Portal de Periódicos da CAPES

ATP Synthase of Yeast Mitochondria

1999; Elsevier BV; Volume: 274; Issue: 1 Linguagem: Inglês

10.1074/jbc.274.1.36

1083-351X

Isabel Arnold, Kathy Pfeiffer, Walter Neupert, Rosemary A. Stuart, Hermann Schägger,

Photosynthetic Processes and Mechanisms

The subunit composition of the mitochondrial ATP synthase from Saccharomyces cerevisiae was analyzed using blue native gel electrophoresis and high resolution SDS-polyacrylamide gel electrophoresis. We report here the identification of a novel subunit of molecular mass of 6,687 Da, termed subunit j (Su j). An open reading frame of 127 base pairs (ATP18), which encodes for Su j, was identified on chromosome XIII. Su j does not display sequence similarity to ATP synthase subunits from other organisms. Data base searches, however, identified a potential homolog fromSchizosaccharomyces pombe with 51% identity to Su j ofS. cerevisiae. Su j, a small protein of 59 amino acid residues, has the characteristics of an integral inner membrane protein with a single transmembrane segment. Deletion of the ATP18gene encoding Su j led to a strain (Δsu j) completely deficient in oligomycin-sensitive ATPase activity and unable to grow on nonfermentable carbon sources. The presence of Su j is required for the stable expression of subunits 6 and f of the F0 membrane sector. In the absence of Su j, spontaneously arising rho−cells were observed that lacked also ubiquinol-cytochrome creductase and cytochrome c oxidase activities. We conclude that Su j is a novel and essential subunit of yeast ATP synthase. The subunit composition of the mitochondrial ATP synthase from Saccharomyces cerevisiae was analyzed using blue native gel electrophoresis and high resolution SDS-polyacrylamide gel electrophoresis. We report here the identification of a novel subunit of molecular mass of 6,687 Da, termed subunit j (Su j). An open reading frame of 127 base pairs (ATP18), which encodes for Su j, was identified on chromosome XIII. Su j does not display sequence similarity to ATP synthase subunits from other organisms. Data base searches, however, identified a potential homolog fromSchizosaccharomyces pombe with 51% identity to Su j ofS. cerevisiae. Su j, a small protein of 59 amino acid residues, has the characteristics of an integral inner membrane protein with a single transmembrane segment. Deletion of the ATP18gene encoding Su j led to a strain (Δsu j) completely deficient in oligomycin-sensitive ATPase activity and unable to grow on nonfermentable carbon sources. The presence of Su j is required for the stable expression of subunits 6 and f of the F0 membrane sector. In the absence of Su j, spontaneously arising rho−cells were observed that lacked also ubiquinol-cytochrome creductase and cytochrome c oxidase activities. We conclude that Su j is a novel and essential subunit of yeast ATP synthase. blue native polyacrylamide gel electrophoresis N-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]glycine. Yeast mitochondrial ATP synthase (1Law R.H.P. Manon S. Devenish R.J. Nagley P. Methods Enzymol. 1995; 260: 133-163Crossref PubMed Scopus (67) Google Scholar) is similar to the corresponding bovine enzyme (2Collinson I.R. Runswick M.J. Buchanan S.K. Fearnley I.M. Skehel J.M. Van Raaij M.J. Griffith D.E. Walker J.E. Biochemistry. 1994; 33: 7971-7978Crossref PubMed Scopus (166) Google Scholar, 3Walker J.E. Collinson I.R. Van Raaij M.J. Runswick M.J. Methods Enzymol. 1995; 260: 163-190Crossref PubMed Scopus (42) Google Scholar) regarding its polypeptide composition, but there are also differences. All components of the bovine catalytic sector of the ATP synthase (F1),i.e. subunits α, β, γ, δ, ε, and the inhibitor protein (IF1), have homologous counterparts inSaccharomyces cerevisiae (4Takeda M. Chen W.J. Saltzgaber J. Douglas M.G. J. Biol. Chem. 1986; 261: 15126-15133Abstract Full Text PDF PubMed Google Scholar, 5Takeda M. Vassarotti A. Douglas M.G. J. Biol. Chem. 1985; 260: 15458-15465Abstract Full Text PDF PubMed Google Scholar, 6Paul M.F. Ackermann S. Yue J. Arselin G. Velours J. Tzagoloff A. J. Biol. Chem. 1994; 269: 26158-26164Abstract Full Text PDF PubMed Google Scholar, 7Giraud M.F. Velours J. Eur. J. Biochem. 