a patient with a moderate mental retardation and a mild exercise intolerance. This child harboured a mtDNA transition (m.6955G>A) in the subunit I of the cytochrome oxidase (MT-CO1) that fulfils most of the requirements to be pathologic. Despite this subunit is the second longest polypeptide encoded in the mtDNA, only one other missense mutation associated with a myopathy has been described. This suggests that we are missing other phenotypes and that the mitochondrial pathology field is broader that previously thought.     

The oli1 gene and flanking sequences in mitochondrial DNA of Saccharomyces cerevisiae: the complete nucleotide sequence of a 1.35 kilobase petite mitochondrial DNA genome covering the oli1 gene

Summary As part of our genetic and molecular analysis of mutants of Saccharomyces cerevisiae affected in the oli1 gene (coding for mitochondrial ATPase subunit 9) we have determined the complete nucleotide sequence of the mtDNA genome of a petite (23-3) carrying this gene. Petite 23-3 (1,355 base pairs) retains a continuous segment of the relevant wild-type (J69-1B) mtDNA genome extending 983 nucleotides upstream, and 126 nucleotides downstream, of the 231 nucleotide oli1 coding region. There is a 15-nucleotide excision sequence in petite 23-3 mtDNA which occurs as a direct repeat in the wild-type mtDNA sequence flanking the unique petite mtDNA segment (interestingly, this excision sequence in petite 23-3 carries a single base substitution relative to the parental wild-type sequence). The putative replication origin of petite 23-3 is considered to lie in its single G,C rich cluster, which differs in just one nucleotide from the standard ori ^s sequence. The DNA sequences in the intergenic regions flanking the oli1 gene of strain J69-1B (and its derivatives) have been systematically compared to those of the corresponding regions of mtDNA in strains derived from the D273-10B parent (sequences from the laboratory of A. Tzagoloff). The nature and distribution of the sequence divergencies (base substitutions, base deletions or insertions, and more extensive rearrangements) are considered in the context of functions associated with mitochondrial gene expression which are ascribed to specialized sequences in the intergenic regions of the yeast mitochondrial genome.     

The cytochrome oxidase subunit III gene in sunflower mitochondria is cotranscribed with an open reading frame conserved in higher plants

Summary The gene encoding subunit III of cytochrome oxidase (COXIII) has been identified in the sunflower mitochondrial genome. The COXIII coding region is located 570 bp downstream of a 477 bp open reading frame (ORFB). Sequence comparisons and hybridization experiments show that ORFB sequences are conserved in other plant mitochondrial genomes. Nucleotide and amino acid sequence comparisons suggest that RNA editing is required in sunflower mitochondria to synthesize a functional COXIII polypeptide.     

Differential expression of the mitochondrial gene cytochrome oxidase II in benign and malignant breast tissue.

Comparative analysis of expression levels of genes in benign and malignant tumours of the breast has been performed. Differential screening of cDNA libraries identified four genes of the mitochondrial genome as being expressed at different levels in the two tissues compared, but further investigations showed that only the gene encoding subunit 2 of cytochrome c oxidase (COII) is expressed at significantly higher levels in carcinomas compared with fibroadenomas. The mitochondrial genes encoding subunits 2 and 4 of NADH dehydrogenase, and subunit 6 of F0F1ATPase, were not found to be differentially expressed in carcinomas and fibroadenomas. All four genes were expressed in the epithelium of human breast carcinomas, as shown by in situ hybridization. The expression level of the COII gene is also correlated with carcinoma grade. No gross alterations to the mitochondrial DNA from these tumours could be detected. The possible implications of these results on the behavioural differences between fibroadenomas and carcinomas are discussed.     

Identification of an aspartate transfer RNA gene in maize mitochondrial DNA

Summary A gene for a transfer RNA (tRNA) specific for aspartic acid was identified in maize mitochondrial DNA. The nucleotide sequence and predicted secondary structure of this tRNA more closely resemble eubacterial and chloroplast aspartate tRNA genes than other mitocondrial aspartate tRNA genes. This gene is located on a 3,123 base pair EcoRl DNA fragment that also contains an elongator methionine tRNA gene. These two tRNA genes are separated by 726 nucleotides and are located on opposite strands of DNA.Paper No. 9755 of the Journal series of the North Carolina Agricultural Research Service, Raleigh