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Journal of Virology, March 2007, p. 2391-2400, Vol. 81, No. 5
0022-538X/07/$08.00+0 doi:10.1128/JVI.01601-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Inhibition of Filovirus Replication by the Zinc Finger Antiviral Protein
Stefanie Müller,1,
Peggy Möller,2,
Matthew J. Bick,1,
Stephanie Wurr,1
Stephan Becker,2,
Stephan Günther,1 and
Beate M. Kümmerer1*
Department
of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20359
Hamburg, Germany,1
Institute of Virology,
Philipps University Marburg, 35043 Marburg,
Germany2
Received 26 July 2006/
Accepted 7 December 2006
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ABSTRACT
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The
zinc finger antiviral protein (ZAP) was recently shown to inhibit
Moloney murine leukemia virus and Sindbis virus replication. We tested
whether ZAP also acts against Ebola virus (EBOV) and Marburg virus
(MARV). Antiviral effects were observed after infection of cells
expressing the N-terminal part of ZAP fused to the product of the
zeocin resistance gene (NZAP-Zeo) as well as after infection of cells
inducibly expressing full-length ZAP. EBOV was inhibited by up to 4 log
units, whereas MARV was inhibited between 1 to 2 log units. The
activity of ZAP was dependent on the integrity of the second and fourth
zinc finger motif, as tested with cell lines expressing NZAP-Zeo
mutants. Heterologous expression of EBOV- and MARV-specific sequences
fused to a reporter gene suggest that ZAP specifically targets L gene
sequences. The activity of NZAP-Zeo in this assay was also dependent on
the integrity of the second and fourth zinc finger motif. Time-course
experiments with infectious EBOV showed that ZAP reduces the level of L
mRNA before the level of genomic or antigenomic RNA is affected.
Transient expression of ZAP decreased the activity of an EBOV replicon
system by up to 95%. This inhibitory effect could be partially
compensated for by overexpression of L protein. In conclusion, the data
demonstrate that ZAP exhibits antiviral activity against filoviruses,
presumably by decreasing the level of viral
mRNA.
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INTRODUCTION
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Ebola virus (EBOV) and Marburg virus (MARV) belong to the family
Filoviridae. Their genome consists of a single-stranded RNA
genome of negative polarity with a length of about 19 kb. The filovirus
genome is transcribed in monocistronic mRNA species, which encode seven
structural proteins: a single surface protein (GP), a matrix protein
(virus protein 40 [VP40]), a second minor matrix protein (VP24), and
four nucleocapsid proteins (nucleoprotein [NP], L protein, VP35, and
VP30) (7,
15,
16,
18,
25). Both EBOV and MARV
cause severe hemorrhagic fever in humans and nonhuman primates
(4,
19). Infections with
filoviruses are characterized by high fever, hemorrhages, and shock
(19,
22). For Zaire-EBOV and
MARV, mortality rates up to 90% have been described; the mortality
rates for Sudan-EBOV are about 60% (from the Centers for Disease
Control and Prevention website
[http://www.cdc.gov/]).
To date, neither a vaccine nor a therapy for treating infected patients
is available.
In contrast to many other viruses, no host cell
proteins with antiviral activity have been identified so far for
filoviruses. However, it is known that filoviruses antagonize the
interferon (IFN) response
(17), suggesting that the
IFN pathway plays a role in the host cell response against filoviruses.
Both VP35 and VP24 of EBOV have been found to be involved in the IFN
antagonism (6,
12,
23).
In an attempt
to search for host cell antiviral proteins active against filoviruses,
we analyzed the effect of the CCCH-type zinc finger antiviral protein
(ZAP) (8) on EBOV and MARV
replication. ZAP was discovered via its ability to inhibit Moloney
murine leukemia virus (MMLV) replication
(8). The cDNA of the
original MMLV-resistant cell clone was derived from a Rat2 fibroblast
library. The cells expressed the N-terminal part of ZAP fused to the
product of the zeocin resistance gene (NZAP-Zeo)
(8). Inhibition of MMLV is
accompanied by a specific loss of viral mRNAs from the cytoplasm,
whereas the level of RNA within the nucleus remained
unimpaired (8). In
addition, it was shown that NZAP-Zeo also inhibits the replication of
alphaviruses by preventing translation of incoming RNA
(2). Further studies
demonstrated that the second and fourth zinc finger motifs of ZAP are
important for inhibition of MMLV and Sindbis virus (SIN)
(11). For SIN, direct
binding of certain genomic RNA fragments to ZAP was described, and
destabilization of the bound RNA was discussed as the mechanism of
action (11). However, the
expression of NZAP-Zeo does not produce a broad-spectrum antiviral
state, as yellow fever virus (YFV), vesicular stomatitis virus, or
poliovirus are not affected by NZAP-Zeo
(2).
In the present
study, we demonstrate that ZAP is also active against filoviruses,
indicating that ZAP's activity is not restricted to positive-strand RNA
viruses and retroviruses. The second and fourth zinc finger motifs
especially were important for inhibition of filovirus replication, as
shown for MMLV and SIN. The mRNA encoding the polymerase seems to be a
target of ZAP.
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MATERIALS AND METHODS
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Cell culture and viruses.
All cells were maintained in
Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine
serum. The Rat2-Zeo cells (named Rat2-HA-Zeo cells in reference
2), Rat2-NZAP-Zeo, and
Rat2-NZAP-Zeo mutant cells
(2) were kept under 100
µg of zeocin/ml (Invitrogen). The tetracycline-inducible
293TRex-ZAP cell line
(11) was passaged under
200 µg of zeocin/ml. Expression of ZAP was induced with 0.5
µg doxycycline/ml (Sigma-Aldrich).
Virus
stocks were produced on Vero-E6 cells. Cells were infected at a
multiplicity of infection (MOI) of 0.01 for 1 h with
Zaire-EBOV (Gabon strain, 2002; unpublished data), Sudan-EBOV (Uganda
strain, 2000; unpublished data), MARV Musoke (Kenya, 1980), or MARV
Popp (West Germany, 1967). Virus was harvested from the supernatant 7
days postinfection (p.i.). All experiments with EBOV and MARV were
performed in a biosafety level 4
laboratory.
