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Journal of Virology, June 2004, p. 6370-6380, Vol. 78, No. 12
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.12.6370-6380.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Intramembrane Proteolysis and Endoplasmic Reticulum Retention of Hepatitis C Virus Core Protein
Kiyoko Okamoto,1 Kohji Moriishi,1 Tatsuo Miyamura,2 and Yoshiharu Matsuura1*
Research Center for Emerging Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka 585-0871,1
Department of Virology II, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan2
Received 27 November 2003/
Accepted 24 February 2004

ABSTRACT
Hepatitis C virus (HCV) core protein is suggested to localize
to the endoplasmic reticulum (ER) through a C-terminal hydrophobic
region that acts as a membrane anchor for core protein and as
a signal sequence for E1 protein. The signal sequence of core
protein is further processed by signal peptide peptidase (SPP).
We examined the regions of core protein responsible for ER retention
and processing by SPP. Analysis of the intracellular localization
of deletion mutants of HCV core protein revealed that not only
the C-terminal signal-anchor sequence but also an upstream hydrophobic
region from amino acid 128 to 151 is required for ER retention
of core protein. Precise mutation analyses indicated that replacement
of Leu
139, Val
140, and Leu
144 of core protein by Ala inhibited
processing by SPP, but cleavage at the core-E1 junction by signal
peptidase was maintained. Additionally, the processed E1 protein
was translocated into the ER and glycosylated with high-mannose
oligosaccharides. Core protein derived from the mutants was
translocated into the nucleus in spite of the presence of the
unprocessed C-terminal signal-anchor sequence. Although the
direct association of core protein with a wild-type SPP was
not observed, expression of a loss-of-function SPP mutant inhibited
cleavage of the signal sequence by SPP and coimmunoprecipitation
with unprocessed core protein. These results indicate that Leu
139,
Val
140, and Leu
144 in core protein play crucial roles in the
ER retention and SPP cleavage of HCV core protein.

INTRODUCTION
Hepatitis C virus (HCV) is a major cause of chronic liver disease
(
5,
19) and has been estimated to infect more than 170 million
people throughout the world (
15). Symptoms of persistent HCV
infection extend from chronic hepatitis to cirrhosis and finally
to hepatocellular carcinoma (
18,
42). HCV belongs to the genus
Hepacivirus in the family
Flaviviridae and possesses a viral
genome consisting of a single, positive-strand RNA with a nucleotide
length of about 9.4 kb (
6,
48). The genome encodes a large precursor
polyprotein of approximately 3,000 amino acids (
6,
17). The
polyprotein is processed co- and posttranslationally into at
least 10 viral proteins by host and viral proteases (
2,
6,
10,
45). The structural proteins of HCV are located in the N-terminal
one-fourth of the polyprotein and are cleaved by host membrane
proteases (
10,
44). Comparison with other flaviviruses suggests
that HCV core protein forms the nucleocapsid, which is surrounded
by the envelope containing glycoproteins E1 and E2 (
6,
48).
Functional analyses suggest that HCV core protein has regulatory
roles in host cellular functions. In tissue culture systems,
HCV core protein regulates signaling pathways and modulates
apoptosis (
4,
29,
40,
41,
46,
54,
55). Moreover, transgenic
mice expressing HCV core protein developed liver steatosis and
thereafter hepatocellular carcinoma (
34,
36). Thus, it has been
suggested that HCV core protein is a multifunctional molecule
that acts as a structural protein but is also involved in the
pathogenesis of hepatitis C. HCV core protein has two major
forms, p23 and p21 (
16,
25,
31,
43,
53). HCV core protein p23
represents a 191-amino-acid product in which the C-terminal
hydrophobic region also acts as a signal sequence for E1. HCV
polyprotein is cleaved between residues 191 and 192 by host
signal peptidase to generate C-terminal and N-terminal polypeptides
encompassing the core and E1 proteins, respectively. For the
full maturation of HCV core protein, the C-terminal signal-anchor
sequence was thought to be further processed by an unidentified
microsomal protease (
25,
30,
31,
43,
53), and the 21-kDa isoform
of core protein is predominantly detected both in cultured cells
by transfection with expression plasmid and in viral particles
obtained from sera of patients with hepatitis C (
53). These
results suggest that p21 is the mature form of HCV core protein
(
53). Immunostaining revealed that most HCV core protein is
distributed diffusely throughout the cell, probably in the endoplasmic
reticulum (ER) (
31,
53). However, a minor population was observed
in the nucleus (
53).
