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Originally published In Press as doi:10.1074/jbc.M105828200 on July 6, 2001
J. Biol. Chem., Vol. 276, Issue 39, 36501-36507, September 28, 2001
A Novel Method to Determine the Topology of Peroxisomal
Membrane Proteins in Vivo Using the Tobacco Etch Virus
Protease*
Klaas Nico
Faber ,
Anita M.
Kram§,
Michael
Ehrmann¶ , and
Marten
Veenhuis**
From the Eukaryotic Microbiology, Groningen Biomolecular Sciences
and Biotechnology Institute, University of Groningen,
P. O. Box 14, 9750 AA Haren, The Netherlands and ¶ Biosi-2,
Cardiff University, Museum Avenue, P. O. Box 911, Cardiff CF10
3US, United Kingdom
Received for publication, June 22, 2001, and in revised form, July 5, 2001
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ABSTRACT |
Most proteins essential for the biogenesis of
peroxisomes (peroxins) that are identified to date are associated with
or are integral components of the peroxisomal membrane. A prerequisite in elucidating their function is to determine their topology in the
membrane. We have developed a novel tool to analyze the topology of
peroxisomal membrane proteins in the yeast Hansenula polymorpha in vivo using the 27-kDa NIa protease subunit from the tobacco etch virus (TEVp). TEVp specifically cleaves peptides containing the
consensus sequence,
EXXYXQ S
(tev). We show that cytosolic TEVp and peroxisomal TEVp.SKL are
selectively active on soluble cytosolic and peroxisomal tev-containing
proteins in vivo, respectively, without affecting the
viability of the yeast cells. The tev sequence was introduced in
between the primary sequence of the peroxisomal membrane proteins Pex3p
or Pex10p and the reporter protein enhanced green fluorescent
protein (eGFP). Co-synthesis of these functional tev-GFP tagged
proteins with either cytosolic TEVp or peroxisomal TEVp.SKL revealed
that the C termini of Pex3p and Pex10p are exposed to the cytosol.
Additional applications of the TEV protease to study peroxisome
biogenesis are discussed.
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INTRODUCTION |
Peroxisomes are organelles present in all eukaryotic organisms
studied so far. Unlike other cellular organelles, their function may be
highly diverse, dependent on cell type and the external stimuli
the cell encounters. In plants they are involved in photorespiration, in trypanosomes they are involved in glycolysis, and in fungi they are
involved in the synthesis of secondary metabolites, such as -lactam
penicillins (1-3). In yeast they are essential for the metabolism of
unusual carbon sources such as oleic acid, primary amines, purines,
D-amino acids, and methanol (4). In humans they are
involved in a variety of anabolic and catabolic pathways, including
plasmalogen and cholesterol biosynthesis as well as fatty acid and
purine degradation. Peroxisome malfunctioning is the cause of severe
inherited human disorders, such as Zellweger syndrome (5, 6).
Peroxisomes do not contain DNA or a protein-synthesizing machinery.
Consequently, peroxisomal proteins are synthesized on cytosolic
polysomes and sorted post-translationally to their target organelle
(7). Two distinct signal sequences for peroxisomal matrix proteins have
been defined (designated as
PTSs)1, the C-terminal PTS1,
SKL, and variants and the N-terminal PTS2 (8). In general, import of
peroxisomal proteins does not involve any significant protein
modification (9). Recently, several genes involved in peroxisome
biogenesis, so-called PEX genes encoding peroxins, have been
cloned by the functional complementation of yeast mutant strains
lacking functional peroxisomes (10). Up to now, 23 PEX genes
have been described, and more are likely to be identified in the near
future. Data base screening has been shown to be a powerful tool to
identify human homologues of the yeast peroxins. Thirteen human PEX
homologues have been identified, so far of which 11 were shown to
restore peroxisome biogenesis in cell lines of patients with
peroxisomal disorders (6).
Most peroxins (18 out of 23) are membrane-associated proteins, either
peripheral or integral. To study the specific functions of these
peroxisomal membrane (PM)-bound peroxins,
information about the topology of these proteins is required. In
particular, the location of functional domains, either catalytic or
domains involved in physical interactions with other proteins, needs to be established to get insight into the roles of the PM peroxins.
