Mitochondrial ATPase complex of Aspergillus nidulans and the dicyclohexylcarbodiimide-binding protein

A mitochondrial reading frame which may code for a second form of ATPase subunit 9 in Aspergillus nidulans

The nucleotide sequence of a 74 codon reading frame from the Aspergillus nidulans mitochondrial genome is presented. The derived amino acid sequence displays typical features of dicyclohexylcarbodiimide (DCCD) binding proteins and is 84% homologous with a mitochondrial reading frame that potentially encodes an ATPase subunit 9 polypeptide in Neurospora crassa. However, in A. nidulans, as in N. crassa, there is strong biochemical and genetic evidence that this subunit is in fact nuclearly-encoded. In both organisms the DCCD-binding protein found in the F0 complexes of mitochondria from actively-growing cultures is almost certainly the product of this nuclear gene, and definitely not that of the mitochondrial reading frame. The discovery of an intact open reading frame than can code for a DCCD-binding protein in the mitochondrial genome of a second species of filamentous fungus strenghthens the possibility that the presence of a mitochondrial version of this gene has some biological significance.

Sequences of members of the human gene family for the c subunit of mitochondrial ATP synthase

Subunit c is an intrinsic membrane component of ATP synthase, and in mammals it is encoded by two expressed nuclear genes, P1 and P2. Both genes encode the same mature c subunit, but the mitochondrial import pre-sequences in the precursors of subunit c are different. The DNA sequences of the human P1 and P2 genes are described. They occupy about 3.0 and 10.9 kb respectively of the human genome, and both genes are split into five exons. The human genome also contains about 14 related spliced pseudogenes, and the sequence of one such pseudogene related to P2 is described. Sequences flanking the 5' ends of the human P1 and P2 coding sequences each contain a CpG-rich island. Potential promoter elements (TATA and CCAAT boxes) are present in the 5' sequences of the P1 gene, but not that of P2, although there is no direct experimental evidence to show the involvement of these sequences in transcription of the genes.

Genic rearrangements in Phytophthora mitochondrial DNA

To assess evolutionary relationships among the oomycetous fungi we have constructed a physical and genic map of the mtDNA of a broad host range strain (695T) of Phytophthora megasperma. While, like other Phytophthora species, this 43.5 kb circular genome lacks the typical oomycete large inverted repeat, a short 0.5-0.9 kb inverted repeat has been identified. Comparison of the relative order of seven genic regions with host-specific Phytophthora strains reveals both a clustering of these loci within one-third of the host-specific genomes, and two genic inversions relative to the broad host range genome. The location of the short inverted repeat suggests that at least one of the inversions is a consequence of intramolecular recombination between repeat elements.

Processing of mitochondrial RNA in Aspergillus nidulans

Genes for cytochrome oxidase subunit I (oxiA), ATPase subunit 9, NADH dehydrogenase subunit 3 (ndhC) and cytochrome oxidase subunit II (oxiB) are located within a 7.2 kb (1 kb = 10(3) bases or base-pairs) segment of the Aspergillus nidulans mitochondrial genome. Northern hybridization shows that abundant RNA molecules of 4.0, 2.5 and 1.5 kb, each containing copies of two or more genes, are transcribed from this region. The 4.0 kb molecule, which contains copies of each of the four genes but lacks the three oxiA introns, is cleaved at a point just upstream from ndhC to give rise to the 2.5 kb RNA, which contains copies of oxiA and the ATPase subunit 9 gene, and the 1.5 kb RNA, which carries ndhC and oxiB. The ATPase subunit 9 gene, which has no identified function, is therefore transcribed into an abundant RNA. S1 nuclease analysis indicates that there are no additional introns in the amino-terminal region of oxiA and that the 4.0 and 2.5 kb transcripts of this gene have staggered 5' termini, the most upstream of which is adjacent to the 3' end of the histidinyl-tRNA gene. The results suggest that transcription of this genome proceeds via a very limited number of primary transcripts with mature RNAs produced by extensive processing events including tRNA excision. RNA synthesis and processing in A. nidulans mitochondria therefore resembles the events occurring in metazoa rather than yeast.

