Assembly of the mitochondrial membrane system: Sequence analysis of a yeast mitochondrial ATPase gene containing the oli-2 and oli-4 loci

The mitochondrial DNA (mtDNA) segments of several ρ^? mutants carrying the oli-2, oli-4 and pho-1 loci have been sequenced. The segments contain a common structural gene sequence that has been identified to include all three genetic markers. The gene codes for a protein with a molecular weight of 28,257. This new gene is located between 61.5 and 62.6 units on the wild-type map of Saccharomyces cerevisiae and is transcribed from the same DNA strand as most other yeast mitochondrial genes sequenced to date. The amino acid composition and sequence deduced from the DNA sequence indicate that the protein is very hydrophobic, with three long domains (>30 residues) consisting of nonpolar amino acids. Based on its molecular weight, the gene product is tentatively proposed to be either subunit 3 or 6 of the oligomycin-sensitive ATPase.     

Formation of the yeast mitochondrial membrane. 3. Accumulation of mitochondrial proteins synthesized in both the cytoplasm and mitochondria in yeast undergoing glucose depression

The inhibitors of protein synthesis, chloramphenicol and cycloheximide, were added to cultures of yeast undergoing glucose derepression at different times during the growth cycle. Both inhibitors blocked the increase in activity of coenzyme QH₂-cytochrome c reductase, suggesting that the formation of complex III of the respiratory chain requires products of both mitochondrial and cytoplasmic protein synthesis.The possibility that precursor proteins synthesized by either cytoplasmic or mitochondrial ribosomes may accumulate was investigated by the sequential addition of cycloheximide and chloramphenicol (or the reverse order) to cultures of yeast undergoing glucose derepression. When yeast cells were grown for 3 hr in medium containing cycloheximide and then transferred to medium containing chloramphenicol, the activity of cytochrome oxidase increased at the same rate as the control during the first hour in chloramphenicol. These results suggest that some accumulation of precursor proteins synthesized in the mitochondria had occurred when cytoplasmic protein synthesis was blocked during the growth phase in cycloheximide. In contrast, essentially no products of mitochondrial protein synthesis accumulated as precursors for either oligomycin-sensitive ATPase or complex III of the respiratory chain during growth of the cells in cycloheximide.When yeast were grown for 3 hr in medium containing chloramphenicol followed by 1 hr in cycloheximide, the activities of cytochrome oxidase and succinate-cytochrome c reductase increased at the same rate as the control, while the activities of oligomycin-sensitive ATPase and NADH or coenzyme QH₂-cytochrome c reductase were nearly double that of the control. These data suggest that a significant accumulation of mitochondrial proteins synthesized in the cytoplasm had occurred when the yeast cells were grown in medium containing sufficient chloramphenicol to block mitochondrial protein synthesis. The possibility that proteins synthesized in the cytoplasm may act to control the synthesis of mitochondrial proteins for both oligomycin-sensitive ATPase and complex III of the respiratory chain is discussed.     

Mitochondrial sensitivity to Drechslera maydis T-toxin and the synthesis of a variant mitochondrial polypeptide in plants derived from maize tissue cultures with texas male-sterile cytoplasm

Summary Tissue cultures of maize carrying cms-T cytoplasm have been found to regenerate fertile, T-toxin resistant plants, with and without a selective treatment with T-toxin. Progeny of these plants were tested for mitochondrial sensitivity to T-toxin and the translation products synthesised by isolated mitochondria were analysed. The results confirm previous indications of a close correlation between susceptibility to T-toxin and the synthesis of a variant 13,000 M_r mitochondrial polypeptide. Interestingly, there appeared to be a critical level at about 33% maximum synthesis of the 13,000 M_r polypeptide above which male sterility and sensitivity to T-toxin are jointly expressed. The possibility that there is a causal link between synthesis of this additional mitochondrial polypeptide, pollen abortion and sensitivity to T-toxin is discussed.     

Investigation of the structural arrangement of the protein subunits of mitochondrial ATPase.

The structure of initochondrial ATPase from Saccharomyces cerevisiae was investigated to establish spatial relationships among the peptide components of this enzyme complex. Reagents which reversibly cross-linked adjacent polypeptides in complex structures were used to propose tentative assignments of neighboring polypeptides both in F₁ ATPase and in the oligomycin-sensitive ATPase complex. Two-dimensional gel electrophoresis of cross-linked and dissociated samples of the enzyme was used to analyze the sizes and subunit compositions of oligomers formed by cross-linking reactions. Two of the nine major peptide components of the ATPase complex were labeled with [₃H]amino acids in the presence of cycloheximide. Analysis of association of these labeled components with other peptides of the complex was therefore facilitated by autoradiographic techniques. The cross-linking studies give rise to a suggested structural model for ATPase.     

