Analysis of exon and intron mutants in the cytochrome b mitochondrial gene of Saccharomyces cerevisiae

The nucleotide changes present in a group of five cytochrome b mit^– mutants were analyzed at the sequence level. Two single-base changes were found: one (M10-152) generated a nonsense codon in the first exon while the other (M8-181) created a missense substitution in the second exon. The other mutants all have multiple (three) substitutions that either resulted in a missense mutation in a coding region (M17-162) or else changed nucleotides in the last intron of the gene, so blocking its excision (M6-200 and M8-53). The synthesis of mitochondrial polypeptides and the steady state concentration of the complex-III subunits were examined. The Rieske protein and the core-4 and core-5 subunits were much reduced in all mutants. Consequently the overall stability of complex III is very sensitive even to amino-acid substitutions in the cytochrome b protein. Mutant M8-53 provides direct evidence for the proposed role of the P9.1 stem in the core structure of the group-I type last intron of this gene. Received: 12 February 1996 / 28 March 1996     

A screen of yeast respiratory mutants for sensitivity against the mycotoxin citrinin identifies the vacuolar ATPase as an essential factor for the toxicity mechanism

In countries with a hot climate the mycotoxin citrinin represents a serious problem in fungal food-poisoning. In humans the renal system is affected the most and the mitochondrial respiratory chain was identified as a possible sensitive target for this toxin. In addition, citrinin has an antifungal activity that also inhibits the growth of the yeast Saccharomyces cerevisiae. So far the precise mode of action and the subcellular targets for citrinin have not been identified. Therefore, we decided to use the model organism yeast for a genetic approach to identify genes that play a role in the sensitivity against this mycotoxin. A large collection of conditional respiratory deficient yeast mutants was screened for sensitivity against citrinin. One special pet-ts mutant was identified that exhibited a higher sensitivity against citrinin. The genetic system of yeast allowed the isolation of the respective wild-type gene. This yeast gene encodes the Vph2p subunit that is essential for the correct assembly of the vacuolar ATPase. Isolation of the mutated gene and gene-disruption experiments of VPH2 and the partially overlapping small YKL118W gene verified this finding. The wild-type VPH2 gene restores all defects of the mutants. In contrast to this, YKL118W gave no complementation and the null mutant showed no phenotype. Thereby the yeast vacuolar ATPase was found to be important for the toxic effect of citrinin in yeast cells. The consequences of this finding for the molecular mechanism of citrinin action and its relation to the mitochondrial respiratory chain are discussed. Received: 18 November / 27 December 1999     

Molecular analysis of UFE1, a Saccharomyces cerevisiae gene essential for spore formation and vegetative growth

 The UFE1 gene of Saccharomyces cerevisiae was cloned, sequenced and characterized. The coding region of UFE1 is separated from the TMP1 gene on chromosome XV by 624 bp. Gene-disruption experiments demonstrated that UFE1 is essential for both the germination of ascospores and for vegetative growth. Translation of the UFE1 coding region generates a protein with significant similarity to cytokeratin and to the coiled-coil region of SED5, USO1 and restin, suggesting that it is involved in the secretory pathway and may also be related to intermediate filament-associated proteins. Received: 6 May/18 June 1996     

Molecular cloning of the PEL1 gene of Saccharomyces cerevisiae that is essential for the viability of petite mutants

The PEL1 gene of Saccharomyces cerevisiae is essential for the cell viability of mitochondrial petite mutants, for the ability to utilize glycerol and ethanol on synthetic medium, and for cell growth at higher temperatures. By tetrad analysis the gene was assigned to chromosome III, centromere proximal of LEU2. The PEL1 gene has been isolated and cloned by the complementation of a pel1 mutation. The molecular analysis of the chromosomal insert carrying PEL1 revealed that this gene corresponds to the YCL4W open reading frame on the complete DNA sequence of chromosome III. The putative Pel1 protein is characterized by a low molecular weight of approximately 17 kDa, a low codon adaptation index, and a high leucine content.     