1994; 222: 851-859Crossref PubMed Scopus (38) Google Scholar, 8Guelin E. Chevallier J. Rigoulet M. Guerin B. Velours J. J. Biol. Chem. 1993; 268: 161-167Abstract Full Text PDF PubMed Google Scholar, 9Ichikawa N. Yoshida Y. Hashimoto T. Ogasawara N. Yoshikawa H. Imamoto F. Tagawa K. J. Biol. Chem. 1990; 265: 6274-6278Abstract Full Text PDF PubMed Google Scholar). The structural similarity extends to subunits of the membrane sector (F0) and second stalk, i.e. subunit a (Su a or Su 6) (10Macino G. Tzagoloff A. Cell. 1980; 20: 507-517Abstract Full Text PDF PubMed Scopus (172) Google Scholar), Su b (11Velours J. Durrens P. Aigle M. Guerin B. Eur. J. Biochem. 1988; 170: 637-642Crossref PubMed Scopus (37) Google Scholar), Su c (proteolipid or Su 9) (12Macino G. Tzagoloff A. J. Biol. Chem. 1979; 254: 4617-4623Abstract Full Text PDF PubMed Google Scholar), which is mitochondrially encoded in yeast but nuclearly encoded in mammals, Su d (13Norais N. Prome D. Velours J. J. Biol. Chem. 1991; 266: 16541-16549Abstract Full Text PDF PubMed Google Scholar), oligomycin sensitivity conferring protein (14Uh M. Jones D. Mueller D.M. J. Biol. Chem. 1990; 265: 19047-19052Abstract Full Text PDF PubMed Google Scholar), Su 8 (15Macreadie I.G. Novitzki C.E. Maxwell R.J. John U. Ooi B.G. McMullen G.L. Lukins H.B. Linnane A.W. Nagley P. Nucleic Acids Res. 1983; 11: 4435-4451Crossref PubMed Scopus (113) Google Scholar), and Su f (16Spannagel C. Vaillier J. Arselin G. Graves P.V. Velours J. Eur. J. Biochem. 1997; 247: 1111-1117Crossref PubMed Scopus (43) Google Scholar). In addition, a gene encoding a putative homolog of subunit g of the bovine ATP synthase has been identified in the yeast genome (Su g). 1EMBL accession number Z71255, SWISS-PROT accession number Q12233. The corresponding protein, however, has not been observed in the isolated ATP synthase yet. A yeast homolog of bovine subunit e has also been reported recently (17Arnold I. Bauer M.F. Brunner M. Neupert W. Stuart R.A. FEBS Lett. 1997; 411: 195-200Crossref PubMed Scopus (70) Google Scholar). Subunit e, also known as Tim11, was originally reported as being a component of the mitochondrial inner membrane import machinery (18Tokatlidis K. Junne T. Moes S. Schatz G. Glick B.S. Kronidou N. Nature. 1996; 384: 585-588Crossref PubMed Scopus (58) Google Scholar); however, it has subsequently been shown to be a membrane-bound subunit of the ATP synthase complex (17Arnold I. Bauer M.F. Brunner M. Neupert W. Stuart R.A. FEBS Lett. 1997; 411: 195-200Crossref PubMed Scopus (70) Google Scholar). Although in mitochondria it is associated with the ATP synthase complex and can be co-immunoprecipitated with subunits of the F1 sector (17Arnold I. Bauer M.F. Brunner M. Neupert W. Stuart R.A. FEBS Lett. 1997; 411: 195-200Crossref PubMed Scopus (70) Google Scholar), subunit e, like subunit g, has not been identified yet in the purified ATP synthase enzyme. A yeast homologue to bovine subunit F6 (19Fang J.-K. Jacobs J.W. Kanner B.I. Racker E. Bradshaw R.A. Proc. Natl. Acad. Sci. U. S. A. 1984; 81: 6603-6607Crossref PubMed Scopus (23) Google Scholar) so far has not been reported. Conversely, a novel subunit, subunit h, has been found recently in yeast ATP synthase (20Arselin G. Vaillier J. Graves P.V. Velours J. J. Biol. Chem. 1996; 271: 20284-20290Abstract Full Text Full Text PDF PubMed Scopus (82) Google Scholar), which appears not to be related to any of the known subunits of bovine or other ATP synthases. The experiments described in this paper focus on the reassessment of the polypeptide composition of the yeast ATP synthase using a different isolation technique, namely blue native electrophoresis (BN-PAGE).2 BN-PAGE is a microscale technique for the separation of the multiprotein complexes of oxidative phosphorylation directly from isolated mitochondrial membranes (21Schägger H. von Jagow G. Anal. Biochem. 