Organisation of the mitochondrial genome of Trichophyton rubrum III. DNA sequence analysis of the NADH dehydrogenase subunits 1, 2, 3, 4, 5 and the cytochrome b gene

In this paper, we present the nucleotide sequence of a 9761 nt-long segment of the mitochondrial genome of the dermatophyte Trichophyton rubrum that bridges the gap between two previously published segments, making a unique contig that represents approximately 80% of the molecule. The location of all genes on the map is determined except for some tRNA genes expected to flank the LSU rRNA gene not yet sequenced. Starting from the 5′ end of the present sequence, we recognized the ND5 and ND2 genes, the cytochrome b gene, an unusually long intergenic spacer of unknown function, as well as the ND3, ND1 and ND4 genes. This sequence extends and confirms the similarity with the mitochondrial genome of Aspergillus nidulans. Interestingly, two cases of partial overlaps between the terminator and initiator codons of successive genes (ND4–ND5 and ND5–ND2) are encountered. Received: 9 July / 10 November 1998     

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.     

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.     

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.     

Alteration of the cytochrome c oxidase subunit 2 gene in the [exn-5] mutant of Neurospora crassa

Summary The maternally inherited [exn-5] mutant of Neurospora crassa is characterized by its slow-growth rate and deficiency of cytochrome aa ₃ relative to wildtype strains. We have determined the DNA sequence of the COXI and COXII genes of the mutant, which encode subunits 1 and 2 of cytochrome c oxidase, respectively. No changes in the DNA sequence of the COXI gene relative to the corresponding wild-type gene were found. In the region of the COXII gene we found two alterations, one a C to T transition eight base pairs upstream of the coding sequence and the second within the coding sequence for subunit 2 affecting amino acid 27 of the precursor polypeptide (amino acid 15 of the mature polypeptide). The altered codon in [exn-5] specifies an isoleucine residue rather than the wild-type threonine residue. The corresponding position in subunit 2 sequences of all other organisms examined is conserved either as a threonine or a serine residue. Thus, we consider it likely that the mutation directly affecting the coding sequence of the polypeptide is responsible for the [exn-5] phenotype. Analysis of serially passaged heterokaryons constructed between wild-type and [exn-5] shows that both mutations segregate with the [exn-5] phenotype. Examination of mitochondrial translation products in [exn-5] revealed a deficiency of subunit 2, as well as the presence of a polypeptide that corresponds to a previously described precursor of subunit 1 that accumulates in a COXI mutant of N. crassa, [mi-3]. We propose possible relationships between [exn-5], [mi-3], and the nuclear su-1 ^[mi-3] allele, which suppresses both mutations.     

Yeast SCO1 protein is required for a post-translational step in the accumulation of mitochondrial cytochrome c oxidase subunits I and II

Summary Biogenesis of functional cytochrome c oxidase in yeast requires the product of the nuclear gene SCO1. Strains deleted for this gene fail to accumulate the mitochondrially-synthesized cytochrome c oxidase subunits I and II, despite the presence of the respective mRNAs. Here we present data which demonstrate that the observed phenotype does not result from a failure to translate the mRNAs, but from a preferential degradation of the newly synthesized subunits. The SCO1 protein is therefore involved in a post-translational step in the accumulation of cytochrome c oxidase subunits I and II. We propose that the SCO1 protein is required for the correct assembly of both subunits into the cytochrome c oxidase complex.     

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.     

The genes for cytochrome b,ND 4L,ND6 and two tRNAs from the mitochondrial genome of the locust,Locusta migratoria

We have cloned and characterized a 2,778-kb XbaI segment of the mitochondrial genome of the locust, Locusta migratoria. It harbours portions of the ND4 and the ND1 genes, the entire genes for ND6, ND4L and cytochrome b, and the genes for three mitochondrial tRNAs. The genes are arranged in an order which is conserved between orthopteran and dipteran insects. The analysis of the cytochrome b sequence, and its comparison with other systems, supports the current model structure for this polypeptide.     

Location of the genes for cytochrome oxidase subunits I and II,apocytochrome b, α-subunit of the F1 ATPase and the ribosomal RNA genes on the mitochondrial genome of maize (Zea mays L.)

Summary The maize mitochondrial COXI, COXII, COB, ATPA and 5S, 18S and 26S rRNA genes have been located and orientated on the circular 570 kb restriction map. The ATPA gene is present in two copies, being within a 12 kb direct repeat, while the other genes are single copies. The protein coding genes are not obviously clustered whereas the 5S and 18S rRNA genes are closely linked and 16 kb from the 26S rRNA gene. The 5S and 18S mt rRNA genes and the ATPA gene are transcribed from the same mtDNA strand while the 26S rRNA, COXI, COXII and COB are transcribed from the opposite strand.     

Cloning,sequencing and expression of the Schwanniomyces occidentalis NADP-dependent glutamate dehydrogenase gene

Summary The cloned NADP-specific glutamate dehydrogenase (GDH) genes of Aspergillus nidulans (gdhA) and Neurospora crassa (am) have been shown to hybridize under reduced stringency conditions to genomic sequences of the yeast Schwanniomyces occidentalis. Using 5 and 3 gene-specific probes, a unique 5.1 kb BclI restriction fragment that encompasses the entire Schwanniomyces sequence has been identified. A recombinant clone bearing the unique BclI fragments has been isolated from a pool of enriched clones in the yeast/E. coli shuttle vector pWH5 by colony hybridization. The idenity of the plasmid clone was confirmed by functional complementation of the Saccharomyces cerevisiae ghd-1 mutation. The nucleotide sequence of the Schw. occidentalis GDH gene, which consists of 1380 nucleotides in a continuous reading frame of 459 amino acids, has been determined. The predicted amino acid sequence shows considerable homology with GDH proteins from other fungi and significant homology with all other available GDH sequences.