Intragenic rearrangements in the mitochondrial NADH dehydrogenase subunit 6 gene of vertebrates

We have sequenced the mitochondrial-encoded NADH dehydrogenase subunit 6 gene from 19 species of birds. Comparison of the derived amino-acid sequences in 22 avian species, six mammals, and two fishes, reveals an intragenic rearrangement in mammals. The C-terminal half of the mammalian protein includes an internal insertion of 10–15 amino acids and a C-terminal deletion of 8–9 amino acids. Based on comparative sequence alignments and hydropathy profile analysis, five hydrophobic segments (designated I to V) corresponding to transmembrane regions are proposed. In this structural model of NADH dehydrogenase subunit 6, the mammalian insertion is found in a variable loop region between transmembrane segments IV and V.     

Mitochondrial DNA of Chlamydomonas reinhardtii: the ND4 gene encoding a subunit of NADH dehydrogenase

Summary The ND4 gene encoding a subunit of respiratory NADH dehydrogenase has been identified on the linear 15.8 kb mitochondrial DNA of Chlamydomonas reinhardtii. The gene maps downstream of ND5. The 1,332 bp nucleotide sequence presented is the first complete reported ND4 sequence from a photoautotrophic organism. The deduced protein of 443 amino acid residues shows 34%, 29% and 27% homology to the protein sequences of Aspergillus amstelodami, Drosophila yakuba and mouse, respectively. ND4 is the fifth and last mitochondrial gene of the NADH dehydrogenase complex on the 15.8 kb mitochondrial genome of C. reinhardtii.     

The subunit I of the respiratory-chain NADH dehydrogenase from Cephalosporium acremonium: the evolution of a mitochondrial gene

Summary A Cephalosporium acremonium mitochondrial gene equivalent to human URF1 has been identified. The primary structure of the protein is highly homologous to its human (39%) and A. nidulans (66%) counterparts. Hydrophobicity profiles and predicted secondary structures are also very similar suggesting that this gene codes for the subunit I of the respiratory-chain NADH dehydrogenase. The nucleotide sequence of the gene, 70% homologous to the A. nidulans one, presents a high AT content (72%) and this fact is reflected in the codon usage.     

The alpha subunit of the mitochondrial ATP synthetase is mitochondrially made in the unicellular heterotrophPrototheca zopfiii

Summary Prototheca zopfii is a unicellular, colorless alga which grows heterotrophically on several different carbon sources.P. zopfii cells were grown, labeled with [³⁵S] sulfate in the presence of cycloheximide, and the mitochondrial fraction isolated and analyzed by gel electrophoresis and autoradiography. Cycloheximide resistant translation products included a heavily labeled protein with an apparent molecular weight of 60,000. This labeled protein co-fractionated with mitochondria when the mitochondria were purified on Percoll gradients. When F₁-ATPase was isolated from the mitochondria, an active ATPase preparation was obtained which, when analyzed by gel electrophoresis, was found to contain 2 prominent proteins in the 55 kd to 60 kd region of the gel. Autoradiography of this electrophoretically-resolved ATPase preparation revealed that the larger of the two, bands, but not the smaller, was heavily labeled with [³⁵S]. Extraction of ATP synthetase (F₁ -F₀) from mitochondria with the detergent octylglucoside, yielded a preparation containing, as major components, the same two 55 kd to 60 kd proteins seen in the F₁-ATPase preparation. Limited proteolysis of the larger protein, isolated from mitochondria that had been labeled in the presence of cycloheximide, was carried out usingStaphylococcus aureus V8 protease or papain. The pattern of peptide fragments observed by Coomassie Blue staining was essentially identical to that observed by autoradiography. This shows that the labeled protein corresponds to the alpha subunit of the ATPase. Thus the alpha subunit of the mitochondrial ATP synthetase ofP. zopfii is synthesized in the mitochondria.     