Recently, a presenilin-related aspartic protease, signal peptide peptidase (SPP), was identified (50). SPP is located in the ER membrane and promotes intramembrane proteolysis of signal peptides. The chemical compound (Z-LL)2-keton inhibits processing of signal peptides by SPP, and it was shown to suppress intramembrane proteolysis of major histocompatibility complex class I molecules, preprolactin, HCV core protein, and others (21, 30, 51). Replacement of Asp265 with Ala in SPP resulted in a loss of catalytic function, although this mutant could bind to TBL4K, a derivative of (Z-LL)2-keton (50). HLA-A was processed into yeast microsomes following the addition of wild-type SPP but not mutant SPP, suggesting that SPP interacts with HLA-A (50). Processing of the signal sequence of HCV core protein by SPP was inhibited by the addition of (Z-LL)2-keton, and Ser183 and Cys184 in the signal sequence of core protein were demonstrated to be important for flexibility and intramembrane proteolysis by SPP (23). Signal sequences generally have a tripartite structure, including a central hydrophobic H region and hydrophilic N- and C-terminal flanking regions (28). SPP recognizes the N- and C-terminal regions and cleaves in the middle of the H region (28). Mutational analyses suggested that the flexibility of signal peptides is generally required for substrate recognition of SPP (23). SPP contains the aspartic protease motifs YD and LGLGD, which are located in the predicted transmembrane region, and it is thought to cleave type II (N terminus in the cytosol and C terminus in the lumen)-oriented substrates (50). However, the effect of the cytoplasmic region of type II membrane substrates on intramembrane proteolysis by SPP is not known. In this study, we examined the regions of HCV core protein that are essential for ER retention and intramembrane cleavage by SPP.

MATERIALS AND METHODS
Plasmids.
For expression of enhanced green fluorescence protein (EGFP)-fused
HCV core proteins in culture cells, the core protein-coding
region was amplified by PCR from cDNA encoding full-length HCV
polyprotein type 1b (
1). The PCR products were subcloned into
SalI and BamHI sites 3' of the EGFP-coding region of pEGFP-C3
(Clontech, Palo Alto, Calif.). The cDNA fragments encoding amino
acids 1 to 191, 1 to 179, 92 to 191, 123 to 191, 128 to 191,
152 to 191, and 174 to 191 of HCV core proteins were amplified
by PCR and then introduced into pEGFP-C3; these constructs are
designated EGFP-Core 191, EGFP-Core 179, EGFP-Core 123-191,
EGFP-Core 128-191, EGFP-Core 152-191, and EGFP-Core 174-191,
respectively. The genes encoding core proteins with the region
between amino acids 128 and 151 deleted and replacement of Leu
139,
Val
140, and Leu
144 with Ala were generated by the method of
splicing by overlap extension (
11,
14,
49) and introduced into
pEGFP-C3; these constructs are designated EGFP-Core

128-151
and EGFP-Core LVL/3A, respectively (Fig.
1).
Fragments encoding Flag and hemagglutinin (HA) tags were inserted
at both ends of the multicloning site of pcDNA3.1 (pcDNA3.1FlagHA).
PCR products encoding either HCV core protein alone, core protein
followed by E1 (Core-E1), or their mutants were cloned into
pcDNA3.1FlagHA, resulting in plasmids encoding recombinant proteins
sharing Flag and HA tags at the N and C termini, respectively
(Fig.
1). In Flag-Core-HA and its derived mutants, Ala
191 was
replaced by Arg to avoid processing by signal peptidase for
determination of cleavage by SPP, as previously shown for the
processing of the E1-E2 junction (
7). In addition, the region
encoding Flag-Core-E1 or its mutants was cleaved from pcDNA3.1FlagHA
constructs and then introduced between the SacI and XhoI sites
of pcDNA3.1/
myc-His C (Invitrogen Corp., Carlsbad, Calif.).
The resulting plasmids encode HCV proteins sharing Flag and
myc/His epitopes at the N and C termini, respectively (Fig.
1). Genes encoding core protein with a single amino acid (Leu
139,
Val
140, or Leu
144), double amino acids (Leu
139 and Val
140, Leu
139 and Leu
144, or Val
140 and Leu
144), or triple amino acids (Leu
139,
Val
140, and Leu
144) replaced with Ala were generated by splicing
by overlap extension and introduced into pcDNA3.1FlagHA and
pcDNA3.1/
myc-His C (Fig.
1; see Fig.
4).
The genes encoding the ER-targeting and ER retrieval sequences
of calreticulin fused with DsRed at the N and C termini, respectively
(
8,
37,
39), were inserted between the EcoRV and XbaI sites
of pcDNA3.1 (pcDNA ER-DsRed) to visualize the ER in culture
cells. This recombinant protein is designated ER-DsRed in this
study.
Cloning of SPP.
The cDNA encoding SPP was amplified from human liver mRNA (Clontech) by reverse transcription-PCR and cloned into T-vector prepared from pBluescript II SK() (27). The gene encoding SPP with an attached HA tag and ER retrieval signal, KEKK, at the C terminus (SPP-HAER) was cloned into pcDNA3.1 to eliminate the possibility that the HA tag suppresses the endogenous ER retrieval signal of SPP. SPP-HAER was colocalized with ER-DsRed on the ER membrane and glycosylated upon transfection into cells (data not shown).
