Conservation and rearrangement of mitochondrial structural gene sequences

Mitochondrial DNA in the Oocyte and the Developing Embryo

Mitochondria play a primary role in cellular energetic metabolism, homeostasis, and death. They possess their own multicopy genome, which is maternally transmitted. Mitochondria are directly involved at several levels in the reproductive process since their functional status influences the quality of oocytes and contributes to the process of fertilization and embryonic development. This chapter discusses recent findings concerning mitochondrial DNA content and its expression during oogenesis, fertilization, and early embryonic development.

ADN mitochondrial du spermatozoïde

Mitochondria play a primary role in cellular energetic metabolism, homeostasis and death. In spermatozoa, in particular, mitochondria produce the ATP necessary for motility. Mitochondrial functions depend, at least partially, on mitochondrial DNA (mtDNA). The mitochondrial genome, the transmission of which is exclusively maternal contributes to cytoplasmic heredity. Qualitative and quantitative mtDNA abnormalities have been associated with male infertility. This review focuses on the role of mtDNA in human fertility.

Linear mitochondrial deoxyribonucleic acid from the yeast Hansenula mrakii

The mitochondrial deoxyribonucleic acid (mtDNA) from a petite-negative yeast, Hansenula mrakii, was studied. A linear restriction map was constructed with 11 restriction enzymes. The linearity of the genome was confirmed by direct end labeling of the molecule, followed by restriction analysis. The molecular weight of the DNA was found to be 55,000 base pairs. This is the first linear mtDNA found in yeast species. Using specific gene probes obtained from Saccharomyces cerevisiae mtDNA, we have constructed a gene map of H. mrakii mtDNA. The arrangement of genes in this linear genome was very different from the circular mtDNA of other known yeasts.

Mitochondrial DNAs of Suillus: three fold size change in molecules that share a common gene order

We constructed restriction-site and gene maps for mitochondrial DNAs from seven isolates of five species of Suillus (Boletaceae, Basidiomycotina). Each mitochondrial genome exists as a single circular chromosome, ranging in size from 36 to 121 kb. Comparisons within species and between two closely related species revealed that insertions and deletions are the major form of genome change, whereas most restriction sites are conserved. Among more distantly related species, size and restriction-site differences were too great to allow precise alignments of maps, but small clusters of putatively homologous restriction sites were found. Two mitochondrial gene orders exist in the five species. These orders differ only by the relative positions of the genes for ATPase subunit 9 and the small ribosomal RNA and are interconvertible by a single transposition. One of the two gene arrangements is shared by four species whose mitochondrial DNAs span the entire size range of 36 to 121 kb. The conservation of gene order in molecules that vary over three-fold in size and share few restriction sites demonstrates a low frequency of rearrangements relative to insertions, deletions, and base substitutions.

Circular mitochondrial genome of Candida albicans contains a large inverted duplication

The mitochondrial DNA (mtDNA) of the dimorphic fungus Candida albicans has a molecular size of 41 kilobase pairs as judged by summation of the fragment sizes produced by digestion with restriction endonucleases EcoRI, PvuII, and a combination of both enzymes. Five of the six EcoRI fragments comprising the mitochondrial genome have been cloned into the plasmid vector, pBR322. Restriction mapping revealed a circular map as predicted by previous observations with the electron microscope. The use of nick-translated, purified mtDNA to probe digests of mtDNA from other strains of C. albicans revealed a common restriction pattern. Use of nick-translated, cloned EcoRI fragments to probe digests of mtDNA revealed a large (at least 5 kilobase pairs), inverted duplication as well as a smaller (less than 0.4 kilobase pairs) region of related sequences.

Identification and characterization of mitochondrial translation products in various yeasts and in Prototheca zopfii

Mitochondrial genomes of different eucaryotes are not all alike. We have examined mitochondrial translation products in a number of yeasts (Candida krusei, Hansenula saturnus, Rhodotorula glutinis, Rhodotorula rubra, Torulopsis glabrata and Saccharomyces cerevisiae) and in Prototheca zopfii, a colorless alga, in order to determine whether certain proteins are invariably synthesized within mitochondria, how different these proteins are, and what additional proteins, if any, might be synthesized by diverse mitochondria. Using a variety of techniques and criteria, including immunological analysis and peptide mapping, we show that all the yeasts studied, and probably P. zopfii as well, make versions of the 3 large subunits of cytochrome c oxidase. Not all of these oxidase subunits are equally closely related to their counterparts in S. cerevisiae, however. Mitochondria of some of the yeasts studied do not make, or make only small amounts of, a counterpart to Varl, a major mitochondrially made protein in S. cerevisiae. Mitochondria of P. zopfii possibly do not make an apocytochrome b. T. glabrata, H. saturnus and the two Rhodotorula species each make one or more proteins whose relationship, if any, to mitochondrial translation products of S. cerevisiae is not apparent. These results provide new information about mitochondrial diversity. Whereas mitochondria of all the organisms that we have studied devote the major part of their synthetic effort to making the three large subunits of cytochrome c oxidase, and probably make certain other proteins in common, they do not all synthesize a completely identical set of proteins.