Nucleotide-sequence analysis indicates that a DNA plasmid in a diseased isolate of Ophiostoma novo-ulmi is derived by recombination between two long repeat sequences in the mitochondrial large subunit ribosomal RNA gene

The nucleotide sequence of a mitochondrial plasmid (2234 bp) in a diseased isolate of Ophiostoma novo-ulmi, and sequences of the mitochondrial DNA that overlap and flank the plasmid end-points, have been determined. The plasmid was shown to be derived from the O. novo-ulmi mitochondrial large subunit ribosomal RNA gene and contained most of intron 1, the whole of exon 2, and probably the first part of intron 2. Within intron 1 there is an open reading frame with the potential to encode a 323 amino-acid polypeptide which contained dodecapeptide sequences typical of RNA maturases and DNA endonucleases. The endpoints of the plasmid in the mtDNA were located within two 90-bp direct imperfect repeat sequences, one of which comprised the last 7 bp of exon 1 and the first 83 bp of intron 1 whilst the other comprised the last 7 bp of exon 2 and the first 83 bp of intron 2. It is proposed that the Ld plasmid was generated by intramolecular recombination between these two repeats with the crossover point probably within the last 15 bp.     

A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum

A 1 380-bp intervening sequence within the mitochondrial small subunit ribosomal RNA (mt SSU rRNA) gene of the fungus Sclerotinia sclerotiorum has been sequenced and identified as a group-I intron. This is the first report of an intron in the mt SSU rRNA gene. The intron shows close similarity in secondary structure to the subgroup-IC2 introns from Podospora (ND3i1, ND5i2, and COIi5) and Neurospora (ND5i1). The intron has an open reading frame (ORF) that encodes a putative protein of 420 amino acids which contains two copies of the LAGLI-DADG motif. The ORF belongs to a family of ORFs identified in Podospora (ND3i1, ND4Li1, ND4Li2, ND5i2, and COIi5) and Neurospora (ND5i1). The putative 420-aa polypeptide is also similar to a site-specific endonuclease in the chloroplast large subunit ribosomal RNA (LSU rRNA) gene of the green alga Chlamydomonas eugametos. In each clone of S. sclerotiorum examined, including several clones which were sampled over a 3-year period from geographically separated sites, all isolates either had the intron or lacked the intron within the mt SSU rRNA gene. Screening by means of Southern hybridization and PCR amplification detected the intron in the mt SSU rRNA genes of S. minor, S. trifoliorum and Sclerotium cepivorum, but not in other members of the Sclerotiniaceae, such as Botrytis anamorphs of Botryotinia spp., or in other ascomycetous and basidiomycetous fungi.     

Chimeric organization of two genes for the soybean mitochondrial ATPase subunit 6

Summary There are two copies of the ATPase subunit 6 (atp6) gene in the soybean mitochondrial genome which differ in their gene organization but share extensive homology with the maize atp6 gene except at their 5 ends. The two soybean genes are chimeric, containing regions with homology to other known mitochondrial genes at their 5 ends. Sequences homologous to the cytochrome oxidase subunit II (coxII) are located in one copy and sequences homologous to the ATPase subunit 9 (atp9) gene are located in the other copy, both of which contain methionine (ATG) codons that are in-frame with the remainder of the atp6 open reading frame. At least the copy of atp6 that contains the coxII sequence at its 5 end is abundantly transcribed to give an RNA of approximately 1,200 nucleotides.     

The gene for the large (16S) ribosomal RNA from the Locusta migratoria mitochondrial genome

Summary The nucleotide sequence of a segment of the mtDNA molecule of the locust Locusta migratoria containing the complete large rRNA (16S) gene and some nucleotides in its vincinity has been determined. The gene contains 1314 nucleotides, comprising the smallest metazoan gene reported to date. The gene has a low content of GC (21%) and exhibits an extended sequence homology to the corresponding gene of the dipteran insect Drosophila yakuba, suggesting a comparable secondary structure. The gene structure is discussed in an evolutionary and functional context.     

Different mitochondrial gene orders among insects: exchanged tRNA gene positions in the COII/COIII region between an orthopteran and a dipteran species

Summary We have cloned and sequenced a 2.65 kb segment of the mtDNA molecule of the orthopteran insect Locusta migratoria. It harbors the genes for four mitochondrial tRNAs, for cytochrome c oxidase subunits II and III and for ATPase subunits 6 and 8. The order of the locust genes resembles that of Drosophila yakuba: in both insects the genes for C0II and ATPase 8 are separated from each other by the genes encoding tRNA^lys and tRNA^asp, but in the locust, the positions of the two tRNA genes are reversed. This leads to a different mitochondrial gene order in the two insects.