Structures of the genes encoding the α and β subunits of the Neurospora crassa mitochondrial ATP synthase

Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution

To study the tempo and pattern of mitochondrial gene loss in plants, DNAs from 280 genera of flowering plants were surveyed for the presence or absence of 40 mitochondrial protein genes by Southern blot hybridization. All 14 ribosomal protein genes and both sdh genes have been lost from the mitochondrial genome many times (6 to 42) during angiosperm evolution, whereas only two losses were detected among the other 24 genes. The gene losses have a very patchy phylogenetic distribution, with periods of stasis followed by bursts of loss in certain lineages. Most of the oldest groups of angiosperms are still mired in a prolonged stasis in mitochondrial gene content, containing nearly the same set of genes as their algal ancestors more than a billion years ago. In sharp contrast, other plants have rapidly lost many or all of their 16 mitochondrial ribosomal protein and sdh genes, thereby converging on a reduced gene content more like that of an animal or fungus than a typical plant. In these and many lineages with more modest numbers of losses, the rate of ribosomal protein and sdh gene loss exceeds, sometimes greatly, the rate of mitochondrial synonymous substitutions. Most of these mitochondrial gene losses are probably the consequence of gene transfer to the nucleus; thus, rates of functional gene transfer also may vary dramatically in angiosperms.

Interaction of mitochondria with microtubules in the filamentous fungus Neurospora crassa

The establishment and maintenance of the 3D structure of eukaryotic cells depends on active transport and positioning of organelles along cytoskeletal elements. The biochemical basis of these processes is only poorly understood. We analysed the interaction of mitochondria with microtubules in the filamentous fungus Neurospora crassa. Mitochondria were fluorescently labelled by expression of matrix-targeted green fluorescent protein. Upon isolation, mitochondria collapsed to round spherical structures that were still able to interact with microtubules in vitro. Binding of mitochondria to microtubules was dependent on peripherally associated proteins on the organellar surface, and was sensitive to adenine nucleotides. MMM1, a mitochondrial outer membrane protein important for maintenance of normal mitochondrial morphology, was not required. This suggests that the interaction of mitochondria with the cytoskeleton is independent of MMM1. We conclude that mitochondrial morphology is maintained by a complex interplay of extrinsic and intrinsic factors, including ATP-dependent proteins on the organellar surface.

Isolation of differentially expressed cDNA clones from salt-adapted Aspergillus nidulans

Differentially expressed cDNA clones were isolated from salt-adapted Aspergillus nidulans (FGSC #359). Poly (A)+ RNA from adapted mycelia was used to construct a lambda Uni-ZAP cDNA library. The library was screened with mixed subtracted cDNA probes. Three-hundred and fifty-seven positive plaques were isolated in the primary screening. Sixty-two randomly selected plaques were purified and placed into eight different cross-hybridization groups. A representative cDNA from each group was used to study expression under unadapted, salt-adapted and salt-shock conditions. These clones, representing eight different genes, displayed enhanced expression under salt stress. Exploratory nucleotide sequencing was performed, and the predicted amino-acid sequence was compared with known gene sequences in the data-bank. Five of the cDNA clones were identified as a mitochondrial (mt) ATPase beta subunit, a mt ATPase subunit 9, a mt transport protein, a ubiquitin-extension protein and a ribosomal protein. Three cDNA clones could not be identified due to lack of adequate homology with known sequences. These results suggest that at least five genes with known function in cellular processes like ATP generation and protein synthesis, and three other genes of unknown identity, are greatly induced in salt-adapted conditions.

Analysis of the mitochondrial ATP synthase beta-subunit gene in Drosophilidae: structure, transcriptional regulatory features and developmental pattern of expression in Drosophila melanogaster

We have cloned and determined the structure of the gene encoding the H(+)-ATP synthase beta subunit in two distantly related Drosophila species, D. melanogaster and D. virilis. The gene contains three exons that are extremely well conserved at the amino acid level, not only in the region encoding the mature protein but also in that encoding the leader peptide. Primer extension analysis indicates that the 5' untranslated region is extremely short, and reveals the presence of multiple initiation sites of transcription in both Drosophila species. The promoters of D. melanogaster and D. virilis H(+)-ATP synthase beta-subunit genes contain a conserved region surrounding the initiation transcription sites. Nucleotide sequence analysis has revealed the absence of canonical TATA and CCAAT boxes and the presence of several putative regulatory elements in both promoter regions, including GAGA, GATA and Ets binding sites. We have analysed the pattern of gene expression during D. melanogaster development. The mRNA is stored in oocytes, and activation of transcription takes place after 10 h of development. The expression of the nuclear-encoded H(+)-ATP synthase beta subunit is strictly coordinated with the expression of subunits 6 and 8 of the same complex that are encoded in the mitochondrial genome.