Immunofluorescence assay.
Zaire-EBOV-infected
cells were fixed 5 days p.i., and immunofluorescence analysis was
performed using a monoclonal antibody directed against Zaire-EBOV
nucleoprotein NP (MAb B6C1; dilution, 1:500; unpublished data). Bound
antibodies were detected with rhodamine-labeled goat anti-mouse
immunoglobulin G (dilution, 1:100)
(Dianova).
Virus titration.
Titration of EBOV and MARV
was performed on Vero-E6 cells. The inoculum was removed after
1 h, and cells were overlaid with medium containing 0.9%
methylcellulose. Five days p.i., the methylcellulose overlay was
removed and cells were fixed with 4% formaldehyde in phosphate-buffered
saline for at least 1 h. Plaques of MARV Popp were visualized
using crystal violet staining (1% crystal violet in 20% ethanol).
Infected foci of Zaire-EBOV, Sudan-EBOV, and MARV Musoke were detected
by an immunofocus assay using virus-specific polyclonal antibodies
raised in goats (unpublished data). Primary antibodies were diluted
1:1,000, and bound antibodies were detected with a
peroxidase-conjugated rabbit anti-goat antibody (dilution, 1:250;
Dianova) followed by incubation with
3,3',5,5'-tetramethylbenzidine substrate
(Mikrogen).
Real-time PCR.
Isolation of viral RNA from the cell
culture supernatant was performed as described previously
(1). The isolated RNA from
the supernatant was detected by real-time reverse transcription-PCR
(RT-PCR) using the Brilliant single-step quantitative RT-PCR kit
(Stratagene). For detection of EBOV RNA, the 20-µl reaction
contained 2 µl of RNA, 1x RT-PCR buffer, 3 mM
MgCl2, 0.2 µM deoxynucleoside triphosphates, 1 U of
SureStart Taq, 1.25 U of StrataScript reverse transcriptase,
0.4 µM of primer EBOGP-1Dfwd, 0.4 µM of primer
EBOGP-1Drev, and 0.1 µM of the EBOGP-1ZPrb probe
(9). The reactions were
run on an ABI PRISM 7000 (Perkin Elmer) with the following steps: (i)
30 min at 42°C; (ii) 15 min at 95°C; (iii) 45 cycles,
with 1 cycle consisting of 5 s at 95°C and
30 s at 58°C. For detection of MARV, 0.4 µM
primer MBGGP3fwd, 0.4 µM primer MBGGP3rev, and 0.1 µM
MBGGP3prb probe were used
(10). In vitro
transcripts of the target regions were used in the PCR to generate a
standard curve for viral RNA quantification.
For quantitative
analysis of viral RNA within infected cells, total cellular RNA was
isolated using TRIzol (Invitrogen). Total cellular RNA (100 ng) was
denatured for 5 min at 65°C in the presence of 10 nmol
deoxynucleoside triphosphates and 10 pmol primer binding to mRNA,
including L mRNA [oligo (dT)30], genomic RNA (EBOV-18046
forward, 5' GAGTTGATTAGTGTGTGCAATAGGTTTAC
3'), or antigenomic RNA (EBOV-18316 reverse,
5' TAGATCAATATGATGTATGAGAGCAATTTATGAG
3'), respectively. After cooling, the mixture was
complemented with 5 mM dithiothreitol (Invitrogen), 20 U
RNaseOUT (Invitrogen), and 60 U SuperScript III reverse
transcriptase (Invitrogen) in 1x first-strand buffer
(Invitrogen) (final reaction volume of 20 µl). RT was performed
for 1 h at 50°C (mRNA) or for 1 h at
55°C (genomic and antigenomic RNA). After inactivation of the
reverse transcriptase for 15 min at 70°C, 2 µl of each
RT reaction was used as template for quantitative real-time PCR using
the QuantiTect SYBR Green PCR kit (QIAGEN). The 20-µl reaction
contained 2 µl cDNA, 10 µl enzyme mix, and 10 pmol of
primers EBOV-18118 forward (5'
ACCTTATATTTACATAGAATGCAGGATTCTGAAG 3') and
EBOV-18249 reverse (5' TGCAAGTATCAGGATACTATGCACGGT
3'). The reactions were run on a LightCycler (Roche)
with the following steps: (i) 15 min at 95°C and (ii) 45 cycles
of 1 cycle consisting of 15 s at 94°C, 30 s
at 52°C, 15 s at 72°C, and 5 s at
76°C, followed by melting curve analysis. Melting curve
analysis revealed only the presence of the specific
product.
Northern blot analysis.
Total cellular
RNA was isolated using TRIzol (Invitrogen). RNA (3 µg) was
separated on a 1.5% agarose-formaldehyde gel and transferred
onto a Hybond N+ membrane (Amersham Pharmacia Biotech). Primers
BNI-162 (5'
GGCGCAGTCAAGTATTTGGAAG-3') and BNI-163
(5'-TTGTAATACGACTCACTATAGGGAGTTGCTTCTCAGCCTCAGT-3')
were used to generate a Zaire-EBOV NP-specific DNA template
via RT-PCR using SuperScript III reverse transcriptase. To
generate an
-32P-labeled riboprobe, 2 µl of
the DNA template was used in a 20-µl in vitro transcription
reaction mixture containing 1x transcription buffer, 25 U of T7
DNA-dependent RNA polymerase (New England BioLabs), 16 U RNaseOUT, 500
µM each of 5 mM ATP, 5 mM GTP, and 5 mM UTP, and 5 µl
of [
-32P]CTP (15 TBq/mmol; Hartmann Analytic GmbH).
Prehybridization and hybridization were performed as described
previously
(13).
Western blot analysis.
