Integral membrane proteins in the mitochondrial outer membrane of Saccharomyces cerevisiae Lena Burri 1 , Katherine Vascotto 1,2 , Ian E. Gentle 1,2 , Nickie C. Chan 1,2 , Traude Beilharz 1 , David I. Stapleton 2 , Lynn Ramage 3, * and Trevor Lithgow 1,2 1 Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Australia 2 Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia 3 Biozentrum, University of Basel, Switzerland Mitochondria were derived from endosymbiotic bac- teria and the mitochondrial outer membrane shares many features with bacterial outer membranes [1,2]. Polypeptides embedded in the outer membrane of Gram-negative bacteria are either lipoproteins anchored by a covalently linked lipid, or have a b-barrel structure with eight or more antiparallel b-strands hydrogen bonded into a cylindrical barrel [3,4]. The b-barrel proteins have an unusual primary structure with many strands of alternating hydrophi- lic and hydrophobic residues and a high abundance of aromatic residues that tend to be placed at the start of the strands [2,5]. These b-barrel proteins are assembled in the bacterial outer membrane in a process mediated by the integral membrane protein Omp85 [2,3,5–8]. Mitochondria also carry a member of the Omp85 family [8]: this protein, called Sam50, has been shown responsible for the assembly of b-barrel pro- teins in the mitochondrial outer membrane [9–11], and functions together with at least two other sub- units as part of a Sorting and Assembly Machine (SAM) complex [7,9–11]. In addition to b-barrel pro- teins, mitochondrial outer membranes also have pro- teins with a-helical transmembrane domains. These proteins appear to provide functions that were procured after the initial endosymbiont established itself in early eukaryotic cells, including protein Keywords detergent phase; mitochondria; outer membrane; transmembrane segments Correspondence T. Lithgow, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia Fax: +61 39348 2251 Tel: +61 38344 4131 E-mail: t.lithgow@unimelb.edu.au *Present address Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland (Received 30 October 2005, revised 29 January 2006, accepted 9 February 2006) doi:10.1111/j.1742-4658.2006.05171.x Mitochondria evolved from a bacterial endosymbiont ancestor in which the integral outer membrane proteins would have been b-barrel structured within the plane of the membrane. Initial proteomics on the outer mem- brane from yeast mitochondria suggest that while most of the protein components are integral in the membrane, most of these mitochondrial pro- teins behave as if they have a-helical transmembrane domains, rather than b-barrels. These proteins are usually predicted to have a single a-helical transmembrane segment at either the N- or C-terminus, however, more complex topologies are also seen. We purified the novel outer membrane protein Om14 and show it is encoded in the gene YBR230c. Protein sequen- cing revealed an intron is spliced from the transcript, and both transcription from the YBR230c gene and steady-state level of the Om14 protein is dra- matically less in cells grown on glucose than in cells grown on nonfermenta- ble carbon sources. Hydropathy predictions together with data from limited protease digestion show three a-helical transmembrane segments in Om14. The a-helical outer membrane proteins provide functions derived after the endosymbiotic event, and require the translocase in the outer mitochondrial membrane complex for insertion into the outer membrane. Abbreviations DAS, dense alignment surface; PVDF, poly(vinylidene difluoride); TOM, translocase in the outer mitochondrial membrane. FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS 1507 translocation, mitochondrial fission, and the contri- butions made by mitochondria to cellular redox metabolism and programmed cell death [12–15]. Integral membrane proteins with a-helical transmem- brane segments appear to be inserted into the outer membrane by the translocase in the outer mitochon- drial membrane (TOM) complex without assistance from the SAM complex [16,17], but it has not been clear whether the most abundant protein traffic into the outer membrane of mitochondria comes from the b-barrel or a-helical type integral membrane proteins. To identify and characterize a-helical type integral membrane proteins, we fractionated outer membrane vesicles from yeast mitochondria for analysis by pro- tein sequencing and mass spectrometry. We found Tri- ton X-114 phase separation to be the most reliable means of purifying integral membrane proteins from the mitochondrial outer membrane, and of the 11 most abundant integral proteins, 10 had a-helical transmem- brane segments. Of these 10 proteins, most had a single transmembrane segment predicted at the N- or C-terminus. However, more complex topologies are