Tài liệu Báo cáo khoa học: Integral membrane proteins in the mitochondrial outer membrane of Saccharomyces cerevisiae docx

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:
*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.).
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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;
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 ( 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
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