Cells were
washed with phosphate-buffered saline and then lysed in Laemmli loading
buffer (50 mM Tris-HCl, pH 6.8, 15% glycerol, 2% sodium dodecyl sulfate
[SDS], 0.05% bromophenol blue, and 2% ß-mercaptoethanol),
sheared through a 27-gauge needle, and heated for 10 min at
90°C. Proteins were separated by SDS-polyacrylamide gel
electrophoresis (PAGE). After SDS-PAGE, the proteins were transferred
onto nitrocellulose membrane (Schleicher & Schuell). The membrane
was stained with 2.5% fast green in 10% acetic acid for 2
min to visualize blotted proteins. Destaining was performed with 10%
acetic acid for 10 min. The membrane was blocked with 10% Roti Block
(Roth). For detection of ZAP, NZAP-Zeo, or NZAP-Zeo mutants, a rabbit
anti-ZAP antibody (RU-893; kindly provided by M. MacDonald, Rockefeller
University, New York, NY) diluted 1:1,500 was used. Detection of
ZAP-hemagglutinin (HA) was performed using an anti-HA monoclonal
antibody (Covance) at a dilution of 1:10,000. The EBOV NP protein was
detected using a polyclonal goat serum (dilution, 1:5,000; unpublished
data). For detection of glyceraldehyde-3-phosphate dehydrogenase
(GAPDH), a monoclonal antibody (Ambion) was used at a dilution of
1:4,000. Peroxidase-coupled secondary antibodies directed against
rabbit or mouse immunoglobulin (Pierce) were diluted 1:10,000.
Peroxidase-coupled anti-goat antibody (Dianova) was diluted 1:40,000.
Detection of the peroxidase-coupled antibodies was performed with Super
Signal West Pico Chemiluminescent substrate
(Pierce).
Artificial EBOV replicon system.
Huh-T7 cells (5
x 105 in a 7-cm2 well) were transfected
with T7 RNA polymerase promoter plasmids expressing Zaire-EBOV NP (0.5
µg), L protein (1 to 4 µg), VP35 (0.5 µg), VP30
(0.1 µg) (20), a
T7 promoter-driven minigenome encoding Renilla luciferase
reporter (1 µg)
(14), and plasmid
pC-T7Pol (0.5 µg)
(21), as described
previously (3). Different
amounts of plasmid pTM1-ZAP expressing HA-tagged ZAP were added to the
transfection mixture. Empty vector pTM1 was used to keep the amount of
transfected DNA constant. In addition, 0.5 µg pTM1-FFluc
expressing firefly luciferase derived from pGL3-control (Promega) was
added to normalize Renilla luciferase values. Renilla
and firefly luciferase activities were determined 2 days
posttransfection using the Dual-Luciferase Reporter assay system
(Promega) according to the manufacturer's instructions. Replicon
activity was expressed as the Renilla/firefly luciferase
ratio.
Plasmid construction.
Total cellular RNA from
virus-infected cells was isolated by TRIzol (Invitrogen). Reverse
transcription of the RNA was performed using SuperScript III reverse
transcriptase (Invitrogen). DNA fragments were amplified with BioTherm
DNA Polymerase (GeneCraft, Germany) or Phusion DNA Polymerase
(Finnzymes, Finland). To map the sequences responsive to ZAP, mRNAs of
Zaire-EBOV and MARV Musoke were reverse transcribed using primer pairs
matching the sequences of GenBank accession number
AF086833 or Z12132, respectively. The borders of
the amplified genome regions (nucleotide numbers are in parentheses)
for EBOV were the following: NP (56 to 3014), VP35 (3032 to 4396), VP40
(4390 to 5894), GP (5900 to 8307), VP30 (8288 to 9729), VP24 (9885 to
11518), L1 (11501 to 12367), L2 (12083 to 14020), L3 (13501 to 15501),
L4 (15001 to 18271), L4/1 + 2 (15000 to 16802), L4/2 +
3 (15775 to 17610), L4/3 + 4 (16598 to 18271), L4/1 (15000 to
16007), L4/2 (15775 to 16802), L4/3 (16598 to 17610), and L4/4 (17397
to 18271); for MARV they were the following: NP (47 to 2832), VP35
(2851 to 4398), VP40 (4412 to 5807), GP (5822 to 8655), VP30 (8762 to
9998), VP24 (9990 to 11267), L1 (11282 to 13753), L2 (13249 to 15876),
L3 (15218 to 17038), and L4 (16532 to 19017). Fragments derived from
the YFV infectious clone pACNR/FLYF-17x
(5) (kindly provided by
C. M. Rice, Rockefeller University, NY) encompassed the
following nucleotides (in parentheses) according to GenBank accession
number X03700: YF1 (1 to 3212), YF2 (2669 to
5917), YF3 (5401 to 8608), and YF4 (8100 to 10714). Adjacent to the
genome-specific sequences, primer pairs contained either an XbaI or a
BamHI site. Details of the primer sequences are available on request.
In addition, a SIN fragment was amplified from the infectious SIN clone
pToto1101 (24) (kindly
provided by C. M. Rice, Rockefeller University, NY)
using primers BNI-394
(5'-GCTCTAGACCCGTCCTGTTTGGATCATTTG-3')and BNI-395
(5'-GCTCTAGATAGGTAGATGGGTGGATGAT-3').
PCR fragments were cloned either into the XbaI site of
pGL3-Control (Promega) or into the BamHI site of pGL3-B. The latter
plasmid was constructed by removing the original BamHI site. In a
second step, a new BamHI site was introduced next to the XbaI site by
site-directed mutagenesis. Positive orientation of the inserted
sequences was verified by sequencing or digestion with suitable
restriction enzymes.
Mapping of ZAP-sensitive sequences.
Rat2-Zeo, Rat2-NZAP-Zeo,
or Rat2-NZAP-Zeo mutant cell lines were seeded in 24-well plates at 2
x 105 cells per well. The next day, 0.4 µg
of pGL3 derivatives containing virus-specific insertions and 0.1
µg of pRL-TK (Promega) was transfected in serum-free medium
using 2 µl of Lipofectamine 2000 (Invitrogen). Plasmid pRL-TK
is a Renilla luciferase reporter plasmid previously shown not to be
sensitive to ZAP (11)
which was included to normalize the firefly luciferase values. At
5 h after transfection, the medium was exchanged by
Dulbecco's modified Eagle medium containing 10% serum and 100
µg zeocin/ml. At 48 h after transfection, cells were
lysed and Renilla and firefly luciferase activities were
measured using the Dual-Luciferase Reporter assay system according to
the manufacturer's instructions. The level of inhibition was calculated
by forming the ratio between the normalized luciferase activity
expressed in empty Rat2-Zeo cells and the normalized luciferase
activity in Rat2 cells expressing NZAP-Zeo or NZAP-Zeo
mutants.
