The results lead to conclusion that the yeast peroxisomes contain membrane pore-forming proteins that may aid the transfer of small solutes between the peroxisomal lumen and cytoplasm..
Trang 1proteins from the yeast Saccharomyces cerevisiae
Silke Grunau1,2,*, Sabrina Mindthoff1,*, Hanspeter Rottensteiner1, Raija T Sormunen3,
J Kalervo Hiltunen2, Ralf Erdmann1and Vasily D Antonenkov2
1 Institut fu¨r Physiologische Chemie, Abt Systembiochemie, Bochum, Germany
2 Department of Biochemistry and Biocenter Oulu, University of Oulu, Finland
3 Department of Pathology, University of Oulu, Finland
Peroxisomes are ubiquitous subcellular organelles
involved in diverse metabolic activities, ranging from
the oxidation of fatty acids, purines, hydroxyacids,
alcohols and polyamines to the synthesis of
plasmalo-gens, ketone bodies and bile acids [1,2] The protein
composition of peroxisomes depends on both the
spe-cies and environmental conditions For example, the
peroxisomes from fungi and plants, but not from
mammals, contain enzymes of the glyoxylate cycle that
allow the conversion of acetyl-CoA molecules
gener-ated mainly by peroxisomal b-oxidation of fatty acids
into succinate, which can be used in a variety of
reac-tions, including the biosynthesis of amino acids or
carbohydrates [3]
A role for peroxisomal membrane as a permeability
barrier to solutes has been a matter of debate for more
than 40 years Only recently was a ‘consensus’ reached
on the idea that this membrane is impermeable to bulky solutes such as ATP and the cofactors, NAD⁄ H ⁄ , NADP ⁄ H ⁄ , CoA and its acyl derivatives [1,4,5] By contrast, the permeability of the membrane
to small solutes, including inorganic ions and organic metabolites, is still a matter of controversy [1,4,5] For example, contradictory results were obtained concern-ing the existence of pH [6,7] or Ca2+ [8,9] gradients across the peroxisomal membrane Moreover, the assumption that the presence of such gradients con-firms the impermeability of the peroxisomal membrane has recently been challenged [5] Our previous studies
on mammalian peroxisomes showed that the mem-brane of these particles is permeable to small solutes [10] and contains pore-forming proteins [11] Likewise,
Keywords
channels; membranes; peroxisomes;
Saccharomyces cerevisiae; yeast
Correspondence
V D Antonenkov, Department of
Biochemistry and Biocenter Oulu, University
of Oulu, Linnanmaa, PO Box 3000, FI-90014
Oulu, Finland
Fax: +358 8 5531141
Tel: +358 8 5531201
E-mail: vasily.antonenkov@oulu.fi
*These authors contributed equally to this
work
(Received 21 October 2008, revised
8 January 2009, accepted 12 January 2009)
doi:10.1111/j.1742-4658.2009.06903.x
Highly-purified peroxisomes from the yeast Saccharomyces cerevisiae grown
on oleic acid were investigated for the presence of channel (pore)-forming proteins in the membrane of these organelles Solubilized membrane pro-teins were reconstituted in planar lipid bilayers and their pore-forming activity was studied by means of multiple-channel monitoring or single-channel analysis Two abundant pore-forming activities were detected with
an average conductance of 0.2 and 0.6 nS in 1.0 m KCl, respectively The high-conductance pore (0.6 nS in 1.0 m KCl) is slightly selective to cations (PK+⁄ PCl) 1.3) and showed an unusual flickering at elevated (> ±40 mV) holding potentials directed upward relative to the open state
of the channel The data obtained for the properties of the low-conduc-tance pore (0.2 nS in 1.0 m KCl) support the notion that the high-conduc-tance channel represents a cluster of two low-conduchigh-conduc-tance pores The results lead to conclusion that the yeast peroxisomes contain membrane pore-forming proteins that may aid the transfer of small solutes between the peroxisomal lumen and cytoplasm
Abbreviation
VDAC, voltage-dependent anion channel.
