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Journal of Virology, March 1999, p. 2222-2231, Vol. 73, No. 3
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Modulation of Nuclear Localization of the Influenza
Virus Nucleoprotein through Interaction with Actin Filaments
Paul
Digard,1,*
Debra
Elton,1
Konrad
Bishop,1
Elizabeth
Medcalf,1
Alan
Weeds,2 and
Brian
Pope2
Division of Virology, Department of
Pathology, University of Cambridge, Cambridge CB2
1QP,1 and
Medical Research Council
Laboratory of Molecular Biology, Cambridge CB2
2QH,2 United Kingdom
Received 16 September 1998/Accepted 1 December 1998
 |
ABSTRACT |
The influenza virus genome is transcribed in the nuclei of infected
cells but assembled into progeny virions in the cytoplasm. This is
reflected in the cellular distribution of the virus nucleoprotein (NP),
a protein which encapsidates genomic RNA to form ribonucleoprotein structures. At early times postinfection NP is found in the nucleus, but at later times it is found predominantly in the cytoplasm. NP
contains several sequences proposed to act as nuclear localization signals (NLSs), and it is not clear how these are overridden to allow
cytoplasmic accumulation of the protein. We find that NP binds tightly
to filamentous actin in vitro and have identified a cluster of residues
in NP essential for the interaction. Complexes containing RNA, NP, and
actin could be formed, suggesting that viral ribonucleoproteins also
bind actin. In cells, exogenously expressed NP when expressed at a high
level partitioned to the cytoplasm, where it associated with F-actin
stress fibers. In contrast, mutants unable to bind F-actin efficiently
were imported into the nucleus even under conditions of high-level
expression. Similarly, nuclear import of NLS-deficient NP molecules was
restored by concomitant disruption of F-actin binding. We propose that the interaction of NP with F-actin causes the cytoplasmic retention of
influenza virus ribonucleoproteins.
 |
INTRODUCTION |
The influenza A virus genome
consists of eight segments of negative-sense single-stranded RNA (vRNA)
which are transcribed in infected cells to yield two types of
positive-sense transcripts: capped and polyadenylated mRNAs and exact
complements (cRNA) which serve as replicative intermediate RNAs for the
production of further vRNAs (18). Four viral proteins are
necessary and sufficient to carry out this process (16): the
three subunits of an RNA-dependent RNA polymerase (PB1, PB2, and PA)
and a 55-kDa single-stranded RNA-binding nucleoprotein (NP). Indeed,
the v- and cRNA segments are always associated with these polypeptides
to form ribonucleoprotein (RNP) structures, thought to comprise one
copy of the trimeric polymerase and approximately one NP polypeptide
per 20 bases of RNA (18).
Unusually for a virus with no DNA coding stage, influenza virus
transcription occurs in the nuclei of infected cells (15). Thus, on initiation of infection the incoming RNPs are targeted to the
nucleus, and during infection newly synthesized RNP proteins also
undergo nuclear import. Consistent with this, nuclear localization signals (NLSs) have been identified in all four transcriptase proteins
(9, 25, 26-28, 41, 41a), including three in NP, the major
protein component of RNPs. At early times postinfection, the polymerase
subunits and NP accumulate in the nucleus (reviewed in reference
18), and NP has been shown to be necessary for the
nuclear import of vRNA in permeabilized cells (30). However, virion assembly, including packaging of progeny RNPs, occurs in the
cytoplasm and at later times this is reflected in the cytoplasmic accumulation of the four transcriptase proteins, generally assumed to
be in the form of RNPs (18). This differential localization of RNPs necessitates regulatory mechanisms, and evidence points to the
involvement of at least three viral polypeptides: the virion matrix
(M1) protein, the minor virion component NS2, and NP itself. M1 is
capable of binding to membranes, RNA, NS2, and RNPs. In the virion, it
is thought to act as the link between the lipid envelope and the
packaged genome segments (44). Moreover, M1 itself can
localize to the nucleus, where it is thought to promote the export of
RNPs (22, 43). NS2, which binds to RNPs via the M1 protein
(47), has recently been shown to possess a nuclear export
signal (31). Microinjected anti-NS2 antibodies inhibit export of RNPs, and it has therefore been proposed that NS2 is the
viral factor directly responsible for the export of RNPs from the
nucleus (31). Accordingly, import of NP (and RNPs early in
infection) can be postulated to occur because of the presence of NLSs
and export can be postulated to occur because of the subsequent expression of components (M1 and NS2) that target RNPs to an export pathway (31, 44). However, this hypothesis does not fully explain why RNPs accumulate in the cytoplasm in the absence of M1
export (33, 42) or why a mutant influenza virus which
synthesizes very little or no NS2 is fully replication competent
(36, 45). Moreover, since vRNA synthesis is not temporally
separated from RNP export, it is not clear how import of newly
synthesized NP is maintained in the presence of active export of the
same polypeptide in the form of RNP complexes, or why cytoplasmic RNPs
are not simply reimported back into the nucleus by virtue of
their polyvalent NLS sequences. Therefore, there must be other elements
involved in the control of RNP localization.