Immunodetection of a 90 000-Mr polypeptide related to yeast plasma membrane ATPase in plasma membrane from maize shoots

Maize shoot plasma membranes were prepared using either polyethyleneglycol (PEG)-dextran phase partition or centrifugation through a 30% sucrose cushion. The ATPase specific activity of membranes obtained with the phase partition method (1.4 μmol P_i · min⁻¹ · mg⁻¹ protein) was twice that of those prepared with the sucrose cushion method. After solubilization by lysolecithin and precipitation by ammonium sulfate, ATPase activities of the order of 3.0–3.5 μmol P_i · min⁻¹ · mg⁻¹ were obtained. A polypeptide of M_r = 90 000 was enriched during ATPase purification.Antibodies against pure plasma membrane ATPase from Saccharomyces cerevisiae inhibited the plant ATPase activity. Immunodetection during purification of the plant enzyme strongly supported the conclusion that the polypeptide of M_r = 90 000 belongs to plant plasma membrane ATPase.     

Circadian rhythms in Neurospora crassa: the effects of point mutations on the proteolipid portion of the mitochondrial ATP synthetase

Summary Five oligomycin-resistant (oli ^r) mutant strains of Neurospora crassa were analyzed for their growth rate and for the periodicity of their circadian rhythm. The most resistant strains had periods of 18–19 h while the least resistant strain had a normal period of 21.0 h. There was a rough correlation between the in vivo degree of oligomycinresistance and the amount of change in the period. Several of the oli ^r mutations have been previously described by Sebald et al. (1977) in terms of known amino acid changes in the primary structure of the proteolipid, or DCCD-binding protein, found in the F₀ membrane portion of the mitochondrial ATP synthetase. Amino acid changes in the structure of this protein are reported here for two other oli ^r mutations. The proteolipid isolation procedures were slightly modified to include a delipidation step, and an HPLC procedure was developed to separate the hydrophobic peptides of this protein. Analysis of heterocaryons carrying both the oli ^r and oli ^s markers indicated that the oli ^r and oli ^s mutations were codominant to each other in terms of period and growth rate. The changes in the primary structure of this DCCD-binding protein reported here are the first known examples of changes in the primary structure of a protein which alter the period of a circadian rhythm.     

Biogenesis of mitochondria. Defective assembly of the proteolipid into the mitochondrial adenosine triphosphatase complex in an oli2 mit− mutant of Saccharomyces cerevisiae

A single mutation in the oli2 region of the mitochondrial DNA causes a charge alteration in a mitochondrially translated subunit of the mitochondrial ATPase (subunit 6; apparent M_r 20 000; apparent pI 6.9 and 7.1). This alteration leads to the defective assembly of the proteolipid subunit into the enzyme complex. The mutant, which is able to grow only very slowly by oxidative metabolism at 28°C offers new possibilities for studying the assembly of the membrane sector (F₀) into the mitochondrial ATPase complex and the role of subunit 6 in this process.     

The yeast mitochondrial adenosine triphosphatase complex. Purification, subunit composition, and some effects of protease inhibitors.

(i) The method of preparing the oligomycin-insensitive F₁-ATPase by chloroform treatment of mitochondrial membranes (Beechey et al., 1975, Biochem. J.148, 533–537) has been modified such that a five-subunit protein is obtained from yeast with an activity of 140 μmol of ATP hydrolyzed/min/mg of protein. Repetition of this procedure in the presence of protease inhibitors (in particular, p-aminobenzamidine) allows isolation of a four-subunit protein with an activity of 243 μmol of ATP hydrolyzed/min/ mg of protein, (ii) A modified procedure is described for the preparation of the yeast oligomycin-sensitive F₁-F₀ ATPase complex, making use of protease inhibitors throughout and solubilization of the ATPase from mitochondrial membranes using Triton X-100 and sodium deoxycholate simultaneously. Two polypeptides Of 42,000 and 29,000 molecular weight are eliminated, the largest corresponding to the missing band of the F₁ sector. The complex retains oligomycin- and uncoupler-sensitive ATP-³²P_i exchange and ATP-driven proton uptake, indicating the retention of a complete coupling mechanism. (iii) F₁-ATPase is released from the F₁-F₀ complex by brief heating at 50 °C in the presence of ATP. The remaining hydrophobic polypeptides aggregate and are isolated by centrifugation. The F₁ sector can be isolated containing either four or five subunits depending on whether the starting F₁-F₀ complex contained the 42,000 and 29,000 molecular weight polypeptides. (iv) Sensitivity of the F₁-F₀ ATPase complex to oligomycin and dicyclohexylcarbodiimide varies considerably depending on the activity measured and whether the complex was first reconstituted with phospholipids. The degree of inhibitor sensitivity is considered a poor guide to intactness of the complex.     