Trang 2channel-forming activity with properties of
substrate-specific pores has been reported for plant peroxisomes
[12,13]
A study on yeast is beneficial due to its simplicity
with respect to genetic manipulations Yeast
Saccharo-myces cerevisiae grown on oleic acid contains
well-developed peroxisomes involved mainly in the
b-oxidation of fatty acids [14] In the present study, we
report on the discovery and characterization of
pore-forming proteins in the peroxisomal membrane from
baker’s yeast, which were detected by an
electrophysio-logical study of peroxisomal proteins reconstituted into
artificial membranes
Results
Characterization of yeast peroxisomal fraction
Peroxisomes were isolated from oleic acid-grown S
ce-revisiae by Optiprep density centrifugation of freshly
prepared post-nuclear supernatants The purity of
per-oxisomes collected from the bottom of the gradient
(fractions 3–4; Fig 1A,B) was estimated by analysis of
the activity of marker enzymes for different organelles:
peroxisomes (catalase), mitochondria (cytochrome c
oxidase) and lysosomes (acid phosphatase) (Fig 1A),
as well as by immunoblotting using antibodies
gener-ated against marker proteins for peroxisomal
mem-brane (Pex11p), mitochondrial outer membrane
(voltage-dependent anion channel; VDAC),
endoplas-mic reticulum (Kar 2p) (Fig 1B) and membranes of
vacuoles (alkaline phosphatase) (data not shown) The
peroxisomes were well separated from the other
cellu-lar organelles, including mitochondria that may be a
main potential source of contaminating
channel-form-ing activities [15], and the purity was confirmed by
electron microscopic examination (Fig 1C, panels 1
and 2) The images obtained demonstrate that the
frac-tion almost exclusively consists of peroxisomes Most
of them were filled with matrix of variable electron
density, whereas, in some particles, only the membrane
was visible, indicating damage of peroxisomes during
isolation On some occasions, an electron dense
mate-rial that was not surrounded by a membrane was
detected (Fig 1C, panel 1) Apparently, this material
represents aggregates of peroxisomal matrix proteins
escaping from the particles
To study the pore-forming activity, only
peroxi-somal fractions were used that contained less than
0.3% of the total cytochrome c oxidase activity loaded
on the gradient and that showed no traces of the
mar-ker proteins for different organelles on immunoblots
under standard assay conditions (Fig 1B) For control
experiments (see below), the mitochondrial fraction was selected from the same gradients (fractions 14–16; Fig 1A) As judged from the analysis of the distribu-tion of markers for different organelles (Fig 1A,B) and data from electron microscopy (Fig 1C, panel 3), this fraction not only contained mitochondria, but also membranes of other organelles, including endoplasmic reticulum, vacuoles and peroxisomes
Latency of yeast peroxisomal enzymes
To determine whether or not the yeast peroxisomal membrane is permeable to solutes, we measured the latency of some enzymes confined to the particles (Fig 2A) The activity of these enzymes was detected
in the isolated peroxisomal fraction before (‘free’ activ-ity) and then after disruption of the membrane by detergent (‘total’ activity; for details, see Experimental procedures) Only 35% of the ‘total’ catalase activity was registered in the absence of detergent The latency
of catalase is a well known phenomenon that has been attributed to the very high concentration in peroxi-somes of this extremely active enzyme [16] Similar to catalase, the activities of cofactor-dependent peroxi-somal enzymes (i.e NAD-dependent malate dehydro-genase, citrate synthase and malate synthase) were found to be latent, indicating that at least one of the cosubstrates⁄ cofactors involved in the enzymatic reac-tions is unable to freely traverse the peroxisomal mem-brane By contrast, detection under similar conditions
of an aspartate aminotransferase reaction showed that the ‘total’ and ‘free’ activities of the enzyme were almost equal (Fig 2A) Importantly, the latter enzyme does not require addition into the reaction medium of any cofactor or other bulky solute The data of the latency determination support the notion that, similar
to the mammalian peroxisomal membrane [10], the membrane of yeast peroxisomes provides free access to the particles for small solutes but prevents diffusion of bulky solutes such as cofactors (NAD⁄ H ⁄ , NADP ⁄ H ⁄ , CoA and its acylated derivatives) and ATP [5] Such