1991; 199: 223-231Crossref PubMed Scopus (1918) Google Scholar). Combined with SDS-polyacrylamide gel electrophoresis (SDS-PAGE) in a second dimension, an overview on the protein subunits of all oxidative phosphorylation complexes is obtained in a two-dimensional gel (22Schägger H. Cramer W.A. von Jagow G. Anal. Biochem. 1994; 217: 220-230Crossref PubMed Scopus (1043) Google Scholar). Using this two-dimensional electrophoretic technique, we observed in the ATP synthase the presence of a previously undetected protein in the 6–7-kDa range. N-terminal protein sequencing revealed it to be a novel subunit of the ATP synthase, subunit j (Su j). Su j is encoded by a gene termed here ATP18 and has no apparent bovine counterpart. Aminocaproic acid (6-aminohexanoic acid) and imidazole were from Fluka, Tricine and Serva Blue G (Coomassie Blue G-250) were from Serva, and phenylmethylsulfonyl fluoride was from Sigma. Hydroxyapatite was prepared as described recently (23Schägger H. von Jagow G. Schägger H. A Practical Guide to Membrane Protein Purification. Academic Press, Orlando, FL1994: 107-124Crossref Google Scholar). For construction of the Δsu j::HIS3 yeast strain, introduction of the HIS3 gene resulting in a partial deletion and disruption of the ATP18/Su j gene was performed as follows. The HIS3 gene was amplified from the plasmid pFA6a-HIS3MX6 (24Wach A. Brachat A. Poehlmann R. Philippsen P. Yeast. 1994; 10: 1793-1808Crossref PubMed Scopus (2241) Google Scholar) using the following primers: S1, 5′-GTTTAACATACGACGACAGATTAATTGATTGGATTGTACTGCCATGCGTACGCTGCAGGTCGAC-3′ (corresponding to nucleotides −43 to +3 of theATP18/Su j gene locus and 18 nucleotides of the multiple cloning site of pFA6a-HIS3MX6 from the 5′ flanking region of the HIS3 gene); and S2, 5′-TGGATCATTGATAAATTCCTTCGTGTTAGAAGAAAGGTCAGCAGCATCGATGAATTCGAGCTCG-3′ (corresponding to nucleotides +90 to +132 of theATP18/Su j gene and 19 nucleotides of the multiple cloning site of pFA6a-HIS3MX6 from the 3′ flanking region of the HIS3 gene). The resulting polymerase chain reaction product was transformed into the haploid yeast strain W303-1A using the lithium acetate method (25Gietz D. St. Jean A. Woods R.A. Schiestl R.H. Nucleic Acids Res. 1992; 20: 1425Crossref PubMed Scopus (2899) Google Scholar), and HIS3 positive clones were selected. Correct integration of the HIS3 marker into theATP18/Su j locus was confirmed by polymerase chain reaction using oligonucleotides that primed upstream and downstream of the disrupted ATP18 gene. The resulting yeast strain Δsu j, the corresponding wild-type W303-1A, and Δsu f were grown in YPGal medium supplemented with 0.5% lactate at 30 °C (26Herrmann J.M. Fölsch H. Neupert W. Stuart R.A. Celis D.E. Cell Biology: A Laboratory Handbook. 1. Academic Press, San Diego, CA1994: 538-544Google Scholar). Cells were harvested by centrifugation at 1,800 × g, washed three times with sucrose buffer (250 mm sucrose, 5 mm6-aminohexanoic acid, 10 mm Tris/HCl, pH 7.0), and used directly for preparation of mitochondrial membranes. About 5 g (wet weight) of sedimented cells, 5 ml of glass beads (0.25–0.5 mm), and 5 ml of sucrose buffer were vortexed for 10 min in a 50-ml tube. After dilution with sucrose buffer, the sedimented glass beads were removed, and the supernatant was centrifuged for 20 min at 1,250 ×g. Mitochondrial membranes were then collected by centrifugation for 30 min at 18,000 × g, taken up with sucrose buffer at a protein concentration of 10–30 mg/ml, and stored at −80 °C. For the analysis of the submitochondrial localization of Su j, intact mitochondria were isolated according to previously published methods (26Herrmann J.M. Fölsch H. Neupert W. Stuart R.A. Celis D.E. Cell Biology: A Laboratory Handbook. 1. Academic Press, San Diego, CA1994: 538-544Google Scholar). BN-PAGE was performed as described previously (22Schägger H. Cramer W.A. von Jagow G. Anal. Biochem. 