Subcellular localization of wild-type and mutant HCV core proteins.
HeLa cells were maintained in the Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum. HeLa cells were seeded on an eight-well chamber slide at 2 x 104 cells per well 24 h before transfection. The cells were transfected with the various plasmids by lipofection with Lipofectamine 2000 (Invitrogen). To determine protein subcellular localizations, transfected cells were fixed with phosphate-buffered saline (PBS) containing 3% paraformaldehyde at 18 h posttransfection and then observed with a confocal laser-scanning microscope (Bio-Rad, Tokyo, Japan). To confirm subcellular localization of the core proteins, transfected cells were fractionated with a subcellular proteome extraction kit (Calbiochem, Darmstadt, Germany). Stepwise extraction resulted in four distinct fractions, which contain mainly cytosolic, membrane-organelle, nuclear, and cytoskelton proteins, respectively. Each fraction was precipitated with trichloroacetic acid and analyzed by immunoblotting, and the densities of the bands were measured with Multi Gauge version 2.2 (Fujifilm, Tokyo, Japan).
Immunoblotting.
After transfection, 293T cells were harvested, washed twice with PBS, and lysed in 20 mM Tris-HCl (pH 7.4) containing 135 mM NaCl, 1% Triton X-100, and 10% glycerol (lysis buffer) supplemented with 1 mM phenylmethylsulfonyl fluoride, 1 mM NaF, and 1 mM Na2VO3. The lysate was centrifuged at 6,500 x g for 5 min at 4°C. The resulting supernatants were subjected to sodium dodecyl sulfate (SDS)-13.5% polyacrylamide gel electrophoresis. The separated proteins were electroblotted onto a Hybond-P polyvinylidene difluoride membrane (Amersham Bioscience, Piscataway, N.J.). These membranes were blocked with PBS containing 5% skim milk and 0.05% Tween 20 (Sigma, St. Louis, Mo.) and incubated with mouse monoclonal anti-Flag M2 (Sigma), anti-HA 16B12 (HA.11; BabCO, Richmond, Calif.), or monoclonal mouse anti-His6-AD1.1.10 (Genzyme/Techne, Tokyo, Japan) immunoglobulin G (IgG) at room temperature for 30 min and then with horseradish peroxidase-conjugated anti-mouse IgG antibody at room temperature for 30 min. Immunoreactive bands were visualized by using the enhanced chemiluminescence Super Signal West Femto substrate (Pierce, Rockford, Ill.).
Immunoprecipitation.
Immunoprecipitation analysis was carried out as described previously (32). Plasmids were transfected into 293T cells by lipofection. Transfected cells were harvested at 18 h posttransfection and lysed in lysis buffer with 0.5% 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxypropanesulfonic acid (CHAPSO) (Dojindo, Kumamoto, Japan). Cell lysates were incubated with monoclonal anti-HA, anti-Glu-Glu (anti-EE) (BabCO), or anti-Flag antibody at 4°C for 1.5 h and then with protein G-Sepharose CL-4B (Amersham Bioscience) at 4°C for 1.5 h. After centrifugation at 6,500 x g for 3 min at 4°C, the pellets were washed five times with lysis buffer. Immunoprecipitates were subjected to immunoblotting.
Deglycosylation.
Plasmids encoding core and E1 proteins were transfected into 293T cells by lipofection, and cell lysates were immunoprecipitated with anti-HA antibody at 18 h posttransfection. Immunoprecipitates were eluted from protein G-Sepharose CL-4B in 0.5% SDS and 1% 2-mercaptoethanol and digested with endo-ß-N-acetylglucosaminidase H (Endo H) or peptide-N-glycosidase F (PNGase F) according to the protocol of the manufacturer (Roche, Mannheim, Germany). The resulting mixtures were subjected to immunoblotting.

RESULTS
Region required for ER retention of HCV core protein.
To determine the regions within HCV core protein that are responsible
for ER retention, EGFP-fused, N-terminally truncated HCV core
protein (Fig.
1) was coexpressed with the ER marker ER-DsRed.
EGFP-Core 191 colocalized with ER-DsRed to the ER (Fig.
2),
whereas EGFP-Core 179 was localized primarily to the nucleus
as reported previously (
3,
33,
43,
47), suggesting that the
C-terminal signal sequence is essential for anchoring HCV core
protein to the ER membrane. However, EGFP-Core 174-191 exhibited
diffuse staining similar to that of EGFP, suggesting that the
signal sequence alone is not sufficient for ER localization.
EGFP-Core 92-191, EGFP-Core 123-191, and EGFP-Core 128-191 were
colocalized with ER-DsRed in the ER, but EGFP-Core 152-191 stained
similarly to EGFP-Core 174-191 and EGFP. These data suggest
that not only the C-terminal signal sequence but also the region
from amino acids 128 to 151 is required for ER retention of
HCV core protein.