A novel extranuclear mutant of Neurospora with a temperature-sensitive defect in mitochondrial protein synthesis and mitochondrial ATPase

Summary [C93] is a novel, extranuclear mutant of Neurospora crassa which has a normal mitochondrial phenotype when grown at 25°, but which is deficient in cytochromes b and aa ₃ when grown at 37° (Pittenger and West 1979). In the present work, the phenotype of [C93] was characterized in greater detail. When [C93] is grown at 37°, the rate of mitochondrial protein synthesis is decreased to approximately 25% that of wild type; the ratio of mitochondrial small to large ribosomal subunits is decreased to 1:4 and mitochondrial small subunits are deficient in the mitochondrially-synthesized protein, S-5. The mitochondrial ribosome assembly defects in 37°-grown [C93] resemble those in chloramphenicol-treated wild-type cells and could merely be a consequence of the decreased rates of mitochondrial protein synthesis. Analysis of mitochondrial translation products by SDS gel electrophoresis suggests that 37°-grown [C93] is grossly deficient in the 19,000 Mr subunit of the oligomycin-sensitive ATPase relative to other mitochondrially-synthesized proteins. The ATPase defect was not found in other extranuclear or nuclear mutants deficient in mitochondrial protein synthesis. These data and additional evidence suggest that the primary defect in [C93] may be in the assembly of the ATPase complex. The possible connection between the ATPase defect and the deficiency of mitochondrial protein synthesis is discussed.     

Temperature dependence of mitochondrial oligomycin-sensitive proton transport ATPase

The temperature dependence of the oligomycin-sensitive ATPase (complex V) kinetic parameters has been investigated in enzyme preparations of different phospholipid composition. In submitochondrial particles, isolated complex V, and complex V reconstituted in dimirystoyl lecithin vesicles, the Arrhenius plots show discontinuities in the range 18–28°C, while no discontinuity is detected with dioleoyl lecithin recombinant. Van't Hoff plots ofK _m also show breaks in the same temperature interval, with the exception of the dioleoylenzyme vesicles, whereK _m is unchanged. Thermodynamic analysis of the ATPase reaction shows that DMPC-complex V has rather larger values of activation enthalpy and activation entropy below the transition temperature (24°C) than those of the other preparations, while all enzyme preparations show similar free energies of activation (14.3–18.5 kcal/mol). The results indicate that temperature and lipid composition influence to a different extent both kinetic and thermodynamic parameters of ATP hydrolysis catalyzed by the mitochondrial ATPase.     

Cell type-specific differences in protein composition of nuclear pore complex-lamina structures in oocytes and erythrocytes of Xenopus laevis

Nuclear envelopes from oocytes of Xenopus laevis are rich in pore complexes and contain a major polypeptide of apparent molecular weight (M_r) 68,000. A rapid extraction procedure using buffer containing 1% ($\text{v}\text{v}$) Triton X-100 and 1.0 m-KCl allows the preparation of insoluble nuclear envelope skeletons showing only residual pore complex structures, with some interconnecting filament material, and one major polypeptide; i.e. that of M_r 68,000. This skeletal protein, which is not found in nuclear contents, reveals, on two-dimensional gel electrophoresis, a series of distinct isoelectric variants focusing in the pH range from 6.4 to 6.6. In living oocytes, this protein is continuously synthesized, as demonstrated by incorporation of labelled amino acids, and phosphorylated, A similar prominent skeletal protein has been found in nuclear envelopes of oocytes of other amphibia; however, slight but significant differences in electrophoretic mobility can be noted between different amphibian species.For comparison, nucleocortical lamina structures containing few pore complexes have been isolated, using similar extraction procedures, from various somatic cells of X. laevis, including erythrocytes. Laminae from these cells contain two major polypeptides, one (L_I) of M_r 72,000 focusing at approximately pH 5.35 and another (L_II) of M_r 69,000 focusing in several variants between pH 6.20 and 6.35. Similarly extracted “pore complex-lamina” fractions from rat liver contain a polypeptide of similar size and electrical charge as protein L_I from Xenopus and, in addition, two other polypeptides (M_r values: 74,000 and 62,000) both focusing between pH 6.6 and 6.9.It is concluded that the pore complex-lamina structure of the oocyte nucleus is assembled by only one major protein of M_r 68,000. The results also show that the protein composition of this insoluble nucleocortical structure can be different in different cells of the same organism. The compositional differences of these nuclear envelope skeletons are discussed in relation to the relative proportions of pore complex and interporous (lamina) material in the nuclear envelopes of the specific cells. It is suggested that the M_r 68,000 protein predominant in oocyte nuclear envelopes contributes, as an architectural component, to the formation of the highly organized nuclear pore complex.     