an arrangement of the barrier function of the yeast peroxisomal membrane predicts that it contains pore-forming proteins that allow the free diffusion of small solutes
The channel-forming activity in yeast peroxisomes
To detect the predicted channel-forming activity of purified peroxisomal preparations, we applied a multiple-channel recording procedure that allows estimation of the number and conductance of the
Trang 3single-channel events registered Indeed, the proteins
solubilized from purified yeast peroxisomes were able
to form membrane pores (Fig 2B) displaying two
predominant types of the channel-forming activity,
with an average conductance of 0.2 and 0.6 nS in
1.0 m KCl (Fig 2C, upper panel) The pattern of the
conductance distribution differed significantly from that detected in the mitochondrial fraction (compare the upper and lower panels in Fig 2C), indicating that the pore-forming activity is determined by perox-isomal proteins but not by contaminating proteins from other organelles
Fig 1 Purification of peroxisomes from oleate-grown yeast S cerevisiae Organelles from a post-nuclear supernatant were separated by Optiprep density gradient centrifugation and organelle segregation was monitored by (A) enzyme measurements and (B) immunoblot analy-sis of marker proteins (A) Fractions from the linear Optiprep gradient were analyzed for marker enzyme activities: catalase (a, filled bars, peroxisomes), cytochrome c oxidase (a, gray bars, mitochondria), acid phosphatase (b, filled bars, lysosomes) or protein content (b, gray bars) The results obtained are expressed as the relative activity Enzyme (protein) recoveries varied in the range 88–110% The line connect-ing small open squares (b) marks the density of the gradient (B) Proteins from equal volumes (20 lL) of each fraction (fractions 1–8 and 22–28) or every second fraction (fractions 8–22) (Fig 1A) were separated by SDS ⁄ PAGE and analyzed by an immunoblot technique using antibodies against the organelle markers: Pex11p (peroxisomes), VDAC (mitochondria) and Kar2p (endoplasmic reticulum) (C) Electron micro-graphs of subcellular organelles isolated by means of Optiprep gradient centrifugation Gradient fractions enriched in peroxisomes (fractions 3–4; Fig 1A,B) or mitochondria and other organelles (fractions 14–16) were combined and mixed with an equal volume of 2% (w ⁄ v) glutaral-dehyde prepared on 40% (w ⁄ v) Optiprep solution to avoid osmotic damage of peroxisomes (for further details, see Experimental proce-dures) After overnight fixation, the organelles were sedimented and processed for electron microscopy Panels 1 and 2: isolated peroxisomes at lower (1) and higher (2) magnifications, scale bars = 1000 and 200 nm, respectively; panel 3: mitochondrial fraction, scale bar = 2000 nm Amorphous electron-dense material that might indicate aggregates of escaped peroxisomal matrix proteins is marked by an asterisk in (C, panel 1).
Trang 4Next, we investigated the subperoxisomal
localiza-tion of the channel-forming activities Peroxisomal
matrix proteins were separated from membrane
fragments by centrifugation in sucrose gradients after
organelle disruption by sonication When proteins
sol-ubilized from the isolated membrane fragments were
analysed for channel-forming activity, a conductance
pattern analogous to that of the whole peroxisomal
preparations was obtained (data not shown) By
contrast, the matrix proteins did not show any
pore-forming activity The conductance pattern of the
per-oxisomal channels was not affected by a shift in pH of
the bath solution from pH 6.0 (unbuffered 1.0 m KCl)
to pH 7.6 or pH 8.4 by adding 20 mm (final
concentra-tion) Mops or Tris buffers, respectively, or by
preincu-bation of protein preparations with dithiothreitol
(5 mm, final concentration, data not shown) The later
finding may indicate that the redox state of SH groups
in molecules of the channel-forming protein(s) does
not affect the activity of these proteins significantly
As expected for large water-filled channels, the single-channel conductance registered by multiple-single-channel recording increased almost linearly with an increasing KCl concentration (Fig 2D) According to our data, the peroxisomal pore-forming proteins were active not only with KCl as an electrolyte, but also activity was detected with other small ions that were tested at a concentration of 1.0 m (pH 6.8): NH4Cl, LiCl, potas-sium acetate and sodium phosphate However, we were unable to register any activity with some larger electro-lytes [e.g tetraethylammonium chloride (1.0 m) or AMP (0.25 m potassium salt, pH 6.8)], although the activity with these ions was evidently present in frac-tions enriched with mitochondria