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RESULTS
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Inhibitory effect of NZAP-Zeo expression on EBOV.
The effect of ZAP on EBOV replication
was studied using cells stably expressing NZAP-Zeo (Rat2-NZAP-Zeo).
Rat2-NZAP-Zeo cells and Rat2 control cells carrying the empty
expression vector (Rat2-Zeo cells) were infected with Zaire-EBOV at an
MOI of 1. First, virus growth was assessed by indirect
immunofluorescence. Rat2-NZAP-Zeo cells showed no signs of Zaire-EBOV
infection, whereas all control cells were infected (Fig.
1A). To quantify the effect of NZAP-Zeo on the growth of Zaire-EBOV more
precisely, virus release was monitored after infection at an MOI of
0.01 and an MOI of 5 using a quantitative real-time RT-PCR assay. As
shown in Fig. 1B,
expression of NZAP-Zeo resulted in a reduction of EBOV-specific RNA in
the supernatant by 3 to 4 log units at both low and high MOIs. The
measurement of infectious virus titer confirmed a reduction by 3 to 4
log units at day 7 postinfection (Fig.
1C). A similar level of
inhibition could also be demonstrated for Sudan-EBOV after infection at
an MOI of 0.01 (Fig. 1C),
indicating that ZAP inhibits different EBOV subtypes.

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FIG. 1. Inhibition
of EBOV replication in Rat2-NZAP-Zeo cells. (A)
Immunofluorescence analysis of NZAP-Zeo-expressing cells infected with
Zaire-EBOV. Rat2-Zeo cells expressing the empty vector or Rat2-NZAP-Zeo
cells expressing the N-terminal portion of ZAP fused to the product of
the zeocin resistance gene were infected with Zaire-EBOV at an MOI of
1. Five days p.i., cells were fixed and immunofluorescence analysis was
performed using a monoclonal antibody directed against Zaire-EBOV NP
protein. (B) Growth kinetics of Zaire-EBOV. Rat2-Zeo cells or
Rat2-NZAP-Zeo cells were infected with Zaire-EBOV at an MOI of 0.01 or
5. The amount of Zaire-EBOV-specific RNA in the supernatant was
quantified using a Zaire-EBOV-specific real-time RT-PCR. The data
represent the means and ranges of duplicate infection experiments.
Dashed line, detection limit. (C) Determination of infectious
virus titer. Rat2-Zeo or Rat2-NZAP-Zeo cells were infected with
Zaire-EBOV or Sudan-EBOV at an MOI of 0.01 or 5. Seven days p.i., the
amount of infectious virus released into the supernatant was determined
by immunofocus assay on Vero-E6 cells. (D) Northern blot
analysis of Zaire-EBOV NP-specific RNA. Rat2-Zeo or Rat2-NZAP-Zeo cells
were infected with Zaire-EBOV at an MOI of 1. Five days p.i., total RNA
was isolated and Northern blot hybridization was performed with a
32P-labeled probe directed against Zaire-EBOV NP RNA.
Noninfected cells served as a control. The methylene blue-stained 28S
RNA is shown below the blot as a semiquantitative marker for gel
loading and RNA
transfer.
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To confirm
the data on the extracellular level of EBOV RNA and infectious
particles, we analyzed the intracellular level of NP-specific mRNA by
Northern blotting. To this end, Rat2-Zeo and Rat2-NZAP-Zeo cells were
infected with Zaire-EBOV at an MOI of 1. EBOV NP mRNA was not
detectable in Rat2-NZAP-Zeo cells, while there was a strong signal in
Rat2-Zeo control cells (Fig.
1D).
Effect of NZAP-Zeo expression on MARV.
In view of the strong inhibitory effect
of NZAP-Zeo on EBOV replication, we wondered if NZAP-Zeo also acts on
viruses of the MARV genus of the filovirus family. Rat2-NZAP-Zeo and
control cells were infected with MARV Musoke at an MOI of 1 and
analyzed by immunofluorescence at 5 days p.i. Both cell lines showed
positive fluorescence signals, indicating that MARV is not completely
blocked (data not shown). However, there was a quantitative reduction
in virus replication. MARV Musoke-specific RNA level in the supernatant
was reduced by 2 log units after infection at an MOI of 0.01 (Fig.
2A). After infection at an MOI of 5, the released viral RNA was reduced up
to 0.5 log units at an early time point (day 3 p.i.) but
eventually reached the level observed for the control cells at late
time points (Fig. 2A).
Infectious virus titer was also reduced by 2 and 1 log units after
infection at an MOI of 0.01 and an MOI of 5, respectively, at day
7 p.i. (Fig.
2B). Infection of Rat2-Zeo
cells with another MARV strain (Popp) induced a severe cytopathic
effect. Interestingly, expression of NZAP-Zeo largely protected the
Rat2 cells from cytopathic effect (data not shown). This finding made
it difficult to compare the level of virus produced by the two cell
lines but suggested that NZAP-Zeo also has an antiviral effect on MARV
Popp. Taken together, representatives of the MARV genus are also
inhibited by NZAP-Zeo, although to a smaller extent compared to
EBOV.

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FIG. 2. Inhibition
of MARV Musoke replication in Rat2-NZAP-Zeo cells. (A)
Rat2-Zeo cells or Rat2-NZAP-Zeo cells were infected with MARV Musoke at
an MOI of 0.01 or 5. The amount of MARV-specific RNA in the supernatant
was quantified using a MARV-specific real-time RT-PCR. The data
represent the means and ranges of duplicate infection experiments.