A 20 X 10(3)-base mosaic gene identified on the mitochondrial chromosome of Podospora anserina

By DNA sequencing and hybridization experiments we have localized the genes cob and col on the mitochondrial chromosome of Podospora anserina. The positions we have determined for these two genes are different from those previously attributed to them. The presence in the gene col of at least two introns, belonging respectively to class I and II, has been demonstrated. This gene, with a size of about 20 X 10(3) bases, appears to be the longest known mitochondrial mosaic gene.

The mitochondrial genome of the fission yeast Schizosaccharomyces pombe. 2. Localization of genes by interspecific hybridization in strain ade7-50h- and cloning of the genome in small fragments

A series of 18 small overlapping restriction fragments has been cloned, covering the complete mitochondrial genome of Schizosaccharomyces pombe. By hybridizing mitochondrial gene probes from Saccharomyces cerevisiae and Neurospora crassa with restriction fragments of Schizosaccharomyces pombe mitochondrial DNA, the following homologous genes were localized on the mitochondrial genome of S. pombe: cob, cox1, cox2 and cox3, ATPase subunit 6 and 9 genes, the large rRNA gene and both types of open reading frames occurring in mitochondrial introns of various ascomycetes. The region of the genome, hybridizing with cob exon probes is separated by an intervening sequence of about 2500 bp, which is homologous with the first two introns of the cox1 gene in Saccharomyces cerevisiae (class II introns according to Michel et al. 1982). Similarly, in the cox1 homologous region, which covers about 4000 bp, two regions were detected hybridizing with class I intron probes, suggesting the existence of two cox1 introns in Schizosaccharomyces pombe. Hybridization with several specific exon probes with a determined order has revealed that cob, cox1, cox3 and the large rRNA gene are all transcribed from the same DNA strand. The low intensities of hybridization signals suggest a large evolutionary distance between Schizosaccharomyces pombe and Saccharomyces cerevisiae or Neurospora crassa mitochondrial genes. Considering the length of the mitochondrial DNA of Schizosaccharomyces pombe (about 19.4 kbp) and the expected length of the localized genes and intron sequences there is enough space left for encoding the expected set of tRNAs and the small rRNA gene. The existence of leader-, trailer-, ori- and spacer sequences or further unassigned reading frames is then restricted to a total length of about 3000 bp only.

Identification of maxicircle DNA sequences in Leishmania Tarentolae that are homologous to sequences of specific yeast mitochondrial structural genes

Sequences homologous to the yeast mitochondrial structural genes for cytochrome oxidase subunits I and II, ATPase 6 and cytochrome b were identified on the kinetoplast DNA maxicircle molecule by low stringency hybridization of maxicircle blots with heterologous probes derived from mitochondrial DNA of yeast petite mutants. No hybridization was observed with the yeast ATPase 9 gene probe. The relative extent of base sequence mismatch was determined by melting of the heterologous hybrids. Candidates for the transcripts of these presumptive structural genes were proposed with reference to the transcriptional map of the maxicircle of Leishmania tarentolae. These results provide the first indication that maxicircle DNA specifies information for a limited number of conserved mitochondrial gene products similar to those already described for other eukaryotic cells.

Nucleotide sequence of Aspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase subunit 3, seven unidentified proteins, four tRNAs and L-rRNA

The complete nucleotide sequence of a 14 kb segment of A. nidulans mtDNA reveals a rather compact organization of genes transcribed from the same strand and coding for two functionally known proteins, seven unidentified polypeptides (URFs), 24 tRNAs and two rRNAs. One of the URFs is located in the intron of the L-rRNA gene and codes for a basic protein of 410 residues. The other URFs are in spacer regions and code for hydrophobic proteins. URFa is homologous to human URF4, and URFb produces a polypeptide of 48 residues resembling the human URF6L product (hydrophobic N-terminus, basic C-terminus). The ATPase subunit 6 genes from mitochondria and E. coli appear to share a common ancestor. The codon frequencies of identified genes and URFs are similar, and codons ending with G or C are rarely used. The structures of tRNAs specific for arginine, asparagine, tyrosine and histidine are deduced from gene sequences.