Electrophysiological properties of a high-conductance channel
We used a single-channel analysis to describe proper-ties of the peroxisomal membrane channel with an
Fig 2 Latency of peroxisomal enzymes
and multiple-channel monitoring of the
pore-forming activity in yeast peroxisomes (A)
‘Free’ activity of yeast peroxisomal enzymes
presented as a percentage of the ‘total’
activity detected after incubation of purified
peroxisomes with 0.1% (w ⁄ v, final
concen-tration) Triton X-100 (B) Traces of the
multiple-channel monitoring of an artificial
membrane in the presence of
detergent-solubilized peroxisomes (upper panel) or
mitochondria (lower panel) The trace in the
frame (upper panel) shows a
timescale-expanded current recording of the upper
trace The bath solution contained 1 M KCl
on the both sides of the membrane The
temperature was +20 C and the applied
voltage was +20 mV (C) Histograms of
insertion events observed during
multiple-channel monitoring (B) in the presence of
purified detergent-solubilized peroxisomes
(upper panel; combined gradient fractions 3
and 4; see Fig 1A) or fraction-enriched in
mitochondria and other organelles (lower
panel; combined gradient fractions 14–16;
see Fig 1A) The total number of insertion
events was 180–200 for each membrane
preparation analyzed Each experiment was
repeated three times; typical histograms are
presented (D) Channel conductance as a
function of KCl concentration The data for
high-conductance activity ( 0.6 nS in 1.0 M
KCl; see Fig 2C) are shown The
mean ± SD conductance for 30–40 single
insertion events was calculated.
Trang 5average conductance of 0.6 nS in 1.0 m KCl (see
above) Figure 3A displays the current recordings at
holding potentials +20, +60 and )60 mV and an
equal concentration of electrolyte (1.0 m KCl) on both
sides of an artificial membrane, being characteristic of
an ion channel with a slope conductance of
K = 0.68 ± 0.4 nS (n = 6) The channel inserted in
the membrane was mainly fully open during the whole
period of activity registration (minutes) at a wide range
of holding potentials (from )80 to +80 mV) The
channel showed strong flickering that was directed
upwards (at positive voltages), especially at higher
holding potentials This flickering was detected in all
twenty measurements The direct transition of some
spikes down to the fully-closed state of the channel
was observed (Fig 3A, lower trace in the right panel), indicating that the current transitions are substates of
a single channel rather than amplitudes of several inde-pendent channels inserted in the membrane The flick-ering of the channel resembles the behaviour of the CLC-0 chloride channel consisting of two pore-form-ing protein molecules [17] (for details, see Discussion) This may indicate that, similar to the CLC-0 channel, the peroxisomal channel represents a cluster of pore-forming proteins in which only one is in a permanently open state, whereas others display a fast, transient gating The nature of this gating deserves further investigation
The reversal potential of a single channel (Fig 3B,C) under asymmetric salt conditions (1.0 m
Fig 3 Single-channel analysis of the high-conductance channel (A) Current traces of
a bilayer containing a single high-conduc-tance pore-forming protein (the insertion event is marked by asterisk) at different membrane potentials (1.0 M KCl on both sides of the membrane) Applied membrane potentials are indicated Note that the chan-nel displayed an intensive flickering at +60 and )60 mV, respectively The largest cur-rent amplitude of this flickering is approxi-mately threefold higher than the amplitude
of the channel itself The lower trace in the right panel shows the direct transition of one of the spikes down to the fully-closed state of the channel (marked by arrowhead) (B) Current traces of a bilayer containing one high-conductance channel (the insertion event is marked by asterisk) under asym-metric salt conditions: 1.0 M KCl cis ⁄ 0.5 M
KCl trans compartment Control experi-ments demonstrated that, after adjustment
of the electrolyte concentration on both sides of the membrane to 1.0 M KCl, the channel displayed a current amplitude of 12–15 pA at +20 mV, which reflects the conductance detected in the multiple-chan-nel recording experiments (Fig 2C) (C) Current–voltage relationship of the high-con-ductance channel under asymmetric salt concentrations (see Fig 3B); data points are mean ± SD of at least six independent measurements.