NP possesses the ability to locate to both cytoplasm and nucleus. In
the absence of other viral proteins, it shuttles between the two
compartments (43), which suggests that it interacts with the
cellular nuclear export apparatus in the absence of M1 and NS2. NP can
also accumulate in the cytoplasm at "late" times postexpression
(27), indicating that the activities of the NP NLSs are
modulatable. Therefore, RNP localization may also be regulated by
mechanisms acting through NP. One well-documented way of modulating
nuclear import is through interactions with cytoplasmic anchoring
proteins (29, 40), and recent work involving cell
fractionation and fluorescent staining experiments has suggested that
cytoplasmic NP is associated with the cytoskeleton (3, 17).
Here we demonstrate that purified NP shows high-affinity binding to
filamentous actin (F-actin) in vitro with a Kd
on the order of 1 µM and a stoichiometry of 1 per actin subunit.
Additionally, there is a further interaction of lower affinity which
may reflect oligomerization of NP itself. We also show the formation of
complexes containing NP, RNA, and actin and have identified a cluster
of amino acid residues in NP important for the interaction with
F-actin. Localization of exogenously expressed NP was found to depend
on the amount expressed, with small amounts entering the nucleus and
large amounts accumulating in the cytoplasm, where the protein colocalizes with F-actin. Mutations in NP which decrease F-actin binding change the cellular distribution of the protein, favoring accumulation in the nuclei even when the expression level is high. We
propose that F-actin binding acts as a cytoplasmic retention signal for NP.
 |
MATERIALS AND METHODS |
Plasmids, antisera, and viruses.
A cDNA copy of A/PR8/34
segment 5 was excised from plasmid pVB5+ (6) with
EcoRI and ligated into similarly linearized plasmid pMAL-c2
(New England Biolabs). The NP and maltose binding protein (MBP) open
reading frames (ORFs) were then fused by oligonucleotide-directed mutagenesis. The resulting plasmid (pMAL-NP) contains the
lac promoter, the MBP gene, a factor Xa protease recognition
site, an alanine codon, and the NP ORF (with an NcoI
restriction enzyme site flanking the initiation codon). Point mutations
were introduced into this plasmid by standard procedures. All mutations
were confirmed by nucleotide sequencing of the appropriate region of
the NP gene. To construct a glutathione S-transferase
(GST)-NP fusion protein, plasmid pMAL-NP was digested with
NcoI, end filled with the Klenow fragment of DNA polymerase,
and digested with EcoRI. The DNA fragment containing the NP
ORF was then ligated into SmaI-EcoRI-cut plasmid pGEX-2T (Pharmacia) to create plasmid pGEX-NP. To obtain eukaryotic expression of nonfused NP, NP genes were excised from the pMAL constructs by digestion with NcoI and XbaI and
inserted into similarly digested plasmid pKT0 (39). The
resulting plasmids (pKT5 series) contain the NP gene under control of a
T7 RNA polymerase promoter.
Antisera against NP were raised by immunizing rabbits with a
-galactosidase fusion protein containing amino acids 340 to 498 of
A/PR8/34 NP. Rabbit antiserum to RNP cores was the generous gift of S. Inglis.
Recombinant vaccinia viruses expressing the three influenza virus
A/PR8/34 P proteins and NP (37) or bacteriophage T7 RNA polymerase (vTF-7 [11]) have previously been described.