Nucleotide sequence of a region of the mitochondrial genome of Aspergillus nidulans including the gene for ATPase subunit 6

A 1500 bp fragment of the Aspergillus nidulans mitochondrial genome contains genes for arginine and asparagine tRNAs, an unassigned reading frame, and the structural gene for ATPase subunit 6. The tRNA genes possess 66% nucleotide homology and possibly originated by a relatively recent duplication event. The unassigned reading frame displays a low level of homology with the human URF A6L. The predicted amino acid sequence of the A-nidulans ATPase subunit 6 gene is 40% homologous to the yeast polypeptide and includes the short, highly conserved regions also present in the equivalent subunits from other mitochondrial systems and from Escherichia coli.

Are mitochondrial structural genes selectively amplified during senescence in Podospora anserina?

Genetic and transcriptional maps have been constructed for the mitochondrial genome of the Ascomycete Podospora anserina. These data have been plotted on the restriction maps for Sal I, Xho I, Bam HI, Eco RI, BgI II and Hae III. We have characterized and cloned a new and unique senescent mitochondrial DNA (beta-event senDNA) and have organized all of the recognized senDNAs on the genomic maps. We make the observation that all of the known and characterized senDNAs are derived from specific genes or gene regions of the young mitochondrial genome. We have unambiguously assigned the alpha-event senDNA (the 2.6 kb monomer) to the oxi3 gene locus and the beta-event senDNA to the oxi2 gene locus.

Extrachromosomal mutator inducing point mutations and deletions in mitochondrial genome of fission yeast

We report the isolation and characterization of a mutator mutant in the fission yeast Schizosaccharomyces pombe. This mutator is of extrachromosomal, very likely mitochondrial, inheritance and acts exclusively on mitochondrial mtDNA. It greatly enhances the frequency of spontaneous mitochondrial drug-resistance mutants compared to the wild type, but it is not obligatory for their occurrence. In contrast, mitochondrial respiratory deficient mutants can only be isolated from mutator strains. It could be shown that this mutator induces point mutations as well as deletions in the mitochondrial genome which lead to respiratory deficiency. This mutator might prove to have a novel function encoded by the mtDNA.

The Zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons

Cross hybridization between maize mitochondrial DNA fragments and a specific yeast mitochondrial DNA probe from the oxi 1 gene has been used to identify and isolate the maize mitochondrial gene coding cytochrome oxidase subunit II, mox 1. The DNA sequence reveals two coding regions separated from each other by a single centrally located intervening sequence. Hybridization of mox 1 DNA probes to mitochondrial RNA from plants shows that te gene is transcribed and indicates that several transcripts are spliced. TGA codons, which code Trp in the mitochondria of all species examined to date, do not occur in this gene. However, alignment of the mox 1 gene sequence with the amino acid sequences of subunit II from other organisms strongly suggests that codon CGG (normally Arg) codes for Trp in maize mitochondria, in addition to the standard Trp codon TGG.

Nuclear inheritance of oligomycin resistance in mouse L cells

The inheritance of oligomycin resistance was studied in three mouse L-cell mutants, OLI 2, OLI 4, and OLI 14. All three mutants had previously been shown to have oligomycin-resistant mitochondrial ATPase activity. In addition, OLI 14 has DCCD-resistant mitochondrial ATPase activity and an altered DCCD-binding protein. Oligomycin-resistant cells were enucleated and fused with oligomycin-sensitive cells under a variety of selective regimes designed to allow growth of oligomycin-resistant cybrids. No transfer of oligomycin resistance via the cytoplasm of OLI 2, OLI 4, or OLI 14 was detected. In contrast, oligomycin resistance was transferred with the karyoplasts of OLI 14 in karyoplast-cell fusions. Fusions between OLI 14 cells and oligomycin-sensitive cells also produced oligomycin-resistant hybrids. Transfer of oligomycin resistance in the karyoplast-cell and cell-cell fusions were demonstrated at the level of the mitochondrial ATPase. These results indicate that oligomycin resistance in OLI 14 is most likely under nuclear control. Furthermore, nuclear inheritance of oligomycin resistance in a mutant with a modified DCCD-binding protein suggests that the gene for the DCCD-binding protein is encoded in the nucleus of mammalian cells.

Linear mitochondrial deoxyribonucleic acid from the yeast Hansenula mrakii

The mitochondrial deoxyribonucleic acid (mtDNA) from a petite-negative yeast, Hansenula mrakii, was studied. A linear restriction map was constructed with 11 restriction enzymes. The linearity of the genome was confirmed by direct end labeling of the molecule, followed by restriction analysis. The molecular weight of the DNA was found to be 55,000 base pairs. This is the first linear mtDNA found in yeast species. Using specific gene probes obtained from Saccharomyces cerevisiae mtDNA, we have constructed a gene map of H. mrakii mtDNA. The arrangement of genes in this linear genome was very different from the circular mtDNA of other known yeasts.