The oliC3 gene of Aspergillus niger: isolation, sequence and use as a selectable marker for transformation

The oliC3 gene of Aspergillus niger has been isolated and sequenced. This gene encodes an oligomycin-resistant variant of the mitochondrial ATP synthase subunit 9. In transformation experiments the gene can serve as a semi-dominant selectable marker for A. niger. It was possible to recognize transformants in which oliC3 had integrated at the homologous oliC locus, as opposed to elsewhere in the genome, by observation of phenotypes on medium containing oligomycin. DNA sequencing has allowed comparison of the deduced amino acid sequence with subunit 9 proteins from other species and comparison of 5' untranslated sequences with those from other fungi.

Transformation of Penicillium chrysogenum with a dominant selectable marker

We have cloned a mutant oligomycin resistance allele of the mitochondrial ATP synthase subunit 9 gene from the filamentous fungus Penicillium chrysogenum. The gene was isolated using the equivalent gene from Aspergillus nidulans as a hybridisation probe. Using the cloned gene it is possible to select for oligomycin resistance in P. chrysogenum transformation experiments. This transformation system was used to introduce further copies of the P. chrysogenum isopenicillin N synthetase gene, which were stably maintained without selection. An assessment of the frequency with which homologous integration occurs was also made. With this system, it should prove possible to transform any strain of P. chrysogenum.

The ATP synthase subunit 9 gene of Aspergillus nidulans: sequence and transcription

We have determined the nucleotide sequence of the Aspergillus nidulans nuclear gene oliC31, which encodes subunit 9 of mitochondrial ATP synthase. The open reading frame contains no introns and specifies a predicted protein of 143 amino acids comprising a pre-sequence of 62 residues and a mature protein of 81 residues. The amino acid homology with the equivalent Neurospora crassa protein is 50% for the pre-sequence and 80% for the mature protein. A comparison with this and other imported mitochondrial proteins has revealed conserved regions which may be important for transport or subsequent processing. Multiple transcription initiation and polyadenylation sites have been identified. The promoter region of the oliC31 gene is characterised by long pyrimidine-rich tracts preceding the transcription initiation sites.

Mitochondrial gene URFN of Neurospora crassa codes for a long polypeptide with highly repetitive structure

The mitochondrial DNA of Neurospora crassa contains a long potential gene, designated URFN, which is located immediately downstream from the CO1 gene. These two genes are encoded in different reading frames and overlap by 13 codons. URFN is 633 triplets long and terminates at a UAG stop codon. Its codon usage is atypical for N. crassa mitochondrial exons and introns, and resembles that of the long open reading frame (ORF) of the mitochondrial plasmid present in N. crassa strain Mauriceville. Multiple sequence repetitions occur in the presumptive URFN polypeptide, most notably a seven-times reiterated motif of 16 to 18 amino acid residues length. The hydropathy pattern shows that the N-terminal third of the URFN polypeptide is predominantly apolar and includes several potentially membrane-spanning stretches; the remaining part is hydrophilic. Calculation of the secondary structure predicts a high proportion (47%) of alpha-helix conformation. The longest alpha-helix contains 40 residues. No similarities to other mitochondrial genes or reading frames have been found, except a significant homology over a stretch of 16 amino acid residues between the N-terminal part of URFN and a well-conserved sequence in the C-terminal region of CO1. The repetitive region in URFN resembles a similarly repetitive stretch in an unassigned reading frame from bacteriophage lambda. Three arguments support the view that URFN is translated. The open reading frame has a considerable length; URFN is transcribed into a mRNA including the overlapping CO1 gene; URFN is most probably conserved among all the various Neurospora species examined thus far, strongly suggesting that it codes for an essential protein.

Analysis of the mitochondrial and nuclear genomes of two basidiomycetes, Coprinus cinereus and Coprinus stercorarius

The mitochondrial and nuclear genomes of Coprinus stercorarius and C. cinereus were compared to assess their evolutionary relatedness and to characterize at the molecular level changes that have occurred since they diverged from a common ancestor. The mitochondrial genome of C. stercorarius (91.1 kb) is approximately twice as large as that of C. cinereus (43.3 kb). The pattern of restriction enzyme recognition sites shows both genomes to be circular, but reveals no clear homologies; furthermore, the order of structural genes is different in each species. The C. stercorarius mitochondrial genome contains a region homologous to a probe derived from the yeast mitochondrial var1 gene, whereas its nuclear genome does not. By contrast, the C. cinereus nuclear, but not mitochondrial, genome contains a region homologous to the var1 probe. Only a small fraction of either the nuclear or mitochondrial genomes, perhaps corresponding to the coding sequences, is capable of forming duplexes in interspecies solution reassociations, as measured by binding to hydroxylapatite. Those sequences capable of reassociating were found to have approximately 15% divergence for the mitochondrial genomes and 7%-15% divergence for the nuclear genomes, depending on the conditions of reassociation.