Dashed line, detection limit. (B) Determination of infectious
virus titer. Rat2-Zeo or Rat2-NZAP-Zeo cells were infected with MARV
Musoke at an MOI of 0.01 or 5. Seven days p.i., the amount of
infectious virus released into the supernatant was determined by
immunofocus assay on Vero-E6 cells. The data represent the means and
ranges of duplicate infection experiments. neg,
negative.
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Inhibition of EBOV and MARV by full-length ZAP.
Since
Rat2-NZAP-Zeo cells express only the N-terminal part of ZAP fused with
the zeocin resistance gene product, it was investigated if full-length
ZAP without heterologous sequences also possesses anti-filovirus
activity. For these experiments, 293TRex cells inducibly expressing
full-length ZAP (293TRex-ZAP) were used. After induction of ZAP
expression, cells were infected with EBOV and MARV at an MOI of 0.1.
Noninduced cells served as a control. Expression of ZAP reduced the
titer of Zaire-EBOV and Sudan-EBOV by 4 log units 4 days p.i. (Fig.
3A). In contrast to Rat2-Zeo cells, growth of MARV Popp did not result in a
CPE in 293TRex-ZAP cells. Therefore, both MARV Musoke and MARV Popp
could be included in the testing. Induction of ZAP reduced viral titers
of the MARV strains by nearly 1 log unit (Fig.
3A). The
expression level of ZAP in noninduced and induced cells was verified at
day 4 p.i. by Western blot analysis (Fig.
3B). Taken together, these
data demonstrate that the antiviral effect observed with NZAP-Zeo
correspond to that of the natural ZAP gene
product.

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FIG. 3. Inhibition
of filovirus replication in 293TRex-ZAP cells. (A) ZAP
expression was induced with doxycycline in 293TRex-ZAP cells, and
6 h later cells were infected with Zaire-EBOV or Sudan-EBOV
(upper panel) as well as MARV Musoke or MARV Popp (lower panel) at an
MOI of 0.1. Noninduced cells served as a control. Four days p.i., the
amount of infectious virus released into the supernatant was determined
by immunofocus or plaque assay on Vero-E6 cells. The data represent the
means and ranges of duplicate infection experiments. (B)
Western blot analysis of ZAP induction in 293TRex-ZAP cells.
Zaire-EBOV- and MARV Popp-infected noninduced and induced 293TRex-ZAP
cells used for the experiments shown in panel A were lysed 4 days p.i.
and analyzed by Western blotting. Detection of ZAP was performed using
a polyclonal anti-ZAP antibody. As a loading control, GAPDH was
detected using an anti-GAPDH monoclonal
antibody.
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Role of zinc finger motifs of NZAP-Zeo for its antiviral activity against filoviruses.
The N terminus of ZAP contains four
CCCH-type zinc finger motifs. The integrity of the second and fourth
zinc finger motif of ZAP is important for its antiviral effect against
MMLV and SIN (11). To
determine the importance of each zinc finger for inhibition of EBOV
replication, cell lines expressing NZAP-Zeo variants with single
mutations in each zinc finger (H86K, C88R, C168R, and H191R)
(11) were infected with
Zaire-EBOV and Sudan-EBOV at an MOI of 0.01. Viral titers were
determined 7 days p.i. to calculate the level of inhibition for each
mutant. Disruption of the second (C88R) and fourth (H191R) finger
largely abolished the capability of NZAP-Zeo to inhibit growth of EBOV
(Fig.
4A). The loss of inhibitory activity compared to that of wild-type NZAP-Zeo
was in the range of 3 log units for both EBOV subtypes (Fig.
4A). Disruption of the
first (H86K) and third (C168R) zinc finger had a lower impact on the
anti-EBOV activity of NZAP-Zeo (Fig.
4A). A similar inhibition
pattern was also observed for MARV Musoke, although the loss of
NZAP-Zeo activity for the H191R mutant was not as dramatic as found for
EBOV (Fig. 4A).

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FIG. 4. Effect
of mutations within the zinc finger motifs of ZAP on its antiviral
activity. (A) Rat2 cells expressing wild-type NZAP-Zeo or
mutants containing single amino acid exchanges (H86K, C88R, C168R, or
H191R) were infected with Zaire-EBOV, Sudan-EBOV, or MARV Musoke at an
MOI of 0.01. Seven days p.i., the infectious virus titer was determined
by immunofocus assay. Data represent means and ranges of duplicate
infection experiments. Dashed line, immunofocus assay detection limit.
(B) Level of NZAP-Zeo mutant protein expressed by cell lines
as detected by Western blot analysis. Rat2-Zeo cells, Rat2-NZAP-Zeo
cells, and Rat2 cells expressing NZAP-Zeo mutants containing the single
amino acid exchange H86K, C88R, C168R, or H191R were lysed in Laemmli
loading buffer. Proteins were separated by SDS-PAGE and transferred
onto a membrane. NZAP-Zeo and NZAP-Zeo mutants were detected using a
polyclonal anti-ZAP antibody. As a loading control, detection of GAPDH
using an anti-GAPDH monoclonal antibody was
performed.
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To
verify that the different levels of antiviral activity are not due to
different expression levels of the individual ZAP mutants, their
expression levels were analyzed by Western blot analysis. As shown in
Fig. 4B, all cell lines
expressed comparable levels of NZAP-Zeo protein. In conclusion, the
integrity of the second and fourth zinc finger motif is important for
the anti-filoviral effect of
NZAP-Zeo.
Mapping of EBOV and MARV sequences targeted by ZAP.
Previous studies indicated that ZAP
targets and destabilizes specific genomic sequences of MMLV and SIN
(11). Antiviral effects
of ZAP against filoviruses may also involve reduction of virus-specific
RNA. To test this hypothesis, Zaire-EBOV- and MARV Musoke-specific
sequences covering all genes were cloned into a simian virus 40 (SV40)
promoter-driven luciferase reporter plasmid between the 3' end
of the luciferase gene and a poly(A) signal (Fig.