Trang 6KCl cis⁄ 0.5 m KCl trans compartment) was
Erev= +2.0 mV, indicating that the channel has a
slight preference for cations over anions
(PK+⁄ PCl)= 1.3) The slope conductance of the
channel was K = 0.95 nS (in 1.0 m⁄ 0.5 m KCl) As
with symmetric salt conditions, the channel displayed
high-conductance flickering, especially at negative
holding potentials (Fig 3B)
Single-channel analysis of a low-conductance channel
More than 80 insertion events were detected in the sin-gle-channel analysis experiments Approximately 60%
of the inserted channels showed properties of the high-conductance channel (0.6 nS in 1.0 m KCl; see previous section) The second largest group of
inser-Fig 4 Single-channel analysis of the low-conductance channel (A) Upper panel: current trace of the channel (the insertion event is marked
by asterisk) The bath solution (A–D) comprised 1.0 M KCl on both sides of the membrane Lower panel: current trace of the low-conduc-tance channel in response to voltage ramp protocol (from )100 to 100 mV, 10 s) (B) Current trace of the low-conductance channel under-going transition to the high-conductance channel Upper panel: direct transition of the channel-forming activity between the closed state and the fully-open state (marked by asterisk) and between the fully-open state and the intermediate state (marked by an arrowhead) The inter-mediate state corresponds to the low-conductance channel activity Lower panel: current trace of the same channel as that shown in the upper panel but at a higher holding potential The fully-closed state of the channel (marked by an asterisk) side by side with the spikes of the flickering (marked by arrowheads) is visible (C) Upper panel: current trace showing two sub-conductance states with almost equal ampli-tude; each of these states represents the amplitude of the low-conductance channel Lower panel: count rate histogram of the upper current trace (D) Upper panel: current trace of the super-large conductance channel with current amplitude in the fully open state 130 pA (1.0 M
KCl, +20 mV) Lower panel: a timescale-expanded current recording of the part shown in the frame in the upper trace Note the direct transi-tion from the closed to the fully-open state and the short lifetime of the open state The partial closure of the channel leads to the appear-ance of a stable substate with a current amplitude comprising one-third of the amplitude characteristic of the fully-open channel.
Trang 7tion events (Fig 4A) displayed a conductance similar
to that of the low-conductance channel activity
detected by multiple-channel monitoring (i.e 0.2–
0.3 nS in 1.0 m KCl; see above) The current–voltage
relationship measured for these channels revealed a
slope conductance of K = 0.28 nS (1.0 m KCl on both
sides of the membrane; data not shown) Recording of
the activity at elevated holding potentials showed an
upward flickering (at positive potentials) with different
open channel amplitudes (Fig 4A,B, lower panels)
The flickering that was upward relative to the open
state of the main channel (at positive potentials)
resembled the similar behaviour of the
high-conduc-tance channel (for comparison, see Fig 3A,B) The
reversal potential of the low-conductance channel in
asymmetric KCl solutions (1.0 m KCl cis⁄ 0.5 m KCl
trans compartment) was Erev= +2.4 mV (data not
shown), which is close to the result obtained for the
high-conductance channel (Erev= 2.0 mV) Therefore,
it appears that the ion selectivity of low- and
high-con-ductance channels is almost identical Approximately
half of the low-conductance traces displayed multiple
transitions to the level with higher current amplitudes
(Fig 4B,C), which approximately corresponded to the
amplitude of the high-conductance channel under the
same experimental conditions The smaller current
amplitude reached approximately one half of the full
conductance (Fig 4C) Direct transitions from the
closed to the fully-open state (largest current
ampli-tude), and from the closed state to the intermediate
state (smaller amplitude), were observed (Fig 4B) The
partially open state was also approached from the
fully-open state (Fig 4B,C) These observations
indi-cate that the intermediate amplitude is a substate of a
single-channel molecule inserted in the membrane,
rather than amplitudes of two independently active
channel molecules Taken together, the data obtained
in the single-channel analysis lead to the suggestion
that the high-conductance channel may represent a
cluster of two low-conductance channels (for details,
see Discussion)
The selectivity of the channel-forming activities