Biochemical techniques to discriminate between peripheral
versus integral membrane protein (differential extraction by
low salt, high salt, and sodium carbonate) and to determine the
topology of PM peroxins (protease protection assays on purified
organelles or differential permeabilization of cellular membranes) have
been performed on most of the PM peroxins reported. In many cases, however, these procedures have not led to unequivocal information on
the topology of these PM peroxins. Typical examples of this include the
analyses on Pex8p (11-13), Pex10p (14-17), Pex11p (18-24), Pex14p
(25-28), Pex16p (29, 30), and Pex17p (31, 32). Therefore, we set out
to develop an alternative method to establish the topology of PM
peroxins. The basic idea was to introduce a specific, heterologous protease in the yeast Hansenula polymorpha. Prerequisite is
that the protease should be active on a defined amino acid sequence not
present in essential proteins of the yeast, which can be introduced in
substrate PM peroxins. Co-expression of a PM peroxin containing a
protease-processing site with a cytosolic protease in one strain or a
peroxisomal protease in another strain should reveal whether the
processing site is accessible in the cytosol or in the peroxisomal matrix. The major advantage of such a system would be that no other
proteins need to be analyzed to determine the accessibility of the
peroxisomal matrix as it is the strain expressing the cytosolic variant
of the protease that is the control for the strain expressing the
peroxisomal variant and vice versa.
We selected a 239-amino acid fragment of the 346-kDa tobacco etch virus
(TEV) polyprotein containing a proteinase activity specifically
processing the consensus sequence (heptapeptide) EXXYXQ(S/G) in cis and in
trans (33). Cleavage occurs between glutamine and serine or
glycine. This protease has been used for site-specific proteolysis both
in vitro and in vivo in Escherichia coli and Saccharomyces cerevisiae of substrate proteins
containing the consensus sequence for processing (34-36).
Here, we describe the synthesis and sorting of the TEV protease to
H. polymorpha peroxisomes or the cytosol. The protease was
shown to be active in both subcellular compartments without the loss of
cell viability. In an in vivo application, we show that the
C termini of both Pex3p (containing a Pex19p-interaction domain)
(37-39) and Pex10p (containing a zinc-binding domain) (14) face the
cytosol. Additional applications of the TEV protease to study
peroxisome biogenesis are discussed.
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EXPERIMENTAL PROCEDURES |
Strains and Cultivation--
H. polymorpha NCYC495
(leu1.1) and derivatives (Table
I) were grown at 37 °C in batch
cultures in YPD (1% yeast extract, 2% Bacto peptone, 2%
glucose) or in mineral medium (40) containing either 0.5% (w/v)
glucose or 0.5% (v/v) methanol as carbon and energy sources in
combination with 0.25% (w/v) ammonium sulfate or 0.25% (w/v)
ethylamine or 0.25% (w/v) methylamine as sole nitrogen sources. For
growth on solid medium, a 0.67% (w/v) yeast nitrogen base was
used, supplemented with 1% (w/v) glucose and 2% (w/v) agar. When
required, leucine was added to the medium to a final concentration of
30 mg/liter.
Molecular Biological Techniques--
E. coli DH5
and XL1blue were used for the propagation and amplification of plasmid
DNA. Recombinant DNA procedures (enzyme digestion, cloning, plasmid
isolation, PCR, and Southern blotting) were performed as described
(41). Transformation of H. polymorpha strains and
site-specific integration of single and multiple copies of plasmid DNA
in the genomic AOX or AMO locus were performed as
described (37, 42, 43).