1994; 217: 220-230Crossref PubMed Scopus (1043) Google Scholar) with the following modifications. Mitochondrial membranes (400 μg of protein) were sedimented by centrifugation for 10 min at 100,000 × g. The pellet was suspended with 40 μl of 50 mm NaCl, 2 mm6-aminohexanoic acid, 1 mm EDTA, 50 mmimidazole HCl, pH 7.0, and 1.0 μl of 0.5 mphenylmethylsulfonyl fluoride in Me2SO was added. Membrane protein complexes were solubilized by the addition of Triton X-100 (9.6 μl from a 10% (w/v) stock solution, 2.4 g of Triton X-100/g of protein). After centrifugation for 20 min at 100,000 ×g, the supernatant was supplemented with 5 μl of a Coomassie Blue G-250 dye suspension (5% Serva Blue G (w/v) in 750 mm 6-aminohexanoic acid) and immediately applied to a 1.6-mm acrylamide gradient gel for analytical BN-PAGE (1-cm gel well, linear 4–13% acrylamide gradient gel overlaid with a 4% sample gel). For SDS electrophoresis, the Tricine-SDS-PAGE (27Schägger H. von Jagow G. Anal. Biochem. 1987; 166: 368-379Crossref PubMed Scopus (10505) Google Scholar) or the Laemmli system (28Laemmli U.K. Nature. 1970; 227: 680-685Crossref PubMed Scopus (207537) Google Scholar) was used. Two-dimensional electrophoresis (BN-PAGE/Tricine-SDS-PAGE), staining, and densitometric quantification were performed as described previously (29Schägger H. Electrophoresis. 1995; 16: 763-770Crossref PubMed Scopus (70) Google Scholar, 30Schägger H. von Jagow G. Schägger H. A Practical Guide to Membrane Protein Purification. Academic Press, Orlando, FL1994: 59-79Crossref Google Scholar). All steps were performed at 4 °C, and the pH values of all buffers were adjusted to 4 °C unless otherwise indicated. Mitochondrial membranes from the W303-1A strain (50 mg of protein) were washed with a 4-fold volume of buffer 1 (50 mm NaCl, 2 mm 6-aminohexanoic acid, 1 mm EDTA, 1 mm phenylmethylsulfonyl fluoride, 50 mmimidazole HCl, pH 7.0) and collected by centrifugation for 60 min at 100,000 × g. The pellet was homogenized in 2.35 ml of buffer 1, and 0.6 ml of Triton X-100 (20% w/v) was added (2.4 g of Triton X-100/g of protein). After centrifugation for 60 min at 100,000 × g, the supernatant (2.6 ml) was adjusted to 150 mm Na+ phosphate and loaded onto a 3-ml hydroxyapatite column equilibrated with buffer 2 (0.05% Triton X-100, 2 mm 6-aminohexanoic acid, 1 mm EDTA, 1 mm phenylmethylsulfonyl fluoride, 150 mmNa+ phosphate, pH 7.7). Hydroxyapatite-bound ATP synthase was washed at room temperature with 1 column volume of buffer 3 (0.1% Triton X-100, 333 μm egg yolk phospholipid, 200 mm Na+ phosphate, pH 7.3) and eluted with buffer 4 (0.1% Triton X-100, 333 μm egg yolk phospholipid, 300 mm Na+ phosphate, pH 7.3). One ml of the fraction with highest ATP hydrolysis activity (about 30% of the total yield, 0.5 mg of total protein) was supplemented with 200 mm 6-aminohexanoic acid and loaded onto a 3-mm-thick preparative gel for BN-PAGE. The major blue band comprising ATP synthase, which was visible during BN-PAGE, was excised and cut into 4 pieces. A stack of these 4 pieces was processed by Tricine-SDS-PAGE in a second dimension and electroblotted onto Immobilon P membranes (30Schägger H. von Jagow G. Schägger H. A Practical Guide to Membrane Protein Purification. Academic Press, Orlando, FL1994: 59-79Crossref Google Scholar). The transferred proteins were sequenced directly using a 473A protein sequencer (Applied Biosystems) or after incubation in a 1:1 (v/v) mixture of trifluoroacetic acid and methanol (24 h at 37 °C) for deformylation (31Gheorghe M.T. Jörnvall H. Bergman T. Anal. Biochem. 1997; 254: 119-125Crossref PubMed Scopus (24) Google Scholar). Oligomycin-sensitive ATP hydrolysis was measured at 25 °C using an assay coupled to the oxidation of NADH. Shortly before the test, 0.25 mm NADH, 1 mm phosphoenolpyruvate, 2.5 units/ml lactate dehydrogenase, and 2 units/ml pyruvate kinase were added to the test buffer (250 mm sucrose, 50 mm KCl, 5 mmMgCl2, 2 mm NaCN, 20 mm Tris/HCl, pH 7.5). The reaction was started with protein without detergent and stopped by the addition of 25 μg of oligomycin from a 5 mg/ml stock solution in Me2SO. Antisera against the C-terminal region of Su j were raised in rabbits against a chemically synthesized peptide CRFAKGGKFVEVD that had been coupled to activated ovalbumin (Pierce). Hypotonic swelling and carbonate extraction of mitochondria were performed as described previously (32Fölsch H. Guiard B. Neupert W. Stuart R.A. EMBO J. 1996; 15: 479-487Crossref PubMed Scopus (155) Google Scholar, 33Pfanner N. Hartl F.