Region essential for processing of the signal sequence of HCV core protein by SPP and signal peptidase.
Based on hydrophobicity and a cluster of basic amino acids,
HCV core protein was proposed to possess three regions (domains
1 to 3) (Fig.
3A, upper panel) by Hope and McLauchlan (
12).
To assess the involvement of the region encompassing amino acids
128 to 151 in proteolysis of the signal sequence of HCV core
protein by signal peptidase and SPP, three hydrophobic amino
acids, Leu
139, Val
140, and Leu
144, in the most hydrophobic peak
in domain 2 were replaced with Ala to reduce hydrophobicity,
and Ala
191 was replaced with Arg to eliminate processing by
signal peptidase (Fig.
3A, lower panel). When a wild-type Flag-Core-HA
construct was expressed in 293T cells, a single band of 23 kDa
was detected by blotting with anti-Flag, but not with anti-HA,
suggesting that the HA-fused signal sequence was properly processed
by SPP and that Flag-core protein of 23 kDa was generated (Fig.
3B, lanes 2 and 11). In cells expressing the substitution mutants,
25- and 23-kDa bands were detected by the anti-Flag antibody
(Fig.
3B, upper panel, lanes 3 to 9) and 25-kDa bands were detected
by the anti-HA antibody (Fig.
3B, lower panel, lanes 3 to 9),
indicating that the 25- and 23-kDa bands correspond to core
proteins that are unprocessed and processed by SPP, respectively.
Cleavability of the signal sequence of mutant core proteins
by SPP was suppressed in accordance with the number of substitutions,
and almost no processing of the signal sequence was observed
in cells expressing Flag-Core LVL/3A-HA, which has three amino
acid substitutions (Fig.
3B, lane 9). These results indicate
that Leu
139, Val
140, and Leu
144 play crucial roles in the processing
of the signal-anchor of HCV core protein by SPP. Furthermore,
deletion of the hydrophobic region including amino acids 128
to 151 from HCV core protein completely eliminated processing
by SPP, and this species was seen only as a single band of 23.5
kDa which was detected by both the anti-Flag and anti-HA antibodies
(Fig.
3B, lane 10). Taken together with the observation that
Ala
180, Ser
183, and Cys
184 in the signal sequence of HCV core
protein of the type 1a Glasgow strain were demonstrated to be
essential for SPP proteolysis (
13,
23), these results indicate
that the hydrophobic region from amino acid 139 to 144 in domain
2 of HCV core protein also participates in the processing of
the signal sequence by SPP.
To examine the role of the region from amino acid 139 to 144
in the cleavage of the HCV core protein signal sequence by signal
peptidase and SPP in more detail, substitutions of Leu
139, Val
140,
and/or Leu
144 with Ala were introduced into the Flag-Core-E1-HA
polyprotein (Fig.
1). Flag-Core-E1-HA protein was cleaved to
the expected molecular mass of 23 kDa of Flag-Core protein by
signal peptidase and SPP (Fig.
3C, lanes 2 and 11), whereas
slightly larger bands corresponding to a core protein unprocessed
by SPP were detected in cells expressing polyproteins possessing
mutations within amino acids 139 to 144 (Fig.
3C, lanes 3 to
9). A lack of processing by SPP was detected mainly in core
proteins containing double amino acid changes of Leu
139, Val
140,
and/or Leu
144 to Ala (Fig.
3C, lanes 6 to 8), and only an unprocessed
band was detected in a triple amino acid substitution mutant
(Fig.
3C, lane 9) and a deletion mutant lacking amino acids
128 to 151 (Fig.
3C, lane 10). In contrast to the processing
of core protein, E1 protein processed from the mutant polyproteins
exhibited the same molecular mass of 32 to 35 kDa and the same
deglycosylation patterns following digestion with Endo H or
PNGase F (Fig.
3D). These results indicate that the internal
hydrophobic region from amino acid 139 to 144 of HCV core protein
is essential for processing by SPP but not for cleavage of the
core-E1 junction by signal peptidase and the subsequent translocation
of E1 protein into the ER. It was suggested that signal peptides
must be liberated from the precursor protein by cleavage with
signal peptidase in order for them to become substrates for
SPP (
23). Our data indicate that processing by SPP is not a
prerequisite for cleavage of the core-E1 junction by signal
peptidase.
Amino acid sequence essential for SPP cleavage of the signal sequences of HCV core proteins of genotypes 1a and 1b.