Plasmid Constructions--
The oligonucleotides and plasmids
used in this study are listed in Table
II. For co-synthesis of tev-containing
substrate proteins and TEV protease (TEVp) derivatives, novel
H. polymorpha expression vectors were constructed based on
the dominant zeocin resistance gene. Vector pHIPZ4, which contains the
H. polymorpha alcohol oxidase promoter (PAOX) for
heterologous expression, has recently been described (44). pHIPZ5,
which contains the H. polymorpha amine oxidase promoter
(PAMO), was constructed by replacing the
PAOX locus in pHIPZ4 by a 1.0-kilobase pair
NotI-BamHI DNA fragment from pHIPX5 (45)
containing the PAMO. A DNA fragment encoding the 27-kDa
NIa protease subunit from TEVp was obtained by PCR using primers KN11
and KN12 introducing a HindIII, BamHI, and start
codon upstream amino acid sequence SLFKG at amino acid position 2040 in
the full-length TEV and a stop codon followed by a SalI site
downstream amino acid sequence NELVIS at amino acid position 2278 in
full-length TEV. A PTS1-type signal (SKL) and a SalI site
were introduced downstream the TEVp coding region using PCR and primer
KN13. The genes encoding the TEVp-substrate molecules were constructed
as follows. By sequential cloning steps, a DNA fragment encoding the
Myc epitope (MEQKLISEEDL), preceded by a HindIII site, and
followed by an XhoI site (primer KN3) was fused to an
XhoI site upstream of a DNA fragment containing the TEV
protease cleavage sequence (ENLYFQ S,
abbreviated as tev) followed by a BglII site and eGFP with a
PTS1 sequence (primer combination KN2-KN14) or without a PTS1 (primer
combination eGFP-SalI (46)-KN14). The
HindIII site upstream and the SalI site
downstream the hybrid genes (TEVp derivatives and TEVp substrate
molecules) were used for insertion into pHIPX4 and pHIPZ4. For
insertion of TEVp-derivatives into pHIPZ5, BamHI and
SalI digestions were used. For constructing the
PEX10.tev.GFP hybrid gene, a XhoI site was
introduced downstream C-terminal codon R295 of H. polymorpha PEX10 by PCR and primer KN20 and fused to the XhoI site preceding tev-GFP. Similarly, using PCR and primer
KN15, a SalI site was introduced downstream C-terminal codon
A457 of H. polymorpha PEX3 and fused to the
XhoI site preceding tev-GFP to construct the
Pex3.tev.GFP hybrid gene. The PEX3.tev.GFP and PEX10.tev.GFP hybrid genes were inserted as
BamHI-SalI fragments into pHIPX4.
Biochemical Methods--
Preparation of crude extracts of
H. polymorpha (46), SDS-polyacrylamide gel electrophoresis
(47), and Western blot analysis (48) was performed as described;
blots were probed using specific antibodies against various
H. polymorpha proteins. Polyclonal antibodies were generated
in rabbits using the 27-kDa fragment of the TEV protease used in this
study. The antibodies against GFP were a gift from Dr. W.-H. Kunau,
Bochum, Germany. Goat anti-rabbit alkaline phosphatase and goat
anti-rabbit horse radish peroxidase (Roche Molecular
Biochemicals) were used as secondary antibodies that were detected by
bromochloroindolyl phosphate/nitro blue tetrazolium (Roche Molecular
Biochemicals) or ECL (Amersham Pharmacia Biotech) according to the
manufacturers' protocols.
Microscopical Procedures--
Fluorescent microscopy to localize
hybrid proteins containing GFP was performed as described (46) using an
Axioskop H fluorescence microscope (Zeiss Netherlands b.v., The
Netherlands) equipped with a Princeton Instruments CCD camera
(RTE/CCD-1300 Y; Princeton Instruments b.v., The Netherlands).
Whole cells were fixed and prepared for electron microscopy and
immunocytochemistry as described previously (11). Immunolabeling was
performed on ultrathin sections of unicryl-embedded cells using
specific antibodies against various H. polymorpha proteins
and GFP and gold-conjugated goat anti-rabbit (GAR-gold) antibodies
according to the instructions of the manufacturer (Amersham Pharmacia
Biotech).
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RESULTS |
The use of the TEV protease to study the principles of peroxisome
biogenesis in H. polymorpha is critically dependent on the following prerequisites. 1) The protein should be synthesized and
become active in this yeast without loss of cell viability, 2) it
should be active on substrate proteins in the cytosol as well as in
peroxisomes, and 3) the activity of cytosolic and peroxisomal TEVp
should be selective toward cytosolic and peroxisomal substrate molecules. The experiments to analyze these prerequisites are detailed below.
Construction of the Substrate Molecules Nmyc.tev.GFP Containing or
Lacking a PTS1--
To establish the activity and subcellular
localization of TEVp and TEVp.SKL in H. polymorpha in vivo,
we constructed two hybrid genes encoding either a cytosolic or a
peroxisomal tev-containing substrate protein molecule (Fig.