-U. Neupert W. Eur. J. Biochem. 1988; 175: 205-212Crossref PubMed Scopus (90) Google Scholar). Protein determination was performed according to Bradford (34Bradford M.M. Anal. Biochem. 1976; 72: 248-254Crossref PubMed Scopus (217544) Google Scholar) and a Lowry protocol in the presence of SDS (35Helenius A. Simons K. J. Biol. Chem. 1972; 247: 3656-3661Abstract Full Text PDF PubMed Google Scholar). The ATP synthase binds stronger to hydroxyapatite than most other mitochondrial proteins of yeast. Therefore hydroxyapatite chromatography is an efficient technique for its isolation. After this first purification step, some of the known ATP synthase subunits can already be recognized in SDS-PAGE (Fig.1 A, lanes 3–5). The same fractions of the hydroxyapatite column were also applied to a gel for BN-PAGE. The S. cerevisiae ATP synthase (Fig.1 B, lanes 3–5) is slightly smaller than the bovine ATP synthase that was loaded in parallel. BN-PAGE was then repeated on the preparative scale using the hydroxyapatite fraction with the highest amount of ATP synthase complex (Fig. 1 B,lane 4). The band of ATP synthase was excised, and the subunit composition of this complex was analyzed further by SDS-PAGE. N-terminal protein sequencing of the resolved proteins (Fig.1 C) showed the presence of known subunits of the ATPase and one additional protein that was termed subunit j, Su j. To exclude the possibility that this protein may represent a contamination of the ATP synthase, a two-dimensional resolution of the sample from Fig. 1,lane 4, was performed. The two-dimensional gel clearly shows that Su j fits the pattern of established subunits of the complex (Fig.1 D). Because no streaking of this protein was observed, we conclude that Su j is a true constituent of the ATP synthase complex. Subunit j could not be removed from the ATP synthase isolated by hydroxyapatite chromatography by adding 7 g of Triton X-100/g of protein and application to BN-PAGE. After the addition of Triton X-100 and 2 m urea and application to BN-PAGE, most of the ATP synthase was dissociated into the individual subunits. The residual fraction of holo-ATP synthase still contained Su j (data not shown). Direct Edman degradation of the proteins transferred to Immobilon P or after deformylation (Su 8 and Su 9) confirmed the presence of known subunits of ATP synthase. The mature subunits α and β were found to be 4 and 14 amino acids, respectively, shorter than described in protein data bases (Table I). The presence of subunit 6 was confirmed by Western blotting and subsequent immunodecoration using a specific antiserum. The novel Su j was directly accessible to Edman degradation, and a sequence of 13 N-terminal amino acids could be obtained (Table I).Table IProteins identified in isolated ATP synthase of S. cerevisiaeBand in SDS gelAssignmentGeneN-terminal sequenceMature protein AAMassSWISS-PROT accessionDa1Su 9 oligomerATP9MQLVLA(*)767,759P008412Su αATP1ASTKAQPTEV51054,952P072513Su βATP2ASAAQSTPIT47851,254P008304Su γATP3ATLKEVEMRL27830,614P380775Su 4 or Su bATP4MSSTPEKQTD20923,249P056266Su 5 or OSCPATP5ASKAAAPPPV19520,870P094577Su 6 or Su aATP6No sequence24927,956P008548Su dATP7sLAKsAANKL(‡)17319,677P309029Su δATP16AEAAAASSGL13814,553Q1216510Su hATP14DVIQDLYLRE9210,408Q1234911Su fATP17VSTLIPPKVV9510,565Q0640512Inhibitor proteinINH1sEGsTGtPRG637,383P0109713Su εATP15sAwRKAGI616,611P2130614Su jATP18MLKRFPTPILKVY596,687P8145015Su 8ATP8MPQLVPFYF(*)485,822P00856Proteins were identified by direct Edman degradation or after deformylation (*), except Su 6, which was identified by Western blotting. The sequence of Su d was obtained