Martoglio and colleagues reported that HCV core protein is processed by SPP after cleavage by host signal peptidase and that Ala180, Ser183, and Cys184 residues in the signal sequence of HCV core protein of type 1a Glasgow strain are essential for SPP proteolysis, as they maintain the structure of the breaking
-helix (23, 30). To determine the amino acids essential for SPP cleavage of the signal sequence of type 1b HCV core protein, Flag-Core-E1-HA and its substitution mutants were expressed in 293T cells (Fig. 4). Mutation of one, two, or three amino acids, except for Flag-Core IF176/177AL-E1-HA (Fig. 4B, lane 9), did not affect the processing of the core protein signal sequence. Flag-Core IF176/177AL-E1-HA exhibited the same molecular size as Flag-Core LVL/3A-E1-HA (Fig. 4B, lane 2), suggesting that Ile176 and Phe177 in the signal sequence of core protein are essential for cleavage by SPP in our system. However, the triple amino acid substitution (Ala180, Ser183, and Cys184) in the type 1b J1strain (Flag-Core ASC/LVL-E1-HA) (Fig. 4B, lane 11), which is the same as the spmt mutant of the type 1a Glasgow strain (23, 30), did not affect the processing of the signal sequence of HCV core protein by SPP. All derived E1 proteins exhibited a molecular mass of 32 to 35 kDa irrespective of the presence of mutations, and deglycosylation by digestion with endoglycosidases generated uniform 22-kDa bands of E1 proteins (data not shown). These results indicate that Ile176 and Phe177, but not Ala180, Ser183, and Cys184, in the signal sequence of type 1b HCV core protein are essential for processing by SPP and confirm that processing of signal sequence by SPP is not required for cleavage by signal peptidase and translocation of E1 protein into the ER. To determine whether the difference in cleavage of signal sequence depends on the genotype of HCV, Ala180, Ser183, and Cys184 in the HCV core protein of the genotype 1a H77c strain were replaced with Val, Leu, and Val, respectively. The spmt construct of the type 1a H77c strain did not affect the processing of core and E1 proteins in BHK cells (Fig. 4C, lane 3) and 293T cells (data not shown). In contrast, replacement of Leu139, Val140, and Leu144 by Ala and of Ile176 and Phe177 by Ala and Leu suppressed the processing of the core protein signal sequence of the type 1a H77c strain in BHK cells (Fig. 4C, lanes 4 and 5). These results indicate that three hydrophobic amino acids Leu139, Val140, and Leu144 in the hydrophobic peak in domain 2 and the two amino acids Ile176 and Phe177 in the transmembrane domain play important roles in the intramembrane proteolysis of HCV core protein signal sequence of genotypes 1a and 1b by SPP.
To further examine the cleavage of the signal sequence of HCV core proteins by SPP, we prepared IF176/177AL and the spmt mutant core proteins carrying a substitution of Ala191 to Arg to avoid processing by signal peptidase as described above. In cells expressing a wild-type or LVL/3A mutant core protein, a 23-kDa processed or a 25-kDa unprocessed core protein was detected, as seen in Fig. 3B (Fig. 4D, lanes 2 and 4). The IF176/177AL mutant exhibited a 26-kDa unprocessed band which was detected by anti-HA antibody (Fig. 4D, lane 5). In contrast, the spmt core protein exhibited a major band at 23 kDa and a faint 24-kDa band after blotting with the anti-Flag antibody (Fig. 4D, lane 3). Detection of a small amount of the 24-kDa unprocessed band by the anti-HA antibody indicates that most of the spmt mutant core protein was processed by SPP. The unprocessed core proteins of spmt, LVL/3A and IF176/177AL exhibited different electrophoretic mobilities, estimated to be 24, 25, and 26 kDa, respectively (Fig. 4D, lower panel, lanes 3 to 5). Lemberg and Martoglio pointed out that the mobility of a protein does not necessarily correlate with its molecular mass when analyzed in a Tris-glycine gel system due to the unexpected electrophoretic mobility of the proteins (22). However, detection of HA-tagged unprocessed signal sequence in the core mutants clearly demonstrated that LVL/3A and IF176/177AL mutants substituted with Leu139, Val140, and Leu144 in domain 2 and with Ile176 and Phe177 in the transmembrane domain, respectively, have lost the ability to be cleaved by SPP.
Effect of a loss-of-function mutant of SPP on the processing of the signal sequence of HCV core protein.
Although there are two reports suggesting that SPP is involved in the processing of the signal sequence of HCV core protein by using the SPP inhibitor (Z-LL)2-keton (23, 30), a direct interaction of HCV core protein with SPP has not been demonstrated. To determine the direct involvement of SPP in the processing of HCV core protein signal sequence, the C-terminal HA tag in the Flag-Core-E1-HA constructs used in the experiments described above was replaced with a myc/His tag and coexpressed with wild-type SPP (SPP-HAER) or with a mutant SPP with amino acid substitutions in the putative protease active sites, i.e., Asp219 (SPP D219A-HAER) or Asp265 (SPP D265A-HAER) to Ala. The signal sequence of HCV core protein was processed in cells coexpressing Flag-Core-E1-myc/His and SPP-HAER (Fig. 5, anti-Flag, lane 3), whereas two bands corresponding to processed and unprocessed (the same size as Flag-Core LVL/3A-E1-myc/His [lane 6]) core proteins were detected in cells coexpressing Flag-Core-E1-myc/His and the mutant SPP constructs (Fig. 5, anti-Flag, lanes 4 and 5). Proper cleavage and glycosylation of E1 proteins in cells coexpressing Flag-Core-E1-myc/His and the SPP mutants (Fig. 5, anti-His, lanes 4 and 5) and those expressing Flag-Core LVL/3A-E1-myc/His (Fig. 5, anti-His, lane 6) indicates that processing of signal sequence by SPP is not required for the cleavage of the core-E1 junction by signal peptidase and translocation of E1 protein into the ER. These results indicate that loss-of-function mutants of SPP inhibit the intramembrane proteolysis of HCV core protein signal sequence and further confirm that the slightly larger bands detected in cells expressing Flag-Core LVL/3A-E1-HA or Flag-Core IF176/177AL-E1-HA are immature core proteins unprocessed by SPP (Fig. 4B, lanes 3 and 9).