1A). These proteins consist of an N-terminal Myc sequence (MEQKLISEEDL) followed by the TEV
proteolytic consensus sequence (ENLYFQ S,
abbreviated as tev in text and figures) and the reporter protein eGFP
(Nmyc.tev.GFP, cytosolic protein). In the case of the peroxisomal
substrate, a PTS1 sequence, SKL, is added at the C terminus
(Nmyc.tev.GFP.SKL). Synthesis of the TEVp substrate molecules was
controlled by the strong methanol-regulated alcohol oxidase promoter
(PAOX). The production of the hybrid proteins
was determined by Western blot analysis using antibodies directed
against GFP or the Myc epitope. Both antisera specifically recognized a
protein band of the expected size of ~30 kDa in crude extracts
prepared from methanol-grown transformants (Fig.
2, lanes 1 and 2).
These protein bands were undetectable in extracts prepared from the
control host strain (data not shown). The subcellular localization of
the TEVp-substrate proteins was determined by fluorescence microscopy
and immunocytochemistry. As shown in Fig. 1, a diffuse fluorescence was
observed in cells of the strain synthesizing Nmyc.tev.GFP (Fig.
1B), which is indicative of a cytosolic location of the
protein. Immunolabeling experiments using antibodies against the Myc
epitope confirmed that indeed this substrate molecule had accumulated
in the cytosol (Fig. 1D). Also, significant labeling was
localized on the nucleus of these cells, which is however not
unexpected since this substrate molecule has a size that should allow
free passage through the nuclear pore (49, 50). In contrast,
fluorescence was observed as bright dots in the strain producing
Nmyc.tev.GFP.SKL (Fig. 1C). The peroxisomal localization of
this protein was corroborated by immunocytochemical experiments (Fig.
1E) in which Myc antibody-dependent labeling was
exclusively located on these organelles. Unexpectedly, the protein did
not diffuse into the crystalline AO matrix of the organelle as for
instance observed for the endogenous enzyme dihydroxyacetone synthase
(51). Instead, it accumulated in the narrow space in between the
crystalline matrix and the peroxisomal membrane (Fig. 1E), a
location also observed for endogenous catalase protein (51).

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Fig. 1.
Sorting of the TEVp-substrate proteins,
Nmyc.tev.GFP and Nmyc.tev.GFP.SKL. A, schematic
representation of the cytosolic and peroxisomal TEVp substrate
proteins, Nmyc.tev.GFP and Nmyc.tev.GFP.SKL. Strains HF42
(Nmyc.tev.GFP) (B and D) and HF45
(Nmyc.tev.GFP.SKL) (C and E) were grown to the
mid-exponential growth phase in methanol-containing medium. Normaski
images (B and C, left panels),
fluorescence microscopy images (B and C,
right panels), and immunolocalization of the substrate
molecules using antibodies raised against the Myc epitope (D
and E) are shown.
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Fig. 2.
In vivo processing of the
cytosolic and peroxisomal TEVp-substrate proteins. Western blot
analysis of cell-free extracts of various strains synthesizing
TEV-substrate proteins with or without TEV protease. Lanes 1 and 2 are controls showing expression of the TEV-substrates
alone (Nmyc.tev.GFP and Nmyc.tev.GFP.SKL, respectively). Lanes
3-6 show the effect on the substrate proteins when
combined with high level expression (by PAOX) of
the TEV protease (TEVp or TEVp.SKL) when cleavage of the Myc tag is
extensive in all combinations. Lanes 7-10 show
that with reduced expression level (by PAMO) of
the TEV protease, the processing of the substrate proteins still occurs
when it co-localizes with the protease (lanes 7 and
10) but is virtually absent when both proteins do
not co-localize (lanes 8 and 9).
Lanes 1-6, cells grown in methanol/ammonium
sulfate medium. Lane 1, Nmyc.tev.GFP (strain HF42);
lane 2, Nmyc.tev.GFP.SKL (HF45); lane 3,
Nmyc.tev.GFP and TEVp (HF34); lane 4, Nmyc.tev.GFP.SKL and
TEVp (HF35) lane 5, Nmyc.tev.GFP and TEVp.SKL (HF36); and
lane 6, Nmyc.tev.GFP.SKL and TEVp.SKL (HF37). Lanes
7-10, cells grown in methanol/methylamine medium.
Lane 7, Nmyc.tev.GFP and TEVp (HF38); lane
8, Nmyc.tev.GFP.SKL and TEVp (HF39); lane 9,
Nmyc.tev.GFP and TEVp.SKL (HF40); and lane 10,
Nmyc.tev.GFP.SKL and TEVp.SKL (HF41). Equal amounts of protein were
separated by SDS-polyacrylamide gel electrophoresis analyzed by Western
blotting using specific antisera raised against GFP (top
panel), Myc (middle panel), and TEVp (bottom
panel).