towards cations (see above), which is opposite to
ion-selectivity of the VDAC at low holding potentials
[18,19], provided an additional opportunity to assess
whether the activities described in the present study
are truly peroxisomal or determined by mitochondrial
contamination Therefore, using single-channel
analy-sis, we compared ion-selectivity of the channel-forming
proteins from peroxisomal and mitochondrial
frac-tions, respectively At asymmetric salt conditions
(1.0 m KCl cis⁄ 0.5 m KCl trans compartment) and
zero holding potential, all 56 inserted channels
dis-played selectivity towards cations when the peroxi-somal fraction was used in the experiments However, when measurements were made on the mitochondrial fraction, only 19 out of 48 inserted channels showed cation selectivity, whereas the other channels were selective towards anions These results strongly support our conclusion that peroxisomes from baker’s yeast contain cation-selective channel-forming protein
On several occasions, the channel activities regis-tered in the peroxisomal fraction showed very large current amplitudes (Fig 4D) The channels with cur-rent amplitudes in a fully-open state of 30, 60 and
130 pA (1.0 m KCl, +20 mV) were registered They displayed strong downward (relative to the open states) flickering, indicating closure of the channels The average mean lifetime of the fully-open channels was relatively low (sopen< 100 ms) Properties of the
‘super-large’ conductance channels (Fig 4D) were not analysed further because of their low abundance
Discussion
The results of the present study demonstrate that the membrane of peroxisomes from the yeast S cerevisiae contains channel⁄ pore-forming proteins, as concluded from the following data: (a) proteins solubilized from highly-purified peroxisomal preparations showed an abundant channel-forming activity in the multiple-channel recording experiments, the pattern of which is completely different from that of the mitochondrial fraction; (b) the channel-forming activity was shown to associate with membrane proteins of peroxisomes; and (c) the results of the single-channel analysis experi-ments revealed that, in regard to single-channel con-ductance, ion-selectivity and voltage-dependence, the investigated peroxisomal channels was found to be dis-tinctly different from VDAC of the outer mitochon-drial membrane [18,19], which can be expected as a major source of the channel-forming activity contami-nation in the peroxisomal preparations
Our finding regarding channel-forming activity in the yeast peroxisomal membrane is consistent with pre-vious observations describing such activity in plants [12,13] and mammals [11] In addition, the 31 kDa protein isolated from peroxisomal preparations of the yeast Hansenula polymorpha showed channel-forming properties [20] However, further characterization of this protein revealed properties similar to mitochon-drial VDAC [20] An electrophysiological analysis of the channel-forming activity related to the 31 kDa protein has not been described Therefore, it is unclear whether this protein represents a peroxisomal consti-tuent or a mitochondrial contamination
Trang 8The peroxisomal channels from different sources
share features characteristic of bacterial and
mamma-lian porins monitored by the planar lipid bilayer
tech-nique: (a) the pores remain open for a prolonged
period of time (seconds to minutes); (b) the
conduc-tance of the channels is relatively large (> 0.2 nS in
1.0 m KCl); and (c) there is a total absence or weak
voltage-dependence of channel gating Interestingly,
according to our preliminary data (unpublished
results), the diameter of the peroxisomal channel is
rather small (< 0.6 nm) and, in this sense, the channel
shows similarity to the plant peroxisomal porin [12,13]
However, in contrast to the plant protein, which
displays strong anion selectivity and weak voltage
dependence, the yeast peroxisomal channel is slightly
cation-selective and not voltage-gated The plant
per-oxisomal channel, similar to some porins from the
outer bacterial membranes [21], can be considered as a
specific porin that preferably allows passing through of
mono- and dicarboxylic acids [13] Whether the yeast
peroxisomal channels show similar properties is
currently under investigation
The conductance pattern of the plant peroxisomal
channel detected by the multiple channel recording at
+20 mV using 1.0 m KCl as an electrolyte reveals
two main conductance levels: 0.3 and 0.6 nS,
respec-tively [12], which is very close to the pattern
described in the present study (Fig 2B,C) These
results can be explained by both plant and yeast