Interaction of HCV core protein with SPP.
To examine the specific interaction of HCV core protein with
SPP, Flag-Core-E1-myc/His, Flag-Core LVL/3A-E1-myc/His, or Flag-Core
IF176/177AL-E1-myc/His was coexpressed with SPP-HAER or SPP
D219A-HAER in 293T cells and immunoprecipitated with anti-Flag
or anti-HA antibody. In cells coexpressing the loss-of-function
mutant, SPP D219A-HAER, and one of the three HCV polyprotein
substrates, nonspecific bands were detected by immunoblotting
with the anti-HA and anti-Flag antibodies in the immunoprecipitates
(Fig.
6A, upper and second panels, lanes 3 to 5). Therefore,
lysates immunoprecipitated with anti-Flag and anti-HA antibodies
were evaluated by comparison with those precipitated with anti-EE.
Three bands corresponding to SPP D219A-HAER were coimmunoprecipitated
with core proteins by anti-Flag immunoprecipitation (Fig.
6A,
upper panel, lanes 8 to 10). SPP has two glycosylation sites
(
50), and therefore the upper, middle, and lower bands seem
to correspond to SPP possessing two glycans, one glycan, and
no glycan, respectively. Deglycosylation by PNGase F treatment
reduced the molecular sizes of all bands to that of the lowest
band (data not shown). Only unprocessed core protein was coimmunoprecipitated
with SPP D219A-HAER by anti-HA (Fig.
6A, second panel, lanes
8 to 10). Coexpression of Flag-Core LVL/3A-E1-myc/His or Flag-Core-IF176/177AL-E1-myc/His
reduced the expression of SPP D219A-HAER (Fig.
6A, third panel,
lanes 4 and 5), suggesting that the core mutants suppress the
expression of the SPP mutant. Clear reduction or elimination
of the processing of the HCV core protein signal sequence was
observed in cells coexpressing SPP D219A-HAER in comparison
with those coexpressing wild-type SPP (Fig.
6A and B, bottom
panels, lanes 3 to 5). Conversely, no interaction of HCV core
protein with wild-type SPP was observed in cells coexpressing
SPP-HAER and the HCV polyprotein substrates (Fig.
6B, upper
panels, lanes 8 to 10). Broad bands were detected in immunoprecipitates
with anti-Flag or anti-EE antibody by immunoblotting with the
anti-Flag antibody, probably due to nonspecific binding of the
processed core protein to protein G-Sepharose (Fig.
6B, second
panel, lanes 3 and 8). These results indicate that a direct
interaction of SPP with HCV core protein only between the unprocessed
core protein and the loss-of-function mutant of SPP is verifiable.
SPP should bind to the signal sequence of HCV core protein and
release it after proteolysis, whereas SPP D219A cannot liberate
the substrate after binding due to lack of the catalytic activity,
suggesting that the SPP mutant may possess dominant negative
effects.
Processing of the signal sequence of HCV polyprotein in a human hepatoma cell line.
To confirm the data obtained for 293T cells with human liver
cells, processing of core-E1 polyprotein in FLC4 cells, a human
hepatoma cell line, was examined (Fig.
7). Processing by signal
peptidase and SPP was evident in cells expressing Flag-Core-E1-HA
or Flag-Core ASC/VLV-E1-HA (lanes 2 and 3), whereas clear processing
by signal peptidase, but not complete cleavage by SPP, was observed
in FLC-4 cells expressing Flag-Core LVL/3A-E1-HA or Flag-Core
IF176/177AL-E1-HA (lanes 4 and 5). These results are consistent
with data obtained with 293T cells, suggesting that the processing
of the signal sequence of HCV core protein is not cell type
dependent or an artifact of the techniques used in this study.
Localization of mutant HCV core proteins.
To determine the effect of mutations on the localization of
HCV core protein, EGFP-Core 191and its mutants that are defective
in cleavage by SPP were expressed in HeLa cells (Fig.
8A). EGFP-Core
191 was processed by SPP and colocalized with an ER marker.