also seen, with the novel protein Om14 being an integral membrane protein with three a-helical trans- membrane segments that are assembled into the mito- chondrial outer membrane. Results and Discussion Integral membrane proteins in the mitochondrial outer membrane The protein profile of mitochondrial outer membranes shows at least nine major proteins (Fig. 1A, asterisks), with the three most abundant of these the 45 kDa pro- tein Om45 [18], the 29 kDa protein Por1 [19] and the 14 kDa outer membrane protein we call Om14. At least six other major proteins are present, as judged from the Coomassie-stained protein profile. In order to characterize the proteins of the outer membrane, we set out to determine what proportion was integral and to identify the major protein species. To determine whether the major outer membrane proteins were integral or peripheral, we initially used alkali extraction. Extraction of the membrane vesicles with alkali sodium carbonate releases several proteins that might be peripheral components of the membrane (Fig. 1A). Under these conditions, Om14 and Om45 are partially extracted by alkali, as are several other outer membrane proteins. Om45 is known to be anchored by a single a-helical transmembrane segment [16]. Mitochondrial outer membrane proteins have amphipathic character in their transmembrane segments, A BC Fig. 1. Biochemical characterization of proteins present in purified mitochondrial outer membranes. (A). Outer membrane vesicles were puri- fied and subject to treatment with 0.1 M Na 2 CO 3 . A sample of total vesicle proteins (100 lg) was analyzed by SDS ⁄ PAGE (‘T’) and compared with the proteins resistant to alkali extraction (‘P’) and those extracted into the supernatant (‘S’). The marker protein sizes and the positions of Om45 and Om14 on the Coomassie-stained gel are shown. (B). Outer membrane vesicles were subject to cloud-point extraction with Tri- ton X-114, and SDS ⁄ PAGE used to determine the proteins present in the aqueous extract (‘Aq’), the detergent phase (‘D’) and the phospho- lipid-rich pellet (‘P’). Arrowheads designate the size of proteins enriched in the lipid-rich pellet including the major 29 kDa protein Por1 and Tom40, identified by mass spectrometry and immunoblotting. (C). After in situ digestion with trypsin, mass spectrometry was used to iden- tify the major proteins in the detergent phase of the extracted outer membrane vesicles (see Table 1). Equivalent samples were analyzed by SDS ⁄ PAGE followed by transfer to PVDF membrane for N-terminal sequencing. Integral proteins in the mitochondrial outer membrane L. Burri et al. 1508 FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS and alkali extraction might not always be a reliable indicator of whether a protein is integral in the outer membrane [17,20–22]. As a distinct means to separate integral and peri- pheral membrane proteins we undertook cloud point extraction with Triton X-114 [23,24]. This treatment liberates three fractions from a solubilized membrane: an aqueous phase containing peripheral membrane proteins, a detergent-phase in which proteins with a-helical transmembrane domains are soluble and a ‘phospholipid-enriched’ pellet fraction containing pro- teins that either have lipid modifications or b-barrel characteristics [25–29]. After phase separation, approximately 15 proteins partitioned exclusively into the aqueous phase, while at least 19 integral membrane proteins partitioned into the detergent phase: Om45 and Om14 clearly behaved as integral membrane pro- teins with a-helical transmembrane segments, partition- ing into the detergent phase (Fig. 1B). A combination of N-terminal sequencing and mass spectrometry was used to identify the 11 major integral membrane proteins (Table 1). As reported previously and shown in Fig. 1C, Tom20 and Tom22 migrate closely together on this gel system [30]. Tom70 and Tom71 also migrate closely together on the gel, and the relative intensity of Coomassie staining reflects previous immunoblot analysis that suggested an 10 : 1 ratio of Tom70 to Tom71 [31]. The mitochondrial glycerol-3-phosphate dehydroge- nase Gut2 behaves as an integral protein, though the precise topology of Gut2 remains unclear. Our protein sequencing confirms a predicted processing site [32], and our predictions with the dense alignment surface (DAS) algorithm (see Experimental procedures) agree with the previous proposal that Gut2 has two trans- membrane segments [33]. Previously, Gut2 had been assumed located on the outer surface of the mitoch- ondrial inner membrane. However, since we identified no other inner membrane proteins in our vesicle pre- paration, we suggest that Gut2 is an outer membrane protein with its N-terminal FAD-binding domain facing the intermembrane space. This topology would enable Gut2 to transfer of