Expression and purification of NP.
Exponentially growing
cultures of Escherichia coli TG1 containing plasmid pMAL-NP,
pGEX-NP, or pGEX-2T were induced by the addition of
isopropyl-thiol-
-galactosidase and incubated with shaking for a
further 4 h. Bacteria were pelleted by centrifugation and
resuspended in a 1/5 culture volume of amylose column buffer (ACB) (500 mM NaCl, 20 mM Tris-Cl [pH 7.6], 1 mM EDTA, 0.02% sodium azide)
(pMAL) or phosphate-buffered saline (PBS) (pGEX), containing 0.25 µg
of lysozyme per ml. After incubation for 30 min on ice and overnight at
20°C, the suspension was thawed and sonicated before centrifugation
at an average of 9,000 × g for 30 min. The supernatants were sequentially filtered through Whatman no. 1 filter
paper and a 0.45-µm-pore-size cellulose acetate filter before
chromatography over amylose resin (New England Biolabs) or glutathione
Sepharose (Pharmacia) as appropriate. Columns were washed sequentially
with 10 volumes of ACB or PBS, 10 volumes of buffer containing 2 M
NaCl, and another 10 volumes of ACB or PBS. Bound protein was eluted
with buffer supplemented with 10 mM maltose or 50 mM reduced glutathione.
The MBP moiety of MBP-NP was removed by the addition of 2 mM
CaCl
2 and 0.5% (wt/wt) factor Xa protease (New England
Biolabs)
in an overnight incubation at 14°C. All polypeptides
displayed
the expected mobilities on sodium dodecyl
sulfate-polyacrylamide
gel electrophoresis (SDS-PAGE) gels (see Fig.
1)
and reacted as
predicted in Western blots using anti-MBP, -GST, and -NP
sera
(data not shown). Protein microsequencing confirmed the predicted
N-terminal sequence for NP cleaved from MBP. Proteins were either
dialyzed or gel filtered into 50 mM NaCl-10 mM HEPES (pH 8)-0.1
mM
EDTA-10% glycerol (storage buffer) and kept at 4 or

70°C.
Protein
concentrations were determined by the Bradford method
(
7) or
by absorbance at 280 nm with a molar extinction coefficient
of 119,000 M
1 · cm
1 calculated according to the
formula of Gill and von Hippel (
13).
All samples were
clarified by centrifugation at an average of
390,000 ×
g for 15 min before
use.
Actin-binding assays.
Purified rabbit muscle actin
(38) was polymerized in 100 mM NaCl-10 mM Tris-Cl (pH
8.0)-1 mM MgCl2-0.1 mM ATP-0.2 mM EGTA-1 mM
sodium azide (F buffer). Sedimentation assay mixtures contained 3 µM
actin in 50 mM NaCl-10 mM HEPES (pH 7.6)-1 mM MgCl2-10%
glycerol-0.1 mM EDTA-0.1 mM ATP in a final volume of 100 µl. After
being mixed, the samples were centrifuged at an average of 200,000 × g for 20 min at 20°C before separation into pellet and
supernatant fractions. Equivalent amounts of the two fractions were
analyzed by SDS-PAGE and stained with Coomassie brilliant blue dye.
Quantitation was performed by using a Molecular Dynamics computing
densitometer (32). For electron microscopy, actin (1 µM)
and MBP or MBP-NP were mixed in F buffer and left on ice for 20 min.
Drops (30 µl) were applied to carbon-coated grids for 1 min and then
grids were rinsed with 5 drops of F buffer and 5 drops of 1% uranyl
acetate before being blotted dry and viewed in a Philips 208S electron microscope at a magnification of 20,000 or 30,000.
RNA transcription and binding assays.
For in vitro RNA
binding assays, a radiolabelled 178-nucleotide synthetic RNA target was
generated by in vitro transcription of plasmid pKT8-
3'5' (generous
gift of K. Tibbles) with bacteriophage T7 RNA polymerase in the
presence of
-[32P]CTP (100 µM; specific activity, 2 Ci/mmol) according to standard procedures. The transcript corresponds
to influenza virus A/PR8/34 segment 8 but with nucleotides 84 to 795 (inclusive) deleted and a C-to-A transversion of the penultimate base.