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Synthesis of Cytosolic or Peroxisomal TEV-Protease Does Not
Affect H. polymorpha Viability--
Two TEV protease expression
plasmids were constructed, one designed to produce cytosolic TEVp and
the other one designed to produce peroxisomal TEVp. To this end, the
active 27-kDa domain of the TEV protease (52) was modified by
introducing an initiation codon (ATG/Met) in front of amino acid 2040 and a termination codon (TAA) downstream amino acid 2278 of full-length
TEV. For peroxisomal targeting, the typical C-terminal PTS1 signal,
SKL, was introduced at the extreme C terminus (TEVp.SKL). In initial experiments, expression of the TEVp variants was controlled by the
PAOX. Four strains were constructed in which the TEVp
substrate proteins were co-synthesized with either TEVp or
TEVp.SKL.
Since the TEV protease might act on any endogenous protein containing
the consensus sequence
EXXYXQ (S/G), we
first determined whether the TEV protease affected cell viability. As
shown in Fig. 2, lanes 3-6, synthesis of the TEV
protease destined for the cytosol or peroxisomes was readily
demonstrated in cells grown for 16 h in methanol-containing
medium. All four strains were viable and showed growth characteristics
in methanol-containing medium akin to the host strain. Electron
microscopical analysis did not reveal any significant morphological
difference between cells producing either TEVp or TEVp.SKL as compared
with wild type controls (data not shown).
Cytosolic and Peroxisomal TEV Protease Are Active in Vivo in H. polymorpha--
To determine whether the TEV protease is active in
H. polymorpha in vivo, cell-free extracts of the four
strains described above were analyzed for processing of the
TEVp-substrate proteins (Fig. 2). Western blot analysis of these
extracts probed with antibodies against GFP or the Myc epitope
revealed that in all four strains, most of the substrate proteins were
processed, reducing the size of and eliminating the Myc epitope from
these molecules (Fig. 2, lanes 3-6). These
results suggest that the TEV protease is active in H. polymorpha cells. However, processing of the substrate protein is
also observed when the substrate and protease were supposed to be
spatially separated. At least two possibilities may account for this
phenomenon, namely (i) processing of the substrates occurs either
in vitro during the preparation of the cell free extracts or
(ii) processing occurs in vivo. Since both substrate and
protease are sorted by the same pathway, the peroxisome-destined protease might already function en route to the organelle. Similarly, the peroxisome-destined substrate molecule might become processed by
cytosolic TEVp before import into the organelle. The possibility of
processing in vitro is less likely as it was prevented by
trichloroacetic acid precipitation of whole cells immediately
after harvesting. Therefore, we anticipated that the processing of
the GFP substrate molecules occurred in vivo. Two
alternative experiments were designed to limit the possible in
vivo processing during sorting of GFP substrate proteins and TEVp
to different subcellular locations. First, the expression levels of
TEVp and TEVp.SKL were lowered through the control of weaker promoter
elements while keeping the expression of the GFP substrate molecules
under the control of the AOX promoter. As can be seen in
Fig. 2, lanes 7-10, a reduced production level of
the TEV protease by the amine oxidase promoter element (PAMO)
resulted in a drastic increase in the level of unprocessed substrate
protein when the two are spatially separated in the cell (Fig. 2,
lanes 8 and 9). In contrast, when the protease
and the substrate protein were destined for the same cellular
compartment, most to all of the substrate proteins were processed (Fig.
2, lanes 7 and 10).
These data show that by lowering the level of the protease, the
processing of substrate molecules in the same subcellular location
still proceeds efficiently, whereas unwanted in vivo processing of substrate molecules destined for a different subcellular location is reduced. In a second approach, we sought to prevent in vivo processing of spatially separated substrate proteins
and TEVp by introducing a timely separation in the synthesis of the two
proteins. To achieve this, cells producing TEVp.SKL under the control
of the PAMO together with either Nmyc.tev.GFP or
Nmyc.tev.GFP.SKL under the control of the PAOX were first grown
in glucose/ethylamine-containing medium. Under these conditions, the
PAMO is induced, and thus TEVp.SKL is synthesized and sorted to
peroxisomes. Concurrently, because of the presence of glucose, the
PAOX, and thus the synthesis of the GFP substrate molecule, is
repressed. Subsequently, these cells were shifted to medium containing
methanol and ammonium sulfate as the sole carbon source and nitrogen
source, respectively. Now the PAMO is fully
repressed (by NH4+), and thus production of TEVp.SKL is
prevented, whereas the production of the GFP substrate proteins is now
induced (by PAOX). In a time course of 8 h of the shift of
cells to methanol/ammonium sulfate-containing medium (Fig.