high-conductance channels functioning as dimers
con-sisting of two low-conductance channels This notion
was substantiated by the single-channel analysis
experiments The cluster organization is not a unique
feature of the peroxisomal pore-forming proteins
Some other examples are trimeric organization of
bacterial porins [21] and the dimeric structure of the
CLC chloride channels [17] The latter shares an
unu-sual behavior of the yeast peroxisomal channels: an
upward flickering relative to the main open state (at
positive holding potentials) representing fast-gating
transitions The lifetime in the fully-open state of the
dimer of the monomeric subunits of the chloride
channel is not the same; usually, it is much longer
than that for one of the monomers [17] The fast
gat-ing of one monomer produces an upward flickergat-ing
relative to the baseline, which is determined by the
fully-open state of the counterpart channel This
might comprise one of the mechanistic explanations
for the ‘upward’ flickering of the yeast peroxisomal
channels The proposed mechanism leads to the
pre-diction that the channel is organized in complex
clus-ters containing a dozen, or even more, monomeric
subunits However, at present, we cannot exclude the
possibility of other mechanisms that might lead to the ‘upward’ flickering of the channels
The functional role of the yeast peroxisomal channels remains to be established Presumably, the channels form a general diffusion pore in the membrane and function as a size-selective filter that allows crossing of the membrane by a wide variety of small solutes, but prevents transfer of ‘bulky’ compounds, including ATP and cofactors (NAD⁄ H, NADP ⁄ H and CoA) The channels may provide a route to transfer metabolites such as carnitine or di- and tricarboxilic acids, which participate in the peroxisomal b-oxidation of fatty acids and the glyoxylate cycle, respectively They are also apparently involved in shuttle mechanisms required for metabolic conversion of peroxisomal cofactors [22] Our preliminary data suggest that some peroxisomal metab-olites may be transferred by a so-called ‘specific’ chan-nel This type of channel is characteristic of the outer membrane of Gram-negative bacteria [21] Therefore, the overall functional organization of the yeast peroxi-somal membrane transport system may be similar to that of the outer membrane of bacteria
Experimental procedures
Strains, media and culture conditions
The yeast strain used in the study was S cerevisiae UTL7-A (MATa leu2-3, 112 ura3-52 trp1) [23] Yeast cells were grown under aerobic conditions on YNDO [0.1% (w⁄ v) yeast extract, 0.67% (w⁄ v) yeast nitrogen base without amino acids, 0.1% (w⁄ v) oleic acid, 0.1% (w ⁄ v) glucose, 0.05% (v⁄ v) Tween 40] medium at pH 6.0 [23]
Isolation of peroxisomes
Preparation of yeast spheroplasts, cell homogenization and isolation of a postnuclear supernatant were performed as described previously [23] Peroxisomes (10 mg of protein) were isolated using a preformed linear 2.25–24.0% (w⁄ v) Optiprep (Iodixanol; Axis-shield PoC AS, Oslo, Norway) density gradient The gradients were centrifuged in a verti-cal rotor (TV860; Sorvall; Thermo Fisher Scientific Inc., Waltham, MA, USA) at 48 000 g (maximum) for 1.5 h The fractions were collected from the bottom of the tubes and used immediately for analysis of the activities of marker enzymes for subcellular organelles
Measurement of enzyme activities and latency determination
Catalase and cytochrome c oxidase, marker enzymes for peroxisomes and mitochondria, respectively, were detected
Trang 9as described previously [24] Acid phosphatase was
mea-sured as marker for lysosomes [25] Activities of
NAD-dependent malate dehydrogenase, citrate synthase and
malate synthase [26], and the activity of aspartate
amino-transferase [26,27], were measured in the purified
peroxi-somal fraction Protein content was determined according
to the method of Bradford [27a]
The latency of peroxisomal enzymes was detected after
resedimentation of the particles in a two-step [20% (w⁄ v)
and 50% (w⁄ v) sucrose] gradient in a vertical rotor at
100 000 g (maximum) for 45 min ‘Free’ enzyme activity
was measured prior to disruption of the peroxisomal
mem-brane by Triton X-100 [0.1% (w⁄ v) final concentration] to
reveal the ‘total’ enzyme activity [10]
Antibodies and immunoblot analysis
Polyclonal rabbit antibodies were raised against Pex11p,
VDAC [28], Kar2p [29] and alkaline phosphatase
(Molecu-lar Probes, Leiden, The Netherlands) to detect the
corre-sponding marker proteins for different cellular organelles
SDS⁄ PAGE and immunoblotting were performed according