without deacylation, although the protein was reported to be acetylated (‡). Small letters in the sequences indicate amino acids that were not identified. The masses of the mature proteins do not include N-terminal modifications. AA, number of amino acids. Open table in a new tab Proteins were identified by direct Edman degradation or after deformylation (*), except Su 6, which was identified by Western blotting. The sequence of Su d was obtained without deacylation, although the protein was reported to be acetylated (‡). Small letters in the sequences indicate amino acids that were not identified. The masses of the mature proteins do not include N-terminal modifications. AA, number of amino acids. Using the obtained N-terminal sequence of Su j, a search for an open reading frame corresponding to a 6.5-kDa protein in the yeast genome data base was performed. A 177-base pair sequence on chromosome XIII was identified with the potential to encode for a protein of 59 amino acid residues (Fig.2 A). This gene encoding for Su j was termed ATP18. We identified a potential homolog inSchizosaccharomyces pombe, a hypothetical protein of 6.8 kDa. This potential Su j homolog in S. pombe was 51% identical to the Su j of S. cerevisiae. The hydropathy plots for both proteins were very similar and suggested them to be membrane proteins with a single transmembrane domain (Fig. 2 B). A peptide corresponding to the C-terminal region of the protein was used to raise antibodies against Su j. Su j was localized to mitochondria by immunostaining. It was inaccessible to added protease in intact mitochondria (Fig. 2 C). Disruption of the outer membrane by hypotonic swelling rendered Su j sensitive to the added protease. In addition, Su j was resistant to alkaline extraction and therefore most likely is an integral membrane protein (Fig.2 C). In summary, Su j is a protein anchored to the inner membrane by a single transmembrane segment at its N terminus and has an Nin-Cout orientation. To test whether the presence of Su j is essential for the activity of the F1F0-ATP synthase, the gene encoding Su j was deleted. The resulting yeast strain Δsu j was respiratory incompetent, as it could no longer grow on the nonfermentable carbon source glycerol, in contrast to its isogenic wild-type strain (Fig.3). Enzymatic measurement of the F1F0-ATP synthase activity confirmed the loss of oligomycin-sensitive ATPase activity in isolated Δsu jin contrast to the wild-type control (results not shown); therefore Su j seemed to be an essential subunit of the yeast F1F0-ATP synthase. However, comparison of the mitochondrial proteins of the Δsu j and Δsu fstrains by BN-PAGE (Fig. 4) and two-dimensional resolution (not shown) revealed that not only the ATP synthase but also cytochrome oxidase (complex IV) and ubiquinol-cytochrome c reductase (complexIII) were below the limit of detection (<10% as compared with wild-type W303-1A). The reduced levels of complex III and IV can be explained by the fact that a spontaneous transition of the Δsu j cells to the rho− state was observed. 3I. Arnold, K. Pfeiffer, W. Neupert, R. A. Stuart, and H. Schägger, unpublished observations. Interestingly a similar formation of rho− cells was observed in the Δsu f strain, as reported by Spannagel et al.(16Spannagel C. Vaillier J. Arselin G. Graves P.V. Velours J. Eur. J. Biochem. 1997; 247: 1111-1117Crossref PubMed Scopus (43) Google Scholar).Figure 4BN-PAGE of Triton X-100-solubilized mitochondria from S. cerevisiaewild-type strain (W303-1A) and the deletion strains Δsu jand Δsu f.ATP synthase (complex V) and cytochrome oxidase (complexIV) are missing in both deletion strains. An additional loss of ubiquinol-cytochrome c reductase (complexIII), which gives rise to a broad band not detectable in BN-PAGE, was revealed after resolution by SDS-PAGE in a second dimension (not shown). BHM, bovine heart mitochondria.View Large Image Figure ViewerDownload Hi-res image Download (PPT) The nature of the association of Su j with the inner membrane and its