3), it can be seen that amine oxidase (an
indicator for TEVp synthesis) is present at t = 0 and
is still detectable after 8 h of growth in
methanol/NH4+-containing medium. In contrast, alcohol
oxidase is virtually absent at t = 0 but is readily
detectable after 1 h in methanol medium. In the strain
synthesizing the cytosolic substrate protein (Fig. 3,
-GFP, top panel), no processing is
observed at 8 h after the shift of these cells from
glucose/ethylamine to methanol/ammonium sulfate medium. In contrast,
significant amounts (>50%) of the peroxisomal GFP substrate molecule
were found to be processed after the shift even after 6-8 h (Fig. 3,
-GFP, bottom panel). Unprocessed peroxisomal
substrate protein, however, remained detectable throughout the 8-h time
interval. Most likely, this is attributable to the development of new
peroxisomes in this period that imported Nmyc.tev.GFP.SKL under
conditions that repress TEVp.SKL production and thus was not available
to the protease. These data convincingly show that accumulation of
TEVp.SKL in peroxisomes prior to the synthesis of the substrate protein
in the cytosol prevents in vivo processing of a substrate
molecule at a different subcellular location but will process substrate
molecules targeted to the same location.

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Fig. 3.
Synthesis of TEVp.SKL prior to that of
TEVp-substrate molecules improves the specificity of in vivo
processing. Strains HF40
(PAOX-Nmyc.tev.GFP,PAMO-TEVp.SKL
(A, B, and C)) and HF41
(PAOX-Nmyc.tev.GFP.SKL,PAMO-TEVp.SKL
(D)) were pregrown in glucose/ethylamine-medium to induce
PAMO-expressed genes (A, AMO and
TEVp.SKL, not shown). Subsequently, these cells were
transferred to methanol/ammonium sulfate-medium, thus repressing
further synthesis of TEVp.SKL but inducing PAOX-expressed genes
(B, AOX; C,
Nmyc.tev.GFP; and D,
Nmyc.tev.GFP.SKL). Prior to the shift (t = 0), PAMO-expressed genes (AMO and
TEVp.SKL) are synthesized and gradually decrease over time
after the shift. In contrast, PAOX-expressed genes (AOX,
Nmyc.tev.GFP, and Nmyc.tev.GFP.SKL) only become
detectable after the shift, and the protein levels increase in time.
Significant amounts of the Nmyc.tev.GFP.SKL substrate protein becomes
processed in time (indicated by the arrowhead), whereas only
the unprocessed Nmyc.tev.GFP is detected after the shift.
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Taken together, these data show that heterologously synthesized TEVp
and TEVp.SKL are active in H. polymorpha in the cytosol and
peroxisomes, respectively, and can act specifically in these compartments. Under the experimental conditions, no vital H. polymorpha proteins are targets for the TEVp activity.
The C Termini of the Peroxisomal Membrane Proteins HpPex3p and
HpPex10p Face the Cytosol--
A potential application of the TEV
protease is the determination of the topology of peroxisomal membrane
proteins. For several of these proteins, the data are controversial to
some extent and may vary with the method used. A typical example is
Pex10p. In the yeast Pichia pastoris, the zinc finger
containing the C terminus was reported to reside in the peroxisomal
matrix (15), whereas it was reported to face the cytosol in human cells
(16, 17). Pex3p on the other hand is a peroxisomal membrane protein of
which the C terminus has consistently been reported to face the cytosol (53-55). Therefore, we decided to determine the localization of the C
termini of these two proteins in H. polymorpha using the TEVp-based system. To this end, functional hybrid proteins, consisting of the peroxin tagged at its C terminus to GFP linked by a
tev-processing sequence, were co-synthesized with either TEVp or
TEVp.SKL. The GFP-tagged membrane proteins were expressed by the
PAOX, and the TEV proteases were expressed by the PAMO.
The cells were grown in methanol/methylamine-containing medium, similar to the strains expressing the soluble substrate proteins as shown in
Fig. 2, lanes 7-10. As can be seen in Fig.