Missense exonic mitochondrial mutation in cytochrome b gene of Saccharomyces cerevisiae,resulting in core protein deficiency in complex III of the respiratory chain

Summary The level of core protein I and subunit VI of mitochondrial complex III (which are coded by the nuclear genome) was found to be greatly diminished in a yeast strain carrying a mutation (W7) in the mitochondrial gene coding for cytochrome b. This suggests that intricate interactions occur in complex III biogenesis between proteins of cytoplasmic and mitochondrial origin. This mutant was characterized by a low cytochrome b level and a loss of activity in the b-c₁ segment of the respiratory chain. It was compared to another mutant showing similar biochemical characteristics, but which had integrated core protein I, as shown by antibody binding experiments. In mutant devoid of core protein I, cytochrome b was found to be reducible by NADH but not by succinate, suggesting two different electron transfer pathways inside comples III from each substrate to cytochrome b heme(s).Abbreviations rho° cytoplasmic petite, with all mitochondrial DNA deleted - EPR electron paramagnetic resonance - DNFB 2,4-dinitrofluorobenzene     

Ts mutations in mitochondrial tRNA genes: characterization and effects of two point mutations in the mitochondrial gene for tRNAphe in Saccharomyces cerevisiae

Two new mitochondrial mutations conferring heat sensitivity on glycerol medium to the cells that carry them and affecting mitochondrial protein synthesis were investigated. Both map in the mitochondrial tRNAphe gene and have C-to-U transitions, one at position 2 (ts22b16) and the other at 62 (ts1345). The latter mutation clearly affects the 3′ end-maturation of tRNAphe, while the former presents normal patterns of both tRNA processing and amino-acylation. The defective phenotype resulting from the ts22b16 mutation can be corrected by over-expressing either the mitochondrial elongation factor EF-Tu or the mutated form of the tRNA. These results suggest that this mutation's primary effect might involve modified interactions during the ternary complex formation. Received: 27 July / 14 October 1997     

Cloning and characterization of MRP10, a yeast gene coding for a mitochondrial ribosomal protein

The nuclear gene MRP10 of Saccharomyces cerevisiae was cloned by complementation of a respiratory deficient mutant N518/L1. This mutant is defective in mitochondrial translation and shows a tendency to accumulate deletions in mitochondrial DNA (ρ ^–). Analysis revealed Mrp10p to be a component of the 37 S subunit of the mitochondrial ribosomes. Disruption of MRP10 in a haploid strain of yeast elicits a phenotype identical to that of the original mutant. The respiratory defect of the null mutant is rescued by re-introducing the MRP10 gene in a wild-type mitochondrial DNA background. These results indicate that Mrp10p belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation. Searches of current databases failed to reveal any homologs among known bacterial or eucaryotic cytoplasmic ribosomal proteins. Some sequence similarity, however, was detected between Mrp10p and Yml37p, previously identified as a component of the yeast mitochondrial 50 S ribosomal subunit. Received: 21 November 1996     

RPG1: an essential gene of Saccharomyces cerevisiae encoding a 110-kDa protein required for passage through the G1 phase

In Saccharomyces cerevisiae cells a number of genes are required for progression through, or else to pass beyond, the G₁ phase. We characterized a novel gene, RPG1, which is also involved in this phase. RPG1 is an essential gene encoding a 110-kDa evolutionarily conserved protein. Elutriated or α-factor-synchronized cells of the rpg1-1 temperature-sensitive mutant were arrested in the first cell cycle when shifted to a non-permissive temperature. The cells remained unbudded and neither grew nor duplicated DNA. rpg1-1 cells synchronized in S phase completed mitosis and arrested as unseparated G₁ cells after a shift to a non-permissive temperature. Similarly, the asynchronous rpg1-1 cells accumulated in G₁ at the non-permissive temperature, but mother and daughter cells did not separate. A bulk of Calcofluor-stained material was localized in the region adjacent to the cell septum. Our data show that Rpg1p is required for passage through the G₁ phase and may be involved in growth control. Data published recently indicate that Rpg1p exhibits significant sequence similarity to a subunit of the mammalian translation initiation factor 3. Received: 6 October 1997 / 8 November 1997     

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     

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.     

Evidence for the association of yeast mitochondrial ribosomes with Cox11p, a protein required for the CuB site formation of cytochrome c oxidase

Cytochrome c oxidase is the terminal enzyme of the mitochondrial (mt) respiratory chain. It contains copper ions, which are organized in two centres, Cu_A and Cu_B. The Cu_A site of subunit Cox2p is exposed to the mt intermembrane space, while the Cu_B site of subunit Cox1p is buried in the inner mt membrane. Incorporation of copper into the two centres is crucial for the assembly and activity of the enzyme. Formation of the Cu_B site is dependent on Cox11p, a copper-binding protein of the mt inner membrane. Here, we experimentally prove that Cox11p possesses a N_in–C_out topology, with the C-terminal copper-binding domain exposed in the mt intermembrane space. Furthermore, we provide evidence for the association of Cox11p with the mt translation machinery. We propose a model in which the Cu_B site is co-translationally formed by a transient interaction between Cox11p and the nascent Cox1p in the intermembrane space.     