predicted orientation in the membrane would suggest Su j to be a subunit of the F0 sector of the F1F0-ATP synthase. We therefore asked whether the expression of Su j was required for the stable expression of other F0 sector subunits. Mitochondria from the Δsu j strain were analyzed by Western blotting for the presence of various subunits of the ATP synthase (Fig.5). In the absence of Su j, subunits 6 and f of the F0 sector were not detectable. The α-subunit of the F1 sector was reduced in the Δsu jstrain. Levels of other mitochondrial marker proteins, such as cytochrome c peroxidase and Mge1p, were not altered in the absence of Su j. The subunit composition of the yeast mitochondrial F1F0-ATP synthase was analyzed using the combined techniques of BN-PAGE and high resolution Tricine-SDS-PAGE. We present evidence here for the existence of a novel ATP synthase subunit, Su j. A homologue in the purified bovine ATP synthase complex has so far not been reported. The presence of an open reading frame inS. pombe with 51% amino acid sequence identity to theS. cerevisiae Su j suggests that Su j represents a general component of eukaryotic ATP synthases. The novel Su j protein appears to represent a bona fide subunit of the ATP synthase. Su j purified with the ATP synthase after BN-PAGE. As this technique resolves proteins by their native molecular mass (22Schägger H. Cramer W.A. von Jagow G. Anal. Biochem. 1994; 217: 220-230Crossref PubMed Scopus (1043) Google Scholar), Su j is unlikely to be a contaminant of the ATP synthase; this would require it to have the same native size. No other polypeptides, which could not be assigned to the ATP synthase complex according to the amino acid sequence, were present in the purified ATP synthase fractions. Su j was observed to be tightly bound to the ATP synthase. Treatment of the isolated complex under conditions that led to its almost complete dissociation resulted in a residual fraction of holo-ATP synthase, which still contained Su j. We therefore suggest that Su j is required for the structural integrity of the ATP synthase complex. Consistent with this view, Su j appears to be an essential subunit of the yeast ATP synthase complex. Deletion of the gene encoding Su j (ATP18) gave rise to a respiratory-deficient phenotype and loss of measurable oligomycin-sensitive ATP synthase activity. The tight binding of subunit j to the isolated yeast ATP synthase raises the question as to why subunit j was not previously identified in other ATP synthase preparations. The previous use of SDS gels probably did not yield sufficient resolution of the smaller subunits of the complex. As shown here, the use of high resolution Tricine-SDS-PAGE has optimized the separation of the yeast ATP synthase subunits in the molecular mass range of Su j. Furthermore, although we used mild solubilization with Triton X-100 and BN-PAGE as a one-step procedure, subunits g and e (Tim11) or a potential homologue of bovine subunit F6 were not found in association with the ATP synthase complex. Notably, recent variation of the conditions for protein solubilization and BN-PAGE led to the isolation of an ATP synthase with three more bound proteins, including subunits e (Tim11) and subunit g. The analysis of the role of these proteins for the structure and function of ATP synthase will be discussed separately (37Arnold I. Pfeiffer K. Neupert W. Stuart R.A. Schägger H. EMBO J. 1998; (in press): 17Google Scholar). In conclusion, we demonstrate here that Su j is an integral inner membrane protein, spanning the membrane once in an Nin-Cout orientation. The membrane association of Su j is compatible with it being a subunit of the F0sector of the ATP synthase. We are currently investigating the association of Su j with other known F0 sector subunits. We are grateful to Dr. Jean Velours (Université Bordeaux, France) for the generous gift of the antisera against ATPase subunits f and 6 and the Δsu fyeast strain. We thank Sandra Weinzierl and Monika Krampert for excellent technical assistance.