4, fluorescence microscopic analysis of
these cells showed that when either Pex3.tev.GFP or Pex10p.tev.GFP was
co-expressed with TEVp.SKL, a clear peroxisomal fluorescent staining
was observed (Fig. 4, B and D). In contrast, when
these hybrid proteins were co-expressed with cytosolic TEVp, a
predominantly cytosolic fluorescent staining was observed (Fig. 4,
A and C). Western blot analyses using crude
extracts prepared of these cells confirm that in cells producing
the cytosolic TEVp, specific processing of the hybrid proteins was
observed (Fig. 5, shown for
Pex3p.tev.GFP). Since synthesis of both the hybrid protein and the TEV
protease was induced simultaneously, unprocessed Pex3p.tev.GFP was
expected to be detectable in these strains. In contrast, no significant
processing of Pex3.tev.GFP was observed when it was co-synthesized with
TEVp.SKL. This result implies that the tev site at the C terminus of
Pex3p is not accessible from the peroxisomal matrix.

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Fig. 4.
Determination of the topology of peroxisomal
membrane proteins Pex3.tev.GFP and Pex10p.tev.GFP in vivo.
Fluorescence microscopic analysis of strains HF151
(PAMO-TEVp,PAOX-PEX3.tev.GFP)
(A), HF153 (PAMO-TEVp.SKL,
PAOX-PEX3.tev.GFP) (B), HF191
(PAMO-TEVp,PAOX-PEX10.tev.GFP)
(C), and HF193
(PAMO-TEVp.SKL,PAOX-PEX10.tev.GFP)
(D) in methanol/methylamine medium. Co-synthesis of
Pex3p.tev.GFP (A) or Pex10.tev.GFP (C) with
cytosolic TEVp leads to a predominant cytosolic fluorescent staining,
whereas co-synthesis with peroxisomal TEVp.SKL shows a peroxisomal rim
staining for Pex3.tev.GFP (B) and Pex10.tev.GFP
(D).
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Fig. 5.
Cytosolic TEVp processes pex3p.tev.GFP.
Western blot analysis of total protein extracts prepared from HF151
(PAMO- TEVp,PAOX-PEX3.tev.GFP,
lanes 1 and 3) and HF153
(PAMO-TEVp.SKL,
PAOX-PEX3.tev.GFP, lanes 2 and
4) cells grown in methanol/methylamine medium using specific
antibodies raised against H. polymorpha Pex3p (lanes
1 and 2) or GFP (lanes 3 and 4).
The arrows indicate the hybrid protein Pex3p.tev.GFP and the
processing products Pex3p and GFP as well as endogenous Pex3p.
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DISCUSSION |
In this study we describe the synthesis of the 27-kDa
NIa protease subdomain of the tobacco etch virus in the yeast H. polymorpha. The protease was shown to be selectively active
in vivo on soluble TEVp-substrate molecules that were
produced in the same compartment either in the cytosol (TEVp) or in the
peroxisomal matrix (TEVp.SKL). This system was successfully used to
show that the C termini of two peroxisomal membrane proteins, Pex3p and
Pex10p, face the cytosol.
Besides several other obvious applications of the TEV protease to study
peroxisome biogenesis, this procedure to determine membrane protein
topology seems to be pre-eminently suited to establish the location of
functional domains in PM peroxins. To understand the function of
peroxisomal membrane proteins, knowledge of the topology of these
proteins is crucial. However, the current procedures to determine
protein topology have resulted in virtually controversial data for many
(integral) peroxisomal membrane proteins, including Pex8p (11-13),
Pex10p (14-17), Pex11p (18-24), Pex14p (25-28), Pex16p (29, 30), and
Pex17p (31, 32). For example for Pex10p, these experiments have
resulted in two contradicting topologies. In P. pastoris,
the C-terminal zinc-finger domain was proposed to face the
peroxisomal matrix (15). In human cells, the C terminus was proposed to
face the cytosol (16, 17). Since two other zinc-binding PM peroxins,
Pex2p and Pex12p, are essential for peroxisome biogenesis, it is
important to know whether their zinc-binding domains face the same side
of the peroxisomal membrane.
The TEV-based system was effectively used to resolve the location of
the C terminus of HpPex10p. Co-synthesis of Pex10.tev.GFP with
cytosolic TEVp resulted in cleavage of the Pex10.tev.GFP hybrid.