5A). These constructs express fusion mRNAs containing the
luciferase gene at the 5' end and filovirus sequences at the
3' end. Thus, targeting the filovirus sequences by ZAP will
lead to reduced luciferase expression. The sequences coding for
filovirus L protein were divided into four overlapping fragments (L1 to
L4). Otherwise, the sequences of complete EBOV and MARV genes were
tested. In addition, a SIN fragment previously shown to be sensitive to
ZAP (11) was included as
a positive control. The resulting plasmids were transfected into
Rat2-NZAP-Zeo and control cells, and the level of RNA reduction by ZAP
was calculated from the luciferase activity in cells expressing
NZAP-Zeo relative to control cells (Fig.
5A). The highest level of
inhibition was observed for the L4 fragments of L gene of Zaire-EBOV
and MARV Musoke (Fig. 5A).
Other viral sequences were also targeted, although to a smaller extent.
To map potential target sequences of ZAP more precisely, the L4
fragment was divided into three overlapping fragments of
about 1.8 kb in size (L4/1 + 2, L4/2
+ 3, and L4/3 + 4) or into four overlapping fragments
of about 1 kb in size (L4/1, L4/2, L4/3, and L4/4) (Fig.
5B). Surprisingly,
luciferase expression of all three SV40 expression constructs
containing 1.8-kb L fragments was inhibited to a similar extent as that
observed for L4 (Fig. 5B).
However, dividing the L4 fragment into 1-kb fragments resulted in the
loss of ZAP-mediated inhibition, suggesting that the length
of the RNA fragment is important for the effect of
ZAP.

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FIG. 5. Mapping
of ZAP target sequences in Zaire-EBOV and MARV Musoke genomes.
(A) cDNA fragments of Zaire-EBOV- and MARV Musoke-specific
genes were cloned into pGL3 or pGL3-B between the firefly luciferase
gene and poly(A) site. Inserted sequences as well as the
approximate size of each insert (in kilobases) are indicated below each
bar. The L genes were divided into four fragments (L1 to L4). SIN
corresponds to a SIN genome fragment known to be sensitive to ZAP. The
plasmids were transfected into Rat2-Zeo or Rat2-NZAP-Zeo cells.
Cotransfection of a plasmid not sensitive to ZAP encoding
Renilla luciferase (pRL-TK) was used to normalize firefly
luciferase values. Cells were lysed 48 h posttransfection,
and luciferase activity was measured. The inhibition (n-fold)
was calculated as the normalized luciferase activity in
Rat2-Zeo cells divided by the normalized luciferase activity in
Rat2-NZAP-Zeo cells. Data are means and ranges of duplicate
transfection experiments. (B) The EBOV
L4 fragment
was further divided into three or four overlapping fragments. A
schematic representation of the fragments is shown at the left.
Transfection and calculation of inhibition was performed as described
for panel A. Numbers in brackets depict the approximate size of the
inserts in kilobases. Data represent means and ranges of duplicate
transfection experiments. (C) Four overlapping sequences covering the
genome of YFV (YF1 to YF4) were inserted into pGL-3. The size of each
insert (in kilobases) is shown in brackets. Transfection and
calculation of inhibition was performed as described for panel A. Data
represent means and ranges of duplicate transfection experiments. (D)
The pGL-3 plasmid containing the EBOV L4 fragment was used to analyze
the activity of NZAP-Zeo zinc finger mutants in the luciferase reporter
assay. Transfection was performed with Rat2 cells expressing NZAP-Zeo
mutants (H86K, C88R, C168R, or H191R). Empty pGL3 was used as a
control. Transfection and calculation of inhibition was performed as
described for panel A. Data represent means and ranges of duplicate
transfection
experiments.
|
|
In order to demonstrate the specificity of the effect, it
was tested whether YFV sequences are susceptible to ZAP in our system.
It has been demonstrated previously that YFV replication is not
inhibited by ZAP (2). Four
overlapping fragments of about 3 kb covering the complete 11-kb YFV
genome were tested in the luciferase reporter assay. As shown in Fig.
5C, the level of
inhibition of all constructs was similar to that of the negative
control vector pGL3. Taken together, the data of both sets of
experiments indicate that sequence-specific features of the inserted
fragment rather than its size per se are relevant to mediate the effect
of ZAP.
To test if the integrity of the zinc fingers is important
for the effect of ZAP on the EBOV L4 fragment, the SV40 promoter
construct containing this fragment was transfected into the Rat2 cell
lines expressing NZAP-Zeo mutants. As shown in Fig.
5D, ZAP lost its
destabilizing effect on the L4 fragment if the second and fourth zinc
finger motif was mutated (C88R and C168R mutant cell lines,
respectively). In conclusion, the inhibitory effect of ZAP on EBOV
replication in cell culture correlates with its ability to interfere
with expression of mRNA containing EBOV L4
sequence.
Effect of ZAP on L mRNA level during EBOV infection.
To
provide evidence that L mRNA is a target for ZAP in the natural context
of a virus infection, the levels of L-gene-specific mRNA as well as
genomic and antigenomic RNAs were monitored during viral infection. To
this end, 293TRex-ZAP cells were infected with Zaire-EBOV at an MOI of
3. ZAP expression was induced 1 h following inoculation to
exclude potential interference of ZAP with virus entry. Total cellular
RNA was isolated from induced and noninduced cells at different time
points after infection. The RNA was reverse transcribed with primers
specifically binding to either mRNA (including L mRNA), genomic RNA, or
antigenomic RNA (Fig.
6A). The levels of the three different cDNAs were determined
using a real-time PCR assay targeting the 3' end of the L gene
(Fig. 6A). All three RNA
species were reduced in induced versus noninduced cells between
16 h and 24 h after infection. Importantly, L mRNA
levels were already reduced by up to 1 log unit in ZAP-expressing cells
at 6 h and 10 h after infection (Fig.
6B), while there was no
evidence for an effect of ZAP on the level of genomic and antigenomic
RNA at this time (Fig. 6C and
D). These data indicate that ZAP interferes with L mRNA
synthesis or stability during natural infection. Since the level of
genomic RNA was not yet affected at early time points, the effect
cannot be mediated by a reduction of the transcriptional template of L
mRNA. Reduction of genome and antigenome at a later phase
might be due to reduced expression of L mRNA, and
thus L protein, or due to additional effects of ZAP on genome
replication.