to standard procedures and blots were developed using the
ECL system (GE Healthcare, Chalfont, St Giles, UK)
Electron microscopy
For transmission electron microscopy, the isolated
peroxi-somes were fixed in 1% (w⁄ v) glutaraldehyde overnight at
4C The organelles were sedimented at 20 000 g
(maxi-mum) for 30 min and processed as described previously [30]
Detection of the pore-forming activity
To study pore-forming activities of yeast peroxisomal
pro-teins, multiple-channel recording and single-channel
analy-sis of solubilized membrane proteins reconstituted into an
artificial lipid bilayer were applied The peroxisomal
frac-tion collected from Optiprep gradients was diluted 10-fold
with 20 mm Mops buffer, pH 7.2 (0.02–0.04 mgÆmL)1
protein) and treated with 0.5% (w⁄ v, final concentration)
Genapol X-080 (Fluka, Buchs, Switzerland) by rotating for
1 h at 4C After sedimentation of insoluble material at
100 000 g (maximum) for 45 min, the resulting supernatant
was immediately used for detection of the pore-forming
activity
Multiple-channel recordings were performed as described
previously [31] in a Teflon chamber separated into two
compartments (5 mL each) by the wall containing a circular
hole (0.2 mm2) The lipid bilayer was formed across this
hole by the painting technique using 1% (w⁄ v) diphytanoyl
phosphatidylcholine (Avanti Polar Lipids Inc., Alabaster,
AL, USA), dissolved in n-decane⁄ butanol (9 : 1, v ⁄ v) After
formation of a stable membrane with a typical capacitance
of 400–700 pF, the solubilized membrane proteins (4 lL) were added to both compartments of the chamber, which were equipped with magnetic stirrers One molar bath solutions of KCl were used, unless otherwise stated The temperature was 20C A Planar Lipid Bilayer Worksta-tion equipped with a BC-535 amplifier and an 8 pole low-pass Bessel filter (Warner Instruments, Hamden, CT, USA) was used for the current detection Acquisition and analysis were performed using pCLAMP software (Axon Instru-ments, Foster City, CA, USA) Membrane currents were measured at a holding potential of +20 mV (unless other-wise stated) with a pair of Ag⁄ AgCl electrodes The data were filtered at 30 Hz and collected at 2.0 kHz Multiple-channel recording allows measurements of a large number
of insertion events of reconstituted pore-forming proteins,
as well as quantitative analysis of these activities by using histograms of insertion frequency relative to current ampli-tudes For each histogram, the absolute number of insertion events with a certain current amplitude (bin size = 2.0 pA) was calculated
For a more detailed investigation of the electrophysio-logical properties of the pore-forming proteins, we used a single-channel analysis, which allows characterization at the high-time resolution of a single channel inserted in the artificial membrane Commercial chambers (Warner Instruments) with two compartments (4 mL each) sepa-rated by wall with a circular hole (0.04 mm2) were used The Ag⁄ AgCl electrodes were connected to the compart-ments via 2 m KCl-agar bridges As in the case of multi-ple-channel recordings, the electrode of the trans compartment was directly connected to the headstage of a current amplifier Reported membrane potentials are referred to the trans compartment The capacitance of the bilayer was in the range 70–90 pF The data were filtered
at 1.0 kHz and collected at 2.0 kHz Measurements of reversal potentials were performed by establishing a two-fold (1.0 m KCl cis⁄ 0.5 m KCl trans compartment) salt gradient after formation a stable lipid bilayer After inser-tion of a single channel, the current was initially recorded
at 0 mV and, subsequently, at different membrane poten-tials In a separate set of experiments, the number of cation-selective versus anion-selective channels was calcu-lated in peroxisomal and mitochondrial fractions, respec-tively Asymmetric salt conditions (1.0 m KCl cis⁄ 0.5 m KCl trans compartment) were used and each insertion event was initially detected at zero holding potential fol-lowed by application of a voltage ramp protocol (from )40 to +40 mV, 10 s)
Acknowledgements
This work was supported by grants from the Academy
of Finland, Sigrid Juselius Foundation; the Deutsche Forschungsgemeinschaft (ER 178⁄ 2-4); and the
Trang 10European Union Project ‘Peroxisomes’
(LSHG-CT-2004-512018) We are grateful to Professor R Benz
from the Lehrstuhl fur Biotechnologie, Universita¨t
Wurzburg, Germany, and Professor M Weckstro¨m
from the Department of Physical Sciences, University
of Oulu, Finland, for helpful discussion
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