electrons to Nde1 in the intermembrane space [32]. Alo1 catalyses the final step in d-erythroascorbic acid biosynthesis [34], was previously located to mito- chondria [34,35], and has a predicted a-helical trans- membrane segment from residue 174 to residue 191. The cytochrome b 5 reductase, Mcr1, is an outer mem- brane protein with a single N-terminal, a-helical trans- membrane segment [36], and assists d-erythroascorbic acid biosynthesis [14]. Table 1. Major proteins identified in the Triton X-114 detergent phase from the mitochondrial outer membrane of Saccharomyces cerevisiae. The details of mass spectrometry and N-terminal sequencing are provided in the Experimental procedures section. ND refers to proteins for which no N-terminal sequence could be determined. Note for Gut2, the aspartate residue in position one of the determined sequence cor- responds to D 38 in the precursor protein, as previously predicted by Esser et al. [32]. For Tom22, the valine at position 1 corresponds to V 2 in the predicted protein sequence [31], suggesting removal of the N-terminal methionine. ORF Gene Protein Sequence coverage (%) N-terminal sequence Molecular mass (kDa) Apparent Predicted YNL121c TOM70 70 kDa protein import receptor, isoform 1 41 MKSFITRNKTAILATV 70.123 70 YHR117w TOM71 70 kDa protein import receptor, isoform 2 28 ND 71.856 70 YIL155c GUT2 Mitochondrial glycerol-3- phosphate dehydrogenase 43 DPSYMVQFPTAAPPQV 72.388 68 YMR110c Unknown 28 ND 59.978 63 YML086c ALO1 D-Arabinono-1,4-lactone oxidase 42 ND 59.493 58 YIL136w OM45 Unknown 42 ND 44.580 45 YKL150w MCR1 NADH-cytochrome b5 reductase 22 MSRLSRSHSKALPIALGTV 34.137 34 YNL055c POR1 Voltage-dependent anion channel, isoform 1 66 MSPPVYSDIS 30.428 29 YGR082w TOM20 20 kDa protein import receptor 30 ND 20.317 22 YNL131w TOM22 22 kDa protein import receptor 22 VELTEIKDDVVQLDEPQFSR 16.790 22 YBR230c OM14 Unknown ND MSATAKHDSNAS 14.609 14 L. Burri et al. Integral proteins in the mitochondrial outer membrane FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS 1509 Ymr110c was previously identified as a mitochond- rial protein [35] and the protein encoded from the YMR110c gene fused to GFP shows punctate intra- cellular localization similar to the outer membrane proteins Mmm1 and Mmm2 [37]. The DAS predictor suggests Ymr110c would have a single transmembrane segment, from residues 134–152, which would anchor it in the mitochondrial outer membrane. As reported for bacterial b-barrel proteins and lipid- modified proteins [27–29], Por1, Tom40, and nine other proteins (of relative molecular masses 27, 34, 35, 50, 55, 65, 70, 85 and 105 kDa) precipitate out of the Triton X-114 detergent phase (Fig. 1B, arrowheads). None of the proteins so far identified in this fraction is predicted to have a a-helical transmembrane segment. Of interest, the 50 kDa protein band includes peptides (8% sequence coverage) derived from Xdj1, a mole- cular chaperone previously reported localized to mito- chondria [38]. Xdj1 is likely to carry a C-terminal prenylation that might be responsible for its location in the pellet fraction: a closely related chaperone, Ydj1, is prenylated and known to play a role in pro- tein transport into mitochondria [39,40]. Om14 is a mitochondrial protein encoded from an intron-containing gene N-terminal sequencing showed Om14 to be encoded from the YBR230c gene (Fig. 2A). The protein sequence we obtained confirmed that a 97-basepair intron predicted in the YBR230c gene [41] is spliced from the transcript encoding Om14 at the predicted splice sites between the sequences corresponding to H 7 and D 8 (Fig. 2A). Introns are rare in the genome of S. cerevisiae [42] and Om14 is, to our knowledge, the first mitochondrial protein encoded in an intron- containing gene. Om14 was purified by anion-exchange chromatogra- phy from mitochondrial outer membranes solubilized in the detergent octyl-POE (Ramage, Lithgow and Schatz, unpublished results). An antiserum raised in rabbits to purified Om14 was used in immunoblots on mitochondria derived from wild-type yeast cells and Dom14 yeast cells from which the YBR230c gene had been deleted confirm that Om14 is the product of the YBR230c gene (data not shown). To be sure that Om14 is located exclusively in the mitochondria, GFP fusions were constructed and expressed in yeast. Confocal fluorescence microscopy of live cells revealed the N-terminal fusion (GFP- Om14) localizes exclusively to cortical structures that costain with the mitochondria-specific dye Mitotracker (Fig. 2B). The C-terminal GFP fusion (Om14-GFP) gave identical profiles (Fig. 2B). Mitochondria were isolated from cells expressing the N-terminal GFP- Om14 fusion protein and treated with trypsin. The GFP domain was released with protease, while trypsin- sensitive proteins like cytochrome b 2 (in the mito- A BCD