Mg2+-induced ADP-dependent inhibition of the ATPase activity of beef heart mitochondrial coupling factor F1.

Incubation of F₁ in the presence of Mg²⁺ results in a pronounced lag in its ATPase activity measured with the ATP-regenerating system. A decrease of the initial rate of ATPase induced by Mg²⁺ is also observed when free nucleotides were separated from the enzyme by Sephadex gel filtration. No inhibition is observed when F₁ treated to remove tightly bound nucleotides was preincubated in the presence of Mg²⁺. Mg²⁺-induced inhibition of ATPase activity of nucleotide-depleted F₁ can be restored by an addition of low concentrations of ADP. In all cases the inhibited ATPase can be activated by the ADP-removing system /phosphoenol pyruvate + pyruvate kinase/. It is concluded that i/ Mg²⁺-induced inhibition of the ATPase activity of F₁ is due to the formation of an inactive F₁. ADP complex; and ii/ unusual inhibition of oligomycin-sensitive ATPase by ADP /Fitin et al., Biochem. Biophys. Res. Communs. 1979, $\text{86}$, 434/ is directed to F₁ component of the complete mitochondrial ATPase system.     

In Vitro Processing of Precursors of Thylakoid Membrane Proteins of Chlamydomonas reinhardtii y-1

Studies of in vitro processing of precursors of the major chlorophyll a/b-binding polypeptides of Chlamydomonas reinhardtii y-1 were undertaken to define the precursor-product relationships. Analysis of translates, prepared from C. reinhardtii poly(A)-rich RNA in a rabbit reticulocyte lysate system, which were incubated with the soluble fraction from C. reinhardtii cells, showed that the 31,500 relative molecular mass (M_r) precursor was converted to the M_r 29,500 thylakoid membrane polypeptide whereas the M_r 30,000 precursor was converted to the M_r 26,000 product. Furthermore, the M_r 31,500 polypeptide, when bound to antibodies, was not processed to the mature polypeptide of M_r 29,500, although the presence of antibodies did not prevent the precursor of M_r 30,000 from being converted to the mature M_r 26,000 polypeptide. The mature fraction of M_r 26,000, was separated into two bands corresponding to polypeptides 16 and 17 in the electrophoretic system of Chua and Bennoun (1975 Proc Natl Acad Sci USA 72: 2175-2179).

Processing activity was present in the soluble fraction obtained from cells grown in the light or in the dark. Therefore, processing of the precursor polypeptides does not appear to be involved in the regulation by light of the accumulation of these polypeptides in thylakoid membranes.

     

Mitochondrial Genetics. Xii. an Oligomycin-Resistant Mutant Localized at a New Mitochondrial Locus in SACCHAROMYCES CEREVISIAE

Three antibiotic-resistance mutations were isolated from strain FL496–2B: two are independent Mendelian genes, one conferring both oligomycin and venturicidin resistance (oli^R₄₉₆) and the other conferring cycloheximide resistance (cyh^R₄₉₆). The third is a mitochondrial mutation, O^R₉, and confers a low level of oligomycin resistance to cells (in vivo) but not to the extracted mitochondrial ATPase (in vitro). This mutation is located on the mitochondrial DNA at a new locus [OLI4] linked to [OLI2] and independent from [OLI1] and [OLI3] and from the other mitochondrial loci.

All three mutations (O ^R₉, oli^R₄₉₆, cyh^R₄₉₆ ) were found without any selection, in the same prototrophic haploid strain, which contained unknown resistances to antibiotics.

Some physiological, genetical and biochemical properties of the mitochondrial mutation are described.