EGFP-Core IF176/177AL, which bears a mutation that confers

-helix
structure to the signal sequences, was diffusely distributed
but did not completely colocalize with ER-DsRed as seen with
EGFP-Core 191. EGFP-Core LVL/3A was localized mainly to the
nucleus and, to a lesser extent, the cytoplasm, and EGFP-Core

128-151 exhibited complete nuclear localization. To confirm
the subcellular localization of mutant HCV core proteins, cells
were transfected with expression plasmids encoding N-terminally
Flag-tagged and C-terminally HA-tagged core proteins to minimize
the effect of fusion protein and fractionated, as described
in Materials and Methods (Fig.
8B). Consistent with the subcellular
localization of EGFP-Core proteins, Flag-Core 191-HA was detected
mainly in the membrane-organelle fraction and Flag-Core LVL/3A-HA
and Flag-Core

128-151-HA were localized mainly in the nuclear
fraction. Although EGFP-Core IF176/177AL did not completely
colocalize with the ER marker, 55% of Flag-Core IF176/177AL-HA
was detected in membrane-organelle fraction. Since we could
not separate ER and Golgi fractions by the fractionation method
used, it is possible that Flag-Core IF176/177AL-HA localizes
mainly in the Golgi rather than the ER. These results indicate
that not only the C-terminal signal sequence but also the hydrophobic
region from amino acid 139 to 144 in domain 2 and proper processing
by SPP are involved in the ER retention of HCV core protein.

DISCUSSION
Hope and McLauchlan identified three regions in the HCV core
protein, including two hydrophobic regions in the C-terminal
one-third of the protein and the region from amino acid 119
to 174, which was designated domain 2 (
12). Domain 2 was hypothesized
to interact with lipid droplets and confer stability to the
HCV core protein (
12). Although a mutation in the signal sequence
of core protein that renders it resistant to SPP proteolysis
restored retention on lipid droplets and overall stability (
30),
deletion of domain 2 from HCV core protein leads to diffusion
in the cytoplasm and degradation after processing by signal
peptidase (
30). Indeed, these data suggest that mature HCV core
protein is retained on lipid droplets via domain 2, but they
do not necessarily indicate that the region is required for
the ER retention of HCV core protein. The intramembrane proteolysis
of the signal sequence of HCV core protein by SPP is abolished
when helix-breaking and -bending residues in the C-terminal
signal-anchor sequence are replaced by basic amino acids (
30).
However, the involvement of other regions of HCV core protein
in processing by SPP is not known. In this study, we could demonstrate
that not only the C-terminal signal-anchor domain but also three
hydrophobic amino acids Leu
139, Val
140, and Leu
144 in domain
2 are required for intramembrane proteolysis by SPP. However,
this domain is not essential for the cleavage of the core-E1
junction by signal peptidase or for translocation of E1 into
the ER. Furthermore, the nuclear localization of domain 2 core
mutants possessing an unprocessed C-terminal signal-anchor sequence
indicates that association with the ER membrane through domain
2 is required for ER retention of HCV core protein.
Martoglio and colleagues demonstrated, by using a Semliki Forest virus expression system, that Ala180, Ser183, and Cys184 break the
-helical structure within the signal sequence and are essential for the intramembrane proteolysis of HCV core protein of the type 1a Glasgow strain by SPP in BHK and Huh7 cell lines (23, 30). However, mutation of Ala180, Ser183, and Cys184 in core proteins of the type 1b J1 and type 1a H77 strains could not inhibit signal sequence processing by SPP in the BHK and 293T cell lines by expression with plasmid. HCV core protein of the type 1a Glasgow strain shares 96.3 and 95.8% amino acid homology to those of the H77c and J1 strains, respectively. Furthermore, the signal sequences of the core proteins of these three strains are almost identical, and therefore the observed differences in cleavability by SPP might be attributable to sequence other than the signal sequence or expression system used. We reexamined the HCV core protein signal sequence and, using the method of Garnier et al. (9), chose to further examine Ile176 and Phe177 as residues that may interfere with the assumption of a compact
-helix structure and allow for intramembrane proteolysis by SPP. Mutation of Ile176 and Phe177 (Core IF176/177AL) of genotype 1a and 1b strains, which is predicted to confer
-helical structure to the signal sequences, inhibited processing by SPP. EGFP-Core IF176/177AL exhibited no colocalization with an ER marker; this differs from the case for the wild-type core protein. These data suggest that the processing of the signal sequence by SPP may play a role in the ER retention of HCV core protein.