Transformation of Aspergillus nidulans with a cloned, oligomycin-resistant ATP synthase subunit 9 gene

An allele (oliC31) of the A. nidulans oliC gene has been cloned using homology with the equivalent gene from N. crassa. OliC31 codes for an oligomycin-resistant, triethyltin-hypersensitive form of subunit 9 of the mitochondrial ATP synthase complex. Direct selection for oligomycin-resistance was possible following transformation of A. nidulans with the oliC31 gene. The phenotypes of transformants cultured in the presence of oligomycin were indicative of the position of integration of the transforming plasmid within the genome. Subsequent recombination events involving the integrated oliC31 gene were also apparent from altered levels of resistance to oligomycin or triethyltin. This gene should prove useful as a marker for transformation of strains lacking auxotrophic lesions and in gene replacement or disruption experiments.

The unusual varl gene of yeast mitochondrial DNA

The var1 gene specifies the only mitochondrial ribosomal protein known to be encoded by yeast mitochondrial DNA. The gene is unusual in that its base composition is nearly 90 percent adenine plus thymine. It and its expression product show a strain-dependent variation in size of up to 7 percent; this variation does not detectably interfere with function. Furthermore, var1 is an expandable gene that participates in a novel recombinational event resembling gene conversion whereby shorter alleles are preferentially converted to longer ones. The remarkable features of var1 indicate that it may have evolved by a mechanism analogous to exon shuffling, although no introns are actually present.

The Aspergillus nidulans mitochondrial genome

A brief description is provided of the overall organisation of the Aspergillus nidulans mitochondrial genome, as revealed by DNA sequence analysis.

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.

Effects of inhibitors of F0-F1 proton-translocating ATPase on urinary acidification

A proton pump in diverse biological systems consists of two structural units with separate but integrated functions, the F0-F1-ATPase. We tested by chemical perturbation the possibility that such a proton pump might be involved in urinary acidification conducted by urinary epithelia (UF0-UF1-ATPase). Tyrosine-reactive chemicals and N,N'-dicyclohexylcarbodiimide, known to block the proton channel unit (F0), also inhibited urinary acidification, as measured by the reverse short-circuit current (RSCC) in urinary bladders from toads and turtles. Since these chemicals were equally effective under aerobic and anaerobic conditions, the inhibition appears to occur directly on UF0 rather than on mitochondria. In contrast, an inhibitor of F0-F1-ATPase, oligomycin, only inhibited aerobic RSCC and was ineffective on anaerobic RSCC. Thus, oligomycin appears to inhibit mitochondrial F0-F1 rather than any UF0+UF1. Another inhibitor of the F1-ATPase unit, N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline, was without effect on RSCC at a concentration (0.3 mM) that produced over 50% inhibition of short-circuit current. These results support the concept that acidifying urinary epithelia contain a plasma membrane proton channel, UF0, but that UF1, if it exists, is unique in that it is resistant to known inhibitors.

Conservation and rearrangement of mitochondrial structural gene sequences

Mitochondria contain the simplest DNA molecules that are present in eukaryotes. Mitochondrial DNA (mtDNA) is easily purified, and is an important model system for studying eukaryote gene structure and basic molecular processes. The protein sequences of mitochondrial gene products have been shown to be conserved from yeast to man, and there are definite similarities at the DNA sequence level. In contrast, the overall organization of the mitochondrial genome is drastically different in these organisms. To understand this, we need to extend work on mtDNA to a wider range of species. We have chosen to study the mtDNA of Aspergillus nidulans because a particularly comprehensive analysis of this system can be achieved using genetics as well as biochemistry, and like most eukaryotes it is an obligate aerobe, whereas Saccharomyces cerevisiae is not. We have investigated whether defined pieces of particular yeast mitochondrial genes show enough homology to Aspergillus mtDNA fragments to enable the corresponding Aspergillus genes to be located on the physical map. The results reported here show that this is the case for all five genes tested, and present the first data on the physical organization of the structural genes in the mitochondrial genome of A. nidulans.