     

Author index

The membrane-bound ATPase activity of Bacillus subtilis was inhibited by dicyclohexylcarbodiimide (DCCD). The DCCD-reactive proteolipid of B. subtilis was extracted, from labelled or untreated membranes containing F₁ or depleted of F₁, with neutral or acidic chloroform/methanol. Purification of the [₁₄C]DCCD-binding proteolipid was attempted by column chromatography on methylated Sephadex G-50 and on DEAE-cellulose. The maximal amount of DCCD which could be bound to the purified proteolipid was found to exceed the amount bound by the purified proteolipid extracted from membranes labelled with the lowest [₁₄C]DCCD concentration required for maximal inhibition of the membrane-bound ATPase activity. The radioactive protein peaks eluted by gel filtration and ion-exchange chromatography were analysed by urea-SDS polyacrylamide slab gel electrophoresis and autoradiography. Radioactivity was incorporated into two components of M_r 18 000 and 6000 when proteolipid was purified by methylated Sephadex. The 6000 polypeptide was always present, whatever the extraction and purification procedures. However, the 18 000 polypeptide was present in largest quantity only when proteolipid was extracted from membranes containing F₁ and purified by methylated Sephadex. When proteolipid was purified on DEAE-cellulose this [₁₄C]DCCD binding component of M_r 18 000 was absent.     

Negatively charged phospholipid requirement of the oligomycin-sensitive mitochondrial ATPase

The highly-purified, oligomycin-sensitive mitochondrial adenosine triphosphatase has been reconstituted with phosphatidylserine. Treatment of the phosphatidylserine-reconstituted ATPase with phosphatidylserine decarboxylase produced a 3-fold decrease in the specific activity of the resulting phosphatidylethanolamine-enriched ATPase complex. Subsequent control experiments indicated that the resulting phosphatidylethanolamine was responsible for the lowered ATPase specific activity. These observations indicate that acidic phospholips do more than facilitate an interaction between the highly-purified, lipid-depleted ATPase and phospholipid. The negatively charged phospholipid appears to be essential for maintaining high levels of oligomycin-sensitive activity even after the initial interaction between phospholipid and the ATPase complex has occurred.     

Crystallization of pig mitochondrial aspartate aminotransferase by seeding with crystals of the chicken mitochondrial isoenzyme

Pig mitochondrial aspartate aminotransferase has been crystallized from polyethylene glycol solutions (M_r = 4000) with the aid of small seed crystals of the chicken mitochondrial isoenzyme. The “hanging drop” vapour diffusion technique was used. The unit cells of the pig and chicken mitochondrial isoenzymes are roughly isomorphous. Diffraction data have been collected to a resolution of 2.8 Å.     

Oligomycin sensitivity of mitochondrial sulfhydryl groups

Dithionitrobenzoate has been used to titrate sulfhydryl groups of rat liver mitochondria in glutamate buffer, pH 7.4.Reaction with oligomycin and different SH reagents preceded the SH titration. Under these conditions it was found that 2-mercaptopropionylglycine and N-ethylmaleimide reacted in an oligomycin-sensitive manner, so that the control values (in the absence of SH reagent) were obtained.Similar concentrations of mersalyl and of N-(N-acetyl-4-sulfamoylphenyl) maleimide, in the presence of oligomycin, enhanced reactivity toward Nbs₂.The concentration range of oligomycin-sensitive SH groups was thus defined between approx. 5 and 9 nmol reagent/mg mitochondrial protein.In this way, a differentiation between SH groups, which are implicated in phosphate transport and those, which react in an oligomycin-sensitive manner, and which are probably connected with the coupling mechanism, was achieved.     

Flocculation in Saccharomyces cerevisiae and mitochondrial DNA structure

Summary Mitochondrial mutants of indstrial yeast strains with different flocculation efficiencies were assayed for involvement of mitochondrial DNA (mtDNA) in flocculation. Most of the mutants exhibited a decreased flocculation rate in comparison to that of the wild strains. The mtDNA of a moderately flocculating wild strain was characterized by restriction enzyme analysis and by the localization of several mitochondrial genes. This molecular analysis of mitochondrial mutants revealed two areas of mtDNA involvement in flocculation, namely a region of the subunit 9 of the ATPase gene (oli 1) and a region of the subunit 3 of the cytochrome-c-oxidase gene (oxi 2).     

On the identification of the uncoupler binding protein of bovine mitochondrial oligomycin sensitive ATPase

The 55,000 dalton polypeptide component of the membrane sector of the mitochondrial oligomycin sensitive ATPase has been purified by recycling chromatography on BioGel P-100. The amino acid composition of the purified polypeptide differs significantly from that of the α-subunit of F₁ with which it shares a similar apparent molecular weight. However, the amino acid composition of the former is identical to that of the Factor B polypeptide, which is known to occur in oligomeric forms. Evidence is presented which suggests that the mitochondrial uncoupler binding proteins and the various oligomeric forms of the Factor B polypeptide, including the 55,000 dalton species described in the present report, are identical.