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FIG. 6. Effect
of ZAP on levels of L mRNA, genomic RNA, and antigenomic RNA during
Zaire-EBOV infection. (A) Experimental strategy for
quantification of Zaire-EBOV L mRNA, genomic RNA, and antigenomic RNA.
Reverse transcription was performed with primers (large arrows)
specifically binding either mRNA (RT-mRNA), genomic RNA (RT-g), or
antigenomic RNA (RT-ag). The synthesized cDNA was quantified by
real-time PCR using primers targeting the 3' end of the L gene
(small arrows). UTR, untranslated region; L, L gene. (B to D)
293TRex-ZAP cells were infected with Zaire-EBOV at an MOI of 3 for
1 h. After removing the inoculum, cells were induced with
doxycycline. Noninduced cells served as controls. Total cellular RNA
was isolated at various time points p.i. Zaire-EBOV-specific L mRNA
(B), genomic RNA (C), and antigenomic RNA (D) were quantified
using the PCR method as described for panel A. The amount of RNA
derived from the inoculum (0 h) was defined as 1 (0 after log
transformation).
The average cyclic threshold (Ct) values at
0 h were the following: L mRNA, Ct
= 29; genome, Ct = 22; antigenome,
Ct = 26. Control reactions lacking reverse
transcriptase were negative in the real-time PCR (data not shown). Data
represent means and ranges of duplicate infection experiments (most
error bars are obscured by the
symbols).
|
|
Inhibition of EBOV replicon system by ZAP and effect of L protein overexpression.
Replication and transcription of an
artificial EBOV minigenome is dependent on the expression of NP, L
protein, VP35, and VP30. ZAP expression is expected to inhibit replicon
activity if it reduces the L mRNA level or affects other steps of EBOV
replication and gene expression. To test this hypothesis, expression
plasmids for NP, L protein, VP35, VP30, and an EBOV-specific minigenome
expressing Renilla luciferase as a reporter were cotransfected
with increasing amounts of a plasmid expressing HA-tagged ZAP.
pTM1-FFluc expressing firefly luciferase was included to correct for
variation in transfection efficacy and unspecific effects of ZAP.
Firefly and Renilla luciferase activities were measured 2 days
posttransfection. As little as 10 ng of ZAP-expressing plasmid was
sufficient to reduce reporter gene expression by 30% (Fig.
7). Increasing the amount of ZAP reduced the replicon activity by up to
95%, while there was no major change in NP level as measured by Western
blot analysis (Fig.
7).

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FIG. 7. Inhibition
of Zaire-EBOV replicon system by ZAP. Huh-T7 cells were transfected
with plasmids encoding Zaire-EBOV NP, L protein, VP35, VP30, and
minigenome containing a Renilla luciferase gene. Increasing
amounts of plasmid encoding ZAP-HA were cotransfected as indicated
(ctrl, negative control without L plasmid; +ctrl,
positive control without ZAP-HA plasmid). Empty vector pTM1 was used to
keep the amount of transfected DNA constant. Plasmid pTM1-FFluc was
included to normalize Renilla luciferase values. Luciferase
activities were determined 2 days posttransfection. The expression
levels of ZAP-HA and EBOV NP were analyzed by Western blot using
anti-HA monoclonal antibody and anti-Zaire-EBOV polyclonal antibody,
respectively (bottom). The amount of cell lysate loaded on the protein
gel was adjusted according to the firefly luciferase values to ensure
comparability with the normalized Renilla values. The levels
of GAPDH served as a loading
control.
|
|
If decreased
expression of L protein was indeed involved in reduced luciferase
expression by the minigenome, it might be possible to rescue replicon
activity by increasing the amount of L protein in the cell. To this
end, the amount of L protein expression plasmid in the transfection
mixture was increased stepwise from 1 µg to 4 µg. The
replicon components were transfected in the absence of ZAP or in the
presence of 0.5 µg or 2 µg ZAP expression plasmid (Fig.
8A). Increasing the amount of L protein expression plasmid had no effect on
ZAP expression, as demonstrated by Western blot analysis (Fig.
8B). In the absence of
ZAP, luciferase gene expression was not changed by increased L protein
levels (Fig. 8A). However,
if the replicon was suppressed by cotransfection of 0.5 µg ZAP
expression plasmid, overexpression of L protein increased replicon
activity about twofold (Fig.
8A). A similar partial
rescue effect was seen if 2 µg ZAP expression plasmid was
transfected. In both experiments, a saturation effect was observed upon
transfection of
3 µg L protein plasmid, suggesting
that ZAP exerts additional inhibitory effects that are not related to L
protein expression. Western blot analysis demonstrates that at least NP
expression is not affected by ZAP (Fig.
8B). In conclusion, the
experiments indicate that increased levels of L protein can partially
compensate for the inhibitory effect of ZAP on replicon activity, which
is consistent with the observation that ZAP reduces the L mRNA level
during natural
infection.

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FIG. 8. Effect
of L-protein overexpression on ZAP-induced inhibition of the Zaire-EBOV
replicon system. (A) Huh-T7 cells were transfected with
plasmids encoding Zaire-EBOV NP, VP35, VP30, increasing amounts of
L-protein expression plasmid, and a minigenome containing a
Renilla luciferase gene (ctrl, negative control
without L plasmid). Different amounts of ZAP-HA expression plasmid were
cotransfected. Empty vector pTM1 was used to keep the amount of
transfected DNA constant. Plasmid pTM1-FFluc was included to normalize
Renilla luciferase values. (B) Expression levels of
ZAP-HA and EBOV NP were analyzed by Western blot using anti-HA
monoclonal antibody and anti-Zaire-EBOV polyclonal antibody,
respectively. The amount of cell lysate loaded on the protein gel was
adjusted according to the firefly luciferase values to ensure
comparability with the normalized Renilla values. The levels
of GAPDH served as a loading
control.
|
|
 |
DISCUSSION
|
|---|
This study
provides evidence that ZAP has an antiviral effect against EBOV and
MARV in cell culture. The growth of Zaire-EBOV and Sudan-EBOV was
inhibited by several orders of magnitude. The antiviral effect against
MARV was less pronounced, suggesting that the degree of inhibition is
dependent on the filovirus species. Similar observations have been made
for members of the alphavirus genus. While SIN was strongly inhibited
by 3 to 8 log units, NZAP-Zeo expression affected replication of
Semliki Forest virus and Ross River virus to a lesser degree
(2). Taking these data
together, it seems that ZAP is active against various members within
one virus family, although to different levels. Furthermore, our data
demonstrate that the activity of ZAP is not restricted to plus-strand
RNA viruses and retroviruses.