Cleavage was prevented when Pex10.tev.GFP was co-synthesized with
peroxisomal TEVp.SKL. Identical results were obtained with a
Pex3.tev.GFP hybrid protein, the C terminus of which is known to face
the cytosol in both bakers' yeast and human cells (53-55). These data
convincingly demonstrate that the C terminus of HpPex10p has the same
location as Pex3p and thus protrudes into the cytosol.
Advantages of the TEVp-processing System--
The advantage of the
TEVp-based procedure over other available methods is that no
(endogenous) control proteins need to be characterized that may display
other susceptibility toward a protease or antibody. Rather, one protein
is analyzed with either a protease acting in the peroxisome or one
active in the cytosol, e.g. the strain co-expressing TEVp is
the control for the TEVp.SKL strain and vice versa. Processing can be
detected in cell free extracts and does not require organelle
purification or selective permeabilization of cellular membranes. In
addition, by using a cleavable GFP domain, processing (and thereby
topology) can be determined by fluorescence microscopy or confocal
laser scanning microscopy using living cells. Conclusive data are
obtained if only one of the combinations shows a significant higher
degree of processing as compared with the other, as described here for
Pex3.tev.GFP and Pex10.tev.GFP.
Additional Applications of the TEV Protease in Studies on
Peroxisome Biogenesis--
The use of the TEV protease is clearly not
restricted to protein topology determination. Firstly, the H. polymorpha strain expressing the peroxisomal protease is now being
used to reinitiate our efforts to set up a reliable in vitro
import system for peroxisomes. The development of such a system has
been severely hampered by both the high fragility of peroxisomes and
the lack of an unequivocal criterion for import. Clearly, the
processing of substrate molecules by the peroxisomal TEV protease will
allow an unequivocal detection system (as for mitochondria) to monitor
in vitro import of substrate molecules. Secondly, the TEV
protease will be applicable in determining whether proteins exist
transiently at a different subcellular location, which in wild type
cells occurs at biochemically low or even undetectable levels. Such an
approach is pre-eminently suitable to study the possible sorting of
peroxisomal membrane proteins via the endoplasmic reticulum (56, 57)
and the shuttling of the PTS1-receptor, Pex5p, between the cytosol and
the peroxisomal matrix (58, 59). Both endoplasmic reticulum-localized
TEVp and functional HpPex5p variants that are susceptible to TEVp
processing have been constructed in our laboratory. Thirdly, proteins
containing (internal) tev sites can be inactivated, both in
vivo and in vitro, and the effect on peroxisomal
biogenesis can be studied. These and probably other applications will
further advance our knowledge about the specific function of the peroxins.
 |
ACKNOWLEDGEMENT |
We thank Dr. W.-H. Kunau (Ruhr
University, Bochum, Germany) for the generous gift of
antibodies against GFP.
 |
FOOTNOTES |
*
This work was supported by a Postdoc Universitaire
Loopbaan Stimulans grant from the Netherlands Organization for
Scientific Research through the Earth and Life Science Foundation (to
K. N. F.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
Present address: University Hospital Groningen, Groningen
University Institute for Drug Exploration (GUIDE), Div.
Gastroenterology and Hepatology, P. O. Box 30.001, 9700 RB Groningen,
The Netherlands. E-mail: k.n.faber@med.rug.nl.
§
Supported by the Netherlands Organization for Scientific Research
through the Netherlands Technology Foundation.
Supported by Biotechnology and Biological Sciences
Research Council and German Israeli Foundation.
**
To whom correspondence should be addressed: Eukaryotic
Microbiology, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Biological Centre, Kerklaan 30, 9751 NN Haren, The Netherlands. Tel.: 31-50-363-2176; Fax:
31-50-363-2154; E-mail:
veenhuis@biol.rug.nl.
Published, JBC Papers in Press, July 6, 2001, DOI 10.1074/jbc.M105828200
 |
ABBREVIATIONS |
The abbreviations used are:
PTS, peroxisomal-targeting signal;
TEV, tobacco etch virus;
TEVp, TEV
protease;
GFP, green fluorescent protein;
eGFP, enhanced green
fluorescent protein;
PM, peroxisomal membrane;
PCR, polymerase chain
reaction;
kDa, kilodalton;
PAOX, alcohol oxidase promoter;
PAMO, amine oxidase promoter.
 |
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