A study of 25 patients with chronic granulomatous disease: A new classification by correlating respiratory burst,cytochrome b,and flavoprotein

Twenty-five patients suffering from chronic granulomatous disease (CGD) and their families were investigated. Defects in the superoxide generating system were characterized at the level of the heme-containing cytochrome b and of the FAD-containing flavoprotein, both localized in the plasma membrane of granulocytes. It was confirmed that in most of the typical cases (18 of 22), the complete inability of superoxide generation was associated with the absence of detectable cytochrome b. Mothers but not fathers of such male patients were characterized by a diminished content of cytochrome b, confirming that the affected gene is localized on the X chromosome. In contrast, the granulocytes of four other typical patients (two female and two male) contained normal amounts of cytochrome b, whereas oxidative activity was absent. Since no abnormality of oxidative activity as well as of cytochrome b was found in granulocytes of the mothers and fathers of these patients, an autosomal recessive mode of inheritance of the disease is probable. The flavoprotein deficiency found in the granulocytes of four male patients was always associated with an absence of detectable cytochrome b. This could indicate a structural relationship between flavoprotein and cytochrome b (e.g., a flavocytochrome). Three further patients with mild X-linked CGD contrasted with the patients with severe or classic X-linked disease; the oxidative activity of their phagocytes was diminished but not absent, and the cytochrome b present, albeit in small amounts.     

Mice heterozygous for a deletion of the tumor necrosis factor-α and lymphotoxin-α genes: biological importance of a nonlinear response of tumor necrosis factor-α to gene dosage

The tumor necrosis factors (TNF-α and lymphotoxin, or LT-α) are important mediators of the immune and inflammatory responses, and it has been proposed that a positive feedback loop could boost the expression of the TNF to sufficiently high levels to fend off infections. To investigate this phenomenon and its biological consequences, we have generated LT-α/TNF-α knockout mice and compared mice having one or two functional LT-α/TNF-α alleles. In response to lipopolysaccharide (LPS) stimulation, TNF-α levels in the circulation or in the supernatant of macrophage cultures were 20- to 100-fold lower in heterozygous samples than in their wild-type counterparts. This differential increased with the intensity of stimulation and throughout the response, supporting the involvement of a positive feedback loop. Moreover, the heterozygous mice had an increased bacterial load following Listeria monocytogenes infection and exhibited a bimodal response to the association of D -galactosamine and LPS which was similar to that of wild-type mice at low doses of LPS and more like that of homozygous mutants at high doses. These results therefore establish the biological importance of the nonlinear response of TNF-α levels to gene dosage, and these mice provide a unique tool to study how the propensity to produce TNF can determine the immunological fitness of individuals.     

Group-I introns in the cytochrome c oxidase genes of Dictyostelium discoideum : two related ORFs in one loop of a group-I intron, a cox1/2 hybrid gene and an unusually large cox3 gene

 The DNA sequences of cytochrome oxidase (subunits 1, 2 and 3) genes of the cellular slime mold Dictyostelium discoideum mitochondria were determined. The genes for subunits 1 and 2 have a single continuous ORF (COX1/2) which contains four group-I introns. The insertion sites of the two group-I introns (DdOX1/2.2 and DdOX1/2.3) coincide with those of fungal and algal group-I introns, as well as a liverwort group-I intron, in the cytochrome oxidase subunit 1. Interestingly, intron DdOX1/2.2 has two free-standing ORFs in a loop (L8) which have similar amino-acid sequences and are homologous to ai4 DNA endonuclease (I-Sce II) and bi4 RNA maturase found in group-I introns of Saccharomyces cerevisiae mitochondrial DNA. Two group-I introns (DdOX1/2.3 and DdOX1/2.4) also have a free-standing ORF in loop 1 and loop 2, respectively. These results show that these group-I introns and the intronic ORFs have evolved from the same ancestral origin, but that these ORFs have been propagated independently. Received: 1 May / 16 September 1996