Precursor HCV core protein consists of 191 amino acids and is processed by signal peptidase from a polyprotein after translocation of the C-terminal signal-anchor sequence into the ER. This is then cleaved by SPP into the mature core protein and localizes primarily to the ER. The mature core protein, further processed by an unidentified protease, is composed of amino acids 151 to 153 and is detected in the nucleus (33, 47). Actually, HCV core protein is observed in the cytoplasm, nucleus, and nucleoli in transgenic mice expressing HCV core protein (35). Under normal conditions, the precursor core protein is processed by SPP to 173 to 179 amino acids and localizes to the ER. In contrast, a 179-amino-acid construct containing a limited C-terminal anchor-signal sequence, Core 179, localizes primarily to the nucleus and to the ER to a lesser extent. This striking difference in the subcellular localizations of Core 191 and Core 179, in conjunction with data from the Core IF176/177AL construct, indicates that the presence of the full-length signal-anchor sequence and proper processing by SPP is required for retention of HCV core protein on the ER membrane.
We also demonstrated that the reduction in hydrophobicity in domain 2 affects proteolysis of the signal sequence by SPP and localization of HCV core protein. It was suggested that HCV core protein interacts with lipid droplets containing triacylglycerol and/or ER membrane through domain 2 irrespective of intramembrane proteolysis of the signal sequence (30). A mutant HCV core protein in domain 2, EGFP-Core LVL/3A with Leu139, Val140, and Leu144 replaced by Ala, was processed by signal peptidase but not by SPP and localized to the nucleus in spite of the presence of an unprocessed hydrophobic signal sequence in the C terminus. This result suggests that penetration of the HCV core protein signal sequence into the ER membrane is necessary, but not sufficient, for ER retention of HCV core protein. Insertion of the C-terminal signal-anchor sequence of core protein into the ER may induce conformational changes in domain 2 to render it accessible to the ER membrane and/or lipid droplets by exposure of hydrophobic residues in the domain, residues that are well conserved among various genotypes of HCV. Although it was suggested that processed HCV core protein was retained on the ER membrane via an interaction with unprocessed core protein (25) or with the C-terminal transmembrane region of E1 (26), our data provide a new model of the ER retention of HCV core protein. HCV core protein is a structural protein that forms the nucleocapsid, and virus particles are thought to be released into ER. Therefore, retention of HCV core protein on the ER membrane should be essential for the assembly of HCV.
Intramembrane-cleaving proteases have been shown to play pivotal roles in cell regulation and signaling and are involved in diseases such as Alzheimer's disease (52). SPP belongs to a family of aspartic proteases family and has two aspartic acid residues, Asp219 and Asp265, in the enzyme active site (50). Signal peptidase II also belongs to this aspartic protease family and cleaves the signal sequence by attacking a proton of a water molecule via an aspartic acid of the enzyme (38). Mutant SPP bearing an Asp265-to-Ala substitution was deficient in the processing of HLA-A but retained binding activity to the SPP substrate analogue TBL4K (50). We could demonstrate a direct interaction by immunoprecipitation of unprocessed HCV core proteins with mutant SPP lacking catalytic and substrate-releasing activities by replacement of Asp219 with Ala. Binding of the loss-of-function SPP mutants with unprocessed core proteins irrespective of mutation or deletion in domain 2 indicates that the domain is not directly involved in the interaction.
It has been demonstrated that expression of HCV core protein alone is sufficient for the induction of hepatic steatosis and hepatocellular carcinoma in transgenic mice (24, 34, 35). Furthermore, we demonstrated that nuclear localization and degradation of HCV core protein is regulated by PA28
-dependent proteolysis (33). These findings suggest that HCV core protein plays a pivotal role in the development of hepatocellular carcinoma and that intramembrane proteolysis may regulate the subcellular localization of HCV core protein. Although the SPP inhibitor (Z-LL)2-keton suppresses cleavage of signal sequence essential for homeostasis, host defense, etc., a specific inhibitor against the intramembrane proteolysis of HCV core protein, such as antagonists for the binding of HCV core protein to ER membrane via domain 2, will be an effective antiviral drug for patients with chronic hepatitis C. Furthermore, involvement of intramembrane proteolysis by SPP in the processing of other HCV proteins and the fates of the peptides cleaved by SPP in the replication and pathogenesis of hepatitis C are subjects of future studies.

ACKNOWLEDGMENTS
We gratefully thank T. Shioda for advice on confocal microscopy
and J. McLauchlan for valuable discussions.
This work was supported in part by grants-in-aid from the Ministry of Health, Labor and Welfare; the program for Promotion of Fundamental Studies in Health Sciences of the Organization for Drug ADR Relief, R&D Promotion, and Product Review; the Ministry of Education, Culture, Sports, Science and Technology; and the 21st Century Center of Excellence Program of Japan.

FOOTNOTES
* Corresponding author. Mailing address: Research Center for Emerging Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, 3-1, Yamadaoka, Suita-shi, Osaka 565-0871, Japan. Phone: 81-6-6879-8340. Fax: 81-6-6879-8269. E-mail:
matsuura{at}biken.osaka-u.ac.jp.


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Journal of Virology, June 2004, p. 6370-6380, Vol. 78, No. 12
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.12.6370-6380.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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