As described for MMLV and SIN, the
second and fourth zinc finger motifs particularly were important for
the anti-filoviral effect. This finding suggests that the mechanism of
action is similar for plus- and negative-strand RNA viruses, although
the precise mechanism is not known. The fact that RNA viruses
replicating solely in the cytoplasm are affected suggests that ZAP
exerts its effects in the cytoplasm. Consistent with this speculation,
specific reduction of the cytoplasmic viral RNA levels of MMLV
(8) and inhibition of
translation of incoming SIN RNA have been described
(2). Further studies
indicated that specific regions within the MMLV and SIN genomes are
targeted by ZAP, leading to destabilization of the respective viral
RNAs (11). Using the same
assay as has been used in these studies, we identified a 3.2-kb
sequence within the L gene of EBOV and a 2.5-kb sequence within the L
gene of MARV to be sensitive to ZAP. The precise target region on EBOV
RNA could not be mapped, since all 1.8-kb subfragments appeared to be
targeted by ZAP, suggesting that the L4 fragment contains several
target sites. However, reducing the fragment size to 1 kb resulted in a
drastic loss of inhibition, indicating that a minimum sequence length
is required for interaction with ZAP. On the other hand, the control
experiments with the long YFV sequences indicate that the inhibition
observed in the luciferase reporter assay does not simply correlate
with the size of the inserted fragment. The precise mechanism of
interaction of ZAP with the L-gene sequences is not clear. Guo et al.
showed that ZAP directly binds to SIN RNA
(11). We assume that the
effect seen with filovirus sequences also stems from destabilization of
virus RNA, although the data do not exclude a role of ZAP at the level
of RNA transcription or translation. The observations that ZAP is
active in three different expression systems, i.e., (i) in an SV40
expression system, which is dependent on cellular RNA polymerase II;
(ii) in the context of viral infection, where mRNA synthesis is
dependent on the viral RNA polymerase; and (iii) in an artificial
replicon system, where mRNA synthesis is driven by T7 RNA polymerase,
do not argue for an effect of ZAP on promoter or RNA
polymerase.
In addition to the luciferase gene-L mRNA fusion
experiments, two lines of evidence suggest that L mRNA is a target of
ZAP. First, L mRNA was reduced early after EBOV infection when the
level of genomic RNA still corresponded to that of the inoculum. This
largely excludes that the reduction of L mRNA is due to degradation of
its transcriptional template. Synthesis of antigenomic RNA, which
shares the L gene sequence with the L mRNA, was also reduced in cells
expressing ZAP. However, the synthesis of new antigenomic RNA initiated
later than that of L mRNA. Therefore, it cannot be distinguished if the
antigenomic RNA is also a target for ZAP or if its decrease is a result
of reduced synthesis of L protein. It might be that ZAP is not acting
on antigenomic RNA, as it is encapsidated by the NP. The second
observation arguing for an interference of ZAP with L gene expression,
presumably at the level of mRNA, was that the inhibitory effect of ZAP
in the artificial replicon system could be partially compensated for by
overexpression of L protein. The partial nature of the rescue effect
suggests that there exist additional targets of ZAP.
The data
obtained with the artificial replicon system also indicate that
transiently expressed ZAP is functional. Thus, vector-driven expression
of ZAP might be a tool to downregulate filovirus replication.
Alternatively, upregulation of endogenous ZAP could have a protective
or therapeutic effect. The gene encoding human ZAP is localized on
chromosome 7 (Ensembl Gene ID ENSG00000105939). Two isoforms of about
100 and 77 kDa in size exist, probably representing two splice
variants. Further studies will elucidate if human ZAP is active against
filoviruses and plays a role in the innate response of
humans.
 |
ACKNOWLEDGMENTS
|
|---|
We thank Angelika Lander
for expert technical assistance. We thank Margaret MacDonald
and Guangxia Gao for providing plasmids pBabe-Haz,
pBabe-NZAP-Zeo (wild-type and zinc finger mutants), Rat2-Zeo cells,
Rat2-NZAP-Zeo cells (wild-type and zinc finger mutants), and
293TRex-ZAP cells; V. Gauss-Müller for providing the Huh-T7
cells; C. M. Rice for providing plasmids pToto1101 and
pACNR/FLYF-17x; T. Takimoto and Y. Kawaoka for the plasmid pC-T7Pol;
and Christian Drosten for critical reading of the
manuscript.
This work was supported by the Deutsche
Forschungsgemeinschaft, Sonderforschungsbereich 535 TP A13 and 593 TP
B3, and by the Land Hessen through a fellowship to Peggy Möller.
The Bernhard-Nocht-Institute is supported by the Bundesministerium
für Gesundheit and the Freie und Hansestadt
Hamburg.
 |
FOOTNOTES
|
|---|
* Corresponding
author. Mailing address: Department of Virology, Bernhard-Nocht-Strasse
74, Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg,
Germany. Phone: 49 40 42818 454. Fax: 49 40 42818 378. E-mail:
kuemmerer{at}bni.uni-hamburg.de. 
Published ahead of print on 20 December 2006. 
S. Müller and P. Möller contributed equally to this paper. 
Present
address: The Rockefeller University, 1230 York Avenue, New York, NY
10021. 
Present
address: Robert Koch-Institute, Nordufer 20, 13353 Berlin,
Germany. 
 |
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