Regulation of the expression of three housekeeping genes encoding subunits of the Neurospora crassa vacuolar ATPase

The vacuolar ATPase is a complex enzyme and is encoded by at least nine genes, which appear to be scattered throughout the genome. We have examined the vma-1 vma-2, and vma-3 genes, which encode subunits present in multiple copies within the Neurospora crassa vacuolar ATPase. We wished to see if the expression of these genes is coordinately regulated and if these genes contain similar promoter elements. A region was sequenced of approximately 1 kb located upstream of the protein coding region for each gene. Several sequence elements were found in similar positions in each of the three genes. Each of the genes had several strong transcription initiation sites, clustered within 13-60 bp and located 112-193 bp upstream of the translation start site. The size and abundance of the RNA transcripts was also determined: the amount of RNA transcribed from each gene was roughly proportional to the numbers of each subunit present in the enzyme. A series of plasmids was constructed containing parts of the putative promoter region fused to beta-galactosidase. Analysis of these plasmids indicated that the essential region of the vma promoters lies within 370 bp of the protein coding region. Overall, the vma genes appear to have similar characteristics to "housekeeping" genes described in other organisms.

The proteolipid subunit of the Neurospora crassa vacuolar ATPase: isolation of the protein and the vma-3 gene

We have isolated the proteolipid subunit from the vacuolar ATPase of Neurospora crassa, using ion-exchange chromatography. We have also isolated several cDNA clones and the corresponding genomic DNA that encodes this subunit. The derived protein sequence indicates that the polypeptide is composed of 161 amino acid residues with an M(r) of 16,328 kDa. The gene encoding the proteolipid, named vma-3, is unusual in several respects. It contains four introns and, unlike other fungal genes, has non-coding regions that are as large as the coding regions. The 3' untranslated regions of the cDNAs were quite heterogeneous, with polyadenylation sites more than 300 bp apart. Analysis of the mRNA indicates that two size classes of transcripts are produced, differing in the length of the 3' untranslated region. Mapping of the vma-3 gene showed that it is closely linked, but not adjacent to, vma-1, the gene encoding the 67 kDa subunit of the vacuolar ATPase. This raises the possibility that in N. crassa some of the vacuolar ATPase genes may be clustered.

Characterization of the cit-1 gene from Neurospora crassa encoding the mitochondrial form of citrate synthase

We have isolated the cDNA and corresponding genomic DNA encoding citrate synthase in Neurospora crassa. Analysis of the protein coding region of this gene, named cit-1, indicates that it specifies the mitochondrial form of citrate synthase. The predicted protein has 469 amino acids and a molecular mass of 52,002 Da. The gene is interrupted by four introns. Hybridization experiments show that a cit-1 probe binds to two different fragments of genomic DNA, which are located on different chromosomes. Neurospora crassa may have two isoforms of citrate synthase, one in the mitochondria and the other in microbodies.

The vacuolar ATPase of Neurospora crassa

The filamentous fungus Neurospora crassa has many small vacuoles which, like mammalian lysosomes, contain hydrolytic enzymes. They also store large amounts of phosphate and basic amino acids. To generate an acidic interior and to drive the transport of small molecules, the vacuolar membranes are densely studded with a proton-pumping ATPase. The vacuolar ATPase is a large enzyme, composed of 8-10 subunits. These subunits are arranged into two sectors, a complex of peripheral subunits called V1 and an integral membrane complex called V0. Genes encoding three of the subunits have been isolated. vma-1 and vma-2 encode polypeptides homologous to the alpha and beta subunits of F-type ATPases. These subunits appear to contain the sites of ATP binding and hydrolysis. vma-3 encodes a highly hydrophobic polypeptide homologous to the proteolipid subunit of vacuolar ATPases from other organisms. This subunit may form part of the proton-containing pathway through the membrane. We have examined the structures of the genes and attempted to inactivate them.