Fig. 2. Identification and characterization of Om14. (A) The determined N-terminal sequence of Om14 (Table 1) is shown in bold. Basic resi- dues, representing sites for trypsin cleavage, are circled and predicted transmembrane segments boxed. (B) Yeast cells expressing GFP- Om14 or Om14-GFP were co-stained with the fluorescent dye Mitotracker Red and viewed by confocal microscopy. Filters selective for the green fluorescence of GFP (left panel) or the red fluorescence of Mitotracker Red (middle panel) were used. Green and red fluorescence pic- tures merged is shown in the right panel. (C) Wild-type (lane 1) or GFP-Om14 expressing (lanes 2–4) purified mitochondria (100 lg) were treated with trypsin and 1% Triton (where indicated, ‘+’) for 30 min at 4 °C. After precipitation in trichloroacetic acid, proteins were analyzed by SDS ⁄ PAGE and immunoblotting with antisera recognizing the outer membrane protein Tom70, the intermembrane space protein cyto- chrome b 2 (Cytb 2 ), the matrix-located Mdj1 or GFP. (D) 100 lg purified mitochondria expressing GFP-Om14 was treated with 0.1 M Na 2 CO 3 and centrifuged to separate solubilized proteins (S) from insoluble material (P). Proteins were then analyzed by immunoblotting after SDS ⁄ PAGE using antisera against the matrix-located mtHsp70, the membrane protein porin and GFP. Integral proteins in the mitochondrial outer membrane L. Burri et al. 1510 FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS chondrial intermembrane space) and Mdj1 (in the mat- rix) were protected from the protease by the outer membrane (Fig. 2C). Alkali extraction of puri- fied mitochondria showed only a partial extraction of GFP-Om14 (Fig. 2D), as seen for the untagged pro- tein in Fig. 1(A). Om14 is an integral outer membrane protein with its N-terminus displayed in the cytosol. Transmembrane topology of Om14 Figure 3A shows a hydropathy analysis of the Om14 sequence that predicts two or three a-helical transmem- brane segments, in support of the behavior of the protein in Triton X-114. The transmembrane segments corresponding to residues 71–90 and 104–119 are con- fident predictions and the corresponding sequences are highly conserved in orthologs of Om14 found in other yeasts, including Saccharomyces kluverii, Ashbya gossypii and Candida albicans (Supplementary material). However, the region corresponding to residues 38–54 predicts relatively poorly as a transmembrane segment. With the N-terminus of Om14 exposed in the cytosol, there are two possible models for transmembrane topology (Fig. 3B). To distinguish between these two, mitochondria were isolated from yeast cells expressing Om14-GFP and shaved with trypsin. The outer mem- brane protein Tom70 is degraded by trypsin, while cyto- chrome b 2 is protected in the intermembrane space (Fig. 3C). An antibody recognizing the GFP tag at the C-terminus of Om14-GFP shows the electrophoretic mobility of the fusion protein is reduced, indicating a 2 kDa mass difference. The C-terminal GFP epitope is protected within the intermembrane space, and the proteolysis must therefore represent a loss of 2 kDa from the N-terminus. Given there are seven arginine and lysine residues spread through the N-terminal stretch of Om14, the three transmembrane segment model of Om14 is the only one consistent with our data. Om14 is not a subunit of the TOM, SAM or morphology-related complexes Proteins closely related in sequence to Om14 were found in all budding yeast for which genome sequence data is available (Supplementary material), but we were unable to find closely related proteins from other fungi, or even in the fission yeast Schizosaccharomyces pombe. Both the lack of obvious orthologs in other fungi and the abundance of Om14 in the outer mem- brane would argue against it having a fundamental role in mitochondrial biogenesis. While the function of Om14 remains unclear, it may be related functionally to another major protein in the outer membrane, Om45. No detailed data on the stoi- chiometry of these proteins exists, however, the Coo- massie-stained profile of membrane proteins suggests Om45 and Om14 are present at similar levels in the outer membrane, and their steady-state levels are tightly coregulated [43] suggestive of some link in their function. A previous report on changes to the mito- chondrial proteome during diauxic shift identified only 18 mitochondrial proteins whose steady-state levels change when yeast cultures are shifted from glucose- to glycerol-based growth media [43]. Sixteen of the 18 pro- teins were known to function in metabolic pathways associated with respiration. The only two proteins of unknown function to disappear when cells were grown A B C Fig. 3. Topology of Om14 in the outer mitochondrial membrane. (A) Hydropathy calculations for Om14 were made with DAS [52]. The solid line represents a high confidence limit and the dashed line a medium confidence limit for predictions. (B) Two potential topologies for Om14 in the outer membrane. Amino acid residues that delimit the predicted transmembrane segments are numbered. (C) Wild-type (lane 1) or Om14-GFP expressing (lanes 2–4) purified mitochondria (100 lg) were treated with trypsin and 1% Triton (where indicated, ‘+’) for 20 min at 4 °C. After precipitation in tri- chloroacetic acid, proteins were analyzed by SDS ⁄ PAGE and im- munoblotting with antisera recognizing the outer membrane protein Tom70, the intermembrane space protein cytochrome b 2 (Cytb 2 ), the matrix-located Mdj1 or GFP. L. Burri et al. Integral proteins in the mitochondrial outer membrane FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS 1511 on glucose were Ybr230c (i.e. Om14) and Om45. Like Dom45 cells [18], Dom14 cells have no obvious defects in mitochondrial morphology or inheritance (data not shown) and show no obvious defects in growth on fer- mentable or nonfermentable carbon sources at any temperature between 14 and 37 °C (data not shown). Topography of the mitochondrial outer membrane The data presented here show that most of the protein associated with the yeast mitochondrial outer mem- brane in yeast is integral in the membrane and most of the integral outer membrane proteins behave as if they have a-helical transmembrane segments, partitioning into the detergent phase after Triton X-114 extraction of the outer membrane. This includes a number of proteins whose submitochondrial location was not known. While many of these proteins have a single transmembrane segment at the N- or C-terminus, some like Gut2 are predicted to have multiple transmem- brane segments. Three transmembrane segments were demonstrated for the newly identified protein Om14. Thus, most of the newly synthesized protein flux into the mitochondrial outer membrane consists of integral proteins with a-helical transmembrane segments, and the outer membrane is versatile enough to assemble a large mass of protein with this topology. As the TOM complex is needed to insert these a-helical transmem- brane segments, the development of a TOM complex by the ancestral endosymbiont was a prime face requirement to establish protein targeting to all com- partments of the developing organelle. Experimental procedures Purification of mitochondrial outer membrane vesicles The yeast strain D273–10B (Mata, ATCC 25657) was grown in 30 L cultures of semisynthetic media with lactate as a car- bon source to an A 600 of approximately 3. Cells were harves- ted and mitochondria purified on 14–18% Nycodenz (Sigma, Castle Hill, NSW, Australia) gradients at pH 6.0 (prepared in 10 mm Mops, 0.6 m sorbitol). Mitochondrial outer mem- brane vesicles were prepared and purified as previously des- cribed [44]. Proteomics Mitochondrial outer membrane vesicles were solubilized essentially as described [37] in buffer containing 50 mm Hepes (pH 8.0), 2% octyl-POE (N-octyl-polyoxyethylene, Bachem, Bubendorf, Switzerland), 50 mm NaCl (to a con- centration of 2–3 mgÆmL )1 protein) and the solubilized pro- teins separated by chromatography on Mono-Q (HR5 ⁄ 5 column, Pharmacia), using the same buffer with 1.0 m NaCl to develop the column. Elution of the major integral membrane proteins from the column was monitored by SDS ⁄ PAGE of every second fraction and subsequent Coo- massie staining of the gels. To raise mono-specific antisera, samples of the outer membrane proteins eluted from the column were resolved by SDS ⁄ PAGE. After briefly Coomassie-staining the gels, bands representing proteins of interest were excised and mounted into an electroelution chamber, with a BT2 mem- brane (Schleicher & Schuell, Bottmingen, Switzerland) at one end. Electroelution proceeded for 6 h at 70 V, with two changes of the eletrophoresis buffer (25 mm Tris, 192 mm glycine, 0.025% SDS). The eluted protein sample was preci- pitated with nine volumes of ice-cold ethanol and lyophi- lized for injection into rabbits. For direct protein sequencing, outer membrane proteins (500 lg of total protein per lane) were separated by SDS ⁄ PAGE, blotted to polyvinylidene difluoride (PVDF; Immobilon-P; Millipore, Australia) and stained briefly with Coomassie blue [45]. Slivers of PVDF-carrying protein were excised and loaded into the sample cartridge of a Perkin- Elmer HPG1005A Sequenator, and N-terminal sequences read for up to 20 cycles. For identification by mass spectrometry, proteins were excised from a dried gel using a protein-free blade and rehydrated in water for 15 min. Gel pieces were diced and destained in 100 mm NH 4 HCO 3 ⁄ 50% acetonitrile, dehydra- ted in acetonitrile for 5 min and then air dried. Proteins were reduced with 50 mm dithiothreitol at 60 °C for 60 min and then alkylated with 50 mm iodoacetamide at room tem- perature in the dark. Gel pieces were washed in 20 mm NH 4 HCO 3 ⁄ 50% acetonitrile, dehydrated as above and rehydrated in the presence of 250 ng proteomics grade tryp- sin (Sigma, Australia) in 20 mm NH 4 HCO 3 and the digest allowed to proceed overnight at 30 °C. Tryptic peptides were analyzed by liquid chromatography-tandem MS (LC- MS ⁄ MS). Peptides were injected manually via a Rheodyne injector onto a Waters 3 lm, dC18 Atlantis column (300 lm · 100 mm) fitted with a Waters Atlantis Nanoease guard column that was connected to an Agilent 1100 XCT plus ion trap mass spectrometer. Peptides were separated over a gradient of 3–40% acetonitrile (with 0.1% formic acid) during 25 min, followed by a rapid gradient to 70% acetonitrile (with 0.1% formic acid), with a total run time of 40 min. MS ⁄ MS spectra were analyzed using the Mascot search engine [46]. Plasmids, yeast strains and media The DNA fragment corresponding to Om14 (YBR230c) was amplified from a preparation of S. cerevisiae cDNA by Integral proteins in the mitochondrial outer membrane L. Burri et al. 1512 FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS PCR using primers that generated in-frame restriction sites. The PCR product was cloned into a centromeric plasmid (with the URA3 gene for selection) to encode GFP-Om14 or Om14-GFP. These plasmids were used for transforma- tion into the om14 strain (MATa, leu2, ura3, trp1, his3?, om14::kanMX). Yeast was grown at 30 °C on YPAD (2% (w ⁄ v) glucose, 1% (w ⁄ v) yeast extract, 2% (w ⁄ v) peptone supplemented with adenine sulfate). Characterization of membrane protein insertion and topology Mitochondria were isolated according to [47] and trypsin treatments were performed as described [48]. Membranes were extracted by resuspension in 0.1 m Na 2 CO 3 and incu- bation for 30 min on ice with gentle vortexing. Soluble and insoluble proteins were separated by centrifugation at 100 000 g in a Beckman Airfuge (Beckman Coulter, Gladesville, NSW, Australia) [49]. For Triton X-114 extrac- tions, samples of outer membrane vesicles corresponding to 100 lg protein were treated with detergent as described [50]. Samples of mitochondrial protein (100 lg) were separ- ated by Tris-glycine SDS ⁄ PAGE and western blots were carried out according to published methods [48]. Fluores- cence microscopy was as previously described [51]. Trans- membrane domains were predicted from protein sequence using DAS [51]. Acknowledgements The authors thank Rosemary Condron for protein sequencing, Ian Dawes for the yeast cDNA prepar- ation, Vasyl Demchyshyn for technical assistance and Gottfried Schatz for very many contributions to the early phase of our work. We thank Agilent Technol- ogies for their active collaboration with the Bio21 Molecular Science and Biotechnology Institute. Thanks also to Tony Purcell and Nick Williamson for critical reading of the manuscript. This project was supported by an Early Career Research Grant from the University of Melbourne (to L.B.), Australian Postgraduate Awards (to K.V., I.E.G. and N.C.C.) and a grant from the Australian Research Council (to T.L.). References 1 Gray MW, Burger G & Lang BF (1999) Mitochondrial evolution. Science 283, 1476–1481. 2 Wimley WC (2003) The versatile beta-barrel membrane protein. Curr Opin Struct Biol 13, 404–411. 3 Tamm LK, Arora A & Kleinschmidt JH (2001) Struc- ture and assembly of beta-barrel membrane proteins. J Biol Chem 276, 32399–32402. 4 Tokuda H & Matsuyama S (2004) Sorting of lipopro- teins to the outer membrane in E. coli. Biochim Biophys Acta 1693, 5–13. 5 Bos MP & Tommassen J (2004) Biogenesis of the Gram-negative bacterial outer membrane. Curr Opin Microbiol 7, 610–616. 6 Schulz GE (2002) The structure of bacterial outer mem- brane proteins. Biochim Biophys Acta 1565, 308–317. 7 Pfanner N, Wiedemann N, Meisinger C & Lithgow T (2004) Assembling the mitochondrial outer membrane. Nat Struct Mol Biol 11, 1044–1048. 8 Gentle IE, Burri L & Lithgow T (2005) Molecular architecture and function of the Omp85 family of pro- teins. Mol Microbiol 58, 1216–1225. 9 Paschen SA, Waizenegger T, Stan T, Preuss M, Cyrk- laff M, Hell K, Rapaport D & Neupert W (2003) Evolutionary conservation of biogenesis of beta-barrel membrane proteins. Nature 426, 862–866. 10 Kozjak V, Wiedemann N, Milenkovic D, Lohaus C, Meyer HE, Guiard B, Meisinger C & Pfanner N (2003) An essential role of Sam50 in the protein sorting and assembly machinery of the mitochondrial outer mem- brane. J Biol Chem 278, 48520–48523. 11 Gentle I, Gabriel K, Beech P, Waller R & Lithgow T (2004) The Omp85 family of proteins is essential for outer membrane biogenesis in mitochondria and bac- teria. J Cell Biol 164, 19–24. 12 Mihara K (2000) Targeting and insertion of nuclear- encoded preproteins into the mitochondrial outer mem- brane. Bioessays 22 , 364–371. 13 Rapaport D (2003) Finding the right organelle: target- ing signals in mitochondrial outer-membrane proteins. EMBO Rep 4, 948–952. 14 Lee JS, Huh WK, Lee BH, Baek YU, Hwang CS, Kim ST, Kim YR & Kang SO (2001) Mitochondrial NADH-cytochrome b(5) reductase plays a crucial role in the reduction of d-erythroascorbyl free radical in Saccharomyces cerevisiae. Biochim Biophys Acta 1527, 31–38. 15 Wilson-Annan J, O’Reilly LA, Crawford SA, Haus- mann G, Beaumont JG, Parma LP, Chen L, Lackmann M, Lithgow T, Hinds MG et al. (2003) Proapoptotic BH3-only proteins trigger membrane integration of pro- survival Bcl-w and neutralize its activity. J Cell Biol 162, 877–887. 16 Waizenegger T, Stan T, Neupert W & Rapaport D (2003) Signal-anchor domains of proteins of the outer membrane of mitochondria: structural and functional characteristics. J Biol Chem 278, 42064–42071. 17 Brandner K, Mick DU, Frazier AE, Taylor RD, Mei- singer C & Rehling P (2005) Taz1, an outer mitochon- drial membrane protein, affects stability and assembly of inner membrane protein complexes: implications for Barth syndrome. Mol Biol Cell 16, 5202–5214. L. Burri et al. Integral proteins in the mitochondrial outer membrane FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS 1513 18 Yaffe MP, Jensen RE & Guido EC (1989) The major 45-kDa protein of the yeast mitochondrial outer mem- brane is not essential for cell growth or mitochondrial function. J Biol Chem 264, 21091–21096. 19 Mihara K & Sato R (1985) Molecular cloning and sequencing of cDNA for yeast porin, an outer mito- chondrial membrane protein: a search for targeting sig- nal in the primary structure. EMBO J 4, 769–774. 20 Mokranjac D, Sichting M, Neupert W & Hell K (2003) Tim14, a novel key component of the import motor of the TIM23 protein translocase of mitochondria. EMBO J 22, 4945–4956. 21 Truscott KN, Voos W, Frazier AE, Lind M, Li Y, Geissler A, Dudek J, Muller H, Sickmann A, Meyer HE, et al. (2003) A J-protein is an essential subunit of the presequence translocase-associated protein import motor of mitochondria. J Cell Biol 163, 707–713. 22 D’Silva PD, Schilke B, Walter W, Andrew A & Craig EA (2003) J protein cochaperone of the mitochondrial inner membrane required for protein import into the mitochondrial matrix. Proc Natl Acad Sci USA 100, 13839–13844. 23 Bordier C (1981) Phase separation of integral membrane proteins in Triton X-114 solution. J Biol Chem 256, 1604–1607. 24 Pryde JG & Phillips JH (1986) Fractionation of mem- brane proteins by temperature-induced phase separation in Triton X-114. Application to subcellular fractions of the adrenal medulla. Biochem J 233, 525–533. 25 Cory S, Huang DC & Adams JM (2003) The Bcl-2 family: roles in cell survival and oncogenesis. Oncogene 22, 8590–8607. 26 Cunningham TM, Walker EM, Miller JN & Lovett MA (1988) Selective release of the Treponema pallidum outer membrane and associated polypeptides with Triton X- 114. J Bacteriol 170, 5789–5796. 27 Brown D & Waneck GL (1992) Glycosyl-phosphatidyl- inositol-anchored membrane proteins. J Am Soc Nephrol 3, 895–906. 28 Hooper NM & Bashir A (1991) Glycosyl-phosphatidyl- inositol-anchored membrane proteins can be distin- guished from transmembrane polypeptide-anchored proteins by differential solubilization and temperature- induced phase separation in Triton X-114. Biochem J 280, 745–751. 29 Osanai K, Takahashi K, Nakamura K, Takahashi M, Ishigaki M, Sakuma T, Toga H, Suzuki T & Voelker DR (2005) Expression and characterization of Rab38, a new member of the Rab small G protein family. Biol Chem 386, 143–153. 30 Lithgow T, Junne T, Suda K, Gratzer S & Schatz G (1994) The mitochondrial outer membrane protein Mas22p is essential for protein import and viability of yeast. Proc Natl Acad Sci USA 91, 11973–11977. 31 Bomer U, Maarse AC, Martin F, Geissler A, Merlin A, Schonfisch B, Meijer M, Pfanner N & Rassow J (1998) Separation of structural and dynamic functions of the mitochondrial translocase: Tim44 is crucial for the inner membrane import sites in translocation of tightly folded domains, but not of loosely folded preproteins. EMBO J 17, 4226–4237. 32 Rigoulet M, Aguilaniu H, Averet N, Bunoust O, Cam- ougrand N, Grandier-Vazeille X, Larsson C, Pahlman IL, Manon S & Gustafsson L (2004) Organization and regulation of the cytosolic NADH metabolism in the yeast Saccharomyces cerevisiae. Mol Cell Biochem 256– 257, 73–81. 33 Esser K, Jan PS, Pratje E & Michaelis G (2004) The mitochondrial IMP peptidase of yeast: functional analy- sis of domains and identification of Gut2 as a new nat- ural substrate. Mol Genet Genomics 271, 616–626. 34 Huh WK, Lee BH, Kim ST, Kim YR, Rhie GE, Baek YW, Hwang CS, Lee JS & Kang SO (1998) d-Ery- throascorbic acid is an important antioxidant molecule in Saccharomyces cerevisiae. Mol Microbiol 30, 895–903. 35 Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B et al. (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci USA 100, 13207–13212. 36 Hahne K, Haucke V, Ramage L & Schatz G (1994) Incomplete arrest in the outer membrane sorts NADH- cytochrome b5 reductase to two different submitochon- drial compartments. Cell 79, 829–839. 37 Hobbs AE, Srinivasan M, McCaffery JM & Jensen RE (2001) Mmm1p, a mitochondrial outer membrane pro- tein, is connected to mitochondrial DNA (mtDNA) nucleoids and required for mtDNA stability. J Cell Biol 152, 401–410. 38 Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS & O’Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425, 686–691. 39 Atencio DP & Yaffe MP (1992) MAS5, a yeast homo- log of DnaJ involved in mitochondrial protein import. Mol Cell Biol 12, 283–291. 40 Caplan AJ, Cyr DM & Douglas MG (1992) YDJ1p facilitates polypeptide translocation across different intracellular membranes by a conserved mechanism. Cell 71, 1143–1155. 41 Davis CA, Grate L, Spingola M & Ares M Jr (2000) Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meioti- cally regulated genes of yeast. Nucleic Acids Res 28, 1700–1706. 42 Barrass JD & Beggs JD (2003) Splicing goes global. Trends Genet 19, 295–298. 43 Ohlmeier S, Kastaniotis AJ, Hiltunen JK & Bergmann U (2004) The yeast mitochondrial proteome, a study of Integral proteins in the mitochondrial outer membrane L. Burri et al. 1514 FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS fermentative and respiratory growth. J Biol Chem 279, 3956–3979. 44 Gonzalez-Baro MR, Granger DA & Coleman RA (2001) Mitochondrial glycerol phosphate acyltransferase contains two transmembrane domains with the active site in the N-terminal domain facing the cytosol. J Biol Chem 276, 43182–43188. 45 Beilharz T, Suzuki CK & Lithgow T (1998) A toxic fusion protein accumulating between the mitochondrial membranes inhibits protein assembly in vivo. J Biol Chem 273, 35268–35272. 46 Perkins DN, Pappin DJ, Creasy DM & Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20 , 3551–3567. 47 Lacapere JJ & Papadopoulos V (2003) Peripheral-type benzodiazepine receptor: structure and function of a cholesterol-binding protein in steroid and bile acid bio- synthesis. Steroids 68, 569–585. 48 Joseph-Liauzun E, Delmas P, Shire D & Ferrara P (1998) Topological analysis of the peripheral benzodi- azepine receptor in yeast mitochondrial membranes supports a five-transmembrane structure. J Biol Chem 273, 2146–2152. 49 Wattenberg B & Lithgow T (2001) Targeting of C-term- inal (tail)-anchored proteins: understanding how cytoplasmic activities are anchored to intracellular membranes. Traffic 2, 66–71. 50 Hermann GJ, Thatcher JW, Mills JP, Hales KG, Fuller MT, Nunnari J & Shaw JM (1998) Mitochondrial fusion in yeast requires the transmembrane GTPase Fzo1p. J Cell Biol 143, 359–373. 51 Beilharz T, Egan B, Silver PA, Hofmann K & Lithgow T (2003) Bipartite signals mediate subcellular targeting of tail-anchored membrane proteins in Saccharomyces cerevisiae. J Biol Chem 278, 8219–8223. 52 Cserzo M, Wallin E, Simon I, von Heijne G & Elofsson A (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng 10, 673–676. Supplementary material The following supplementary material is available online: Fig. S1. Alignment of Om14 from various yeast species. Draft form sequence data for Saccharomyces paradoxus, Saccharomyces kudriazevii, Saccharomyces kluveryii and Naumovia castellii were accessed via the Genome Sequence Center (University of St Louis; http://genomeold.wustl.edu/). Final sequences, publicly available through GenBank, have the following acces- sion numbers: Om14 from Ashbya gossypii (NM_ 208072.1), from Kluyveromyces lactis (CAG98233.1), from Saccharomyces cerevisiae (NP_009789.1), from Candida glabrata (CAG58159.1). Sequences were aligned with clustalw, using version 1.81 with default parameters (http://www.ebi.ac.uk/clustalw/). Amino acid residues are colored to show chemically similar residues (pink, basic; blue, acidic; green, polar; red, nonpolar). The three predicted transmembrane seg- ments are shaded grey and numbered TM1-TM3. Asterisks denote truncated sequences; with uncon- firmed introns breaking the open-reading frame in these genome sequences. This material is available as part of the online article from http://www.blackwell-synergy.com L. Burri et al. Integral proteins in the mitochondrial outer membrane FEBS Journal 273 (2006) 1507–1515 ª 2006 The Authors Journal compilation ª 2006 FEBS 1515 . is integral in the membrane and most of the integral outer membrane proteins behave as if they have a-helical transmembrane segments, partitioning into the. Discussion Integral membrane proteins in the mitochondrial outer membrane The protein profile of mitochondrial outer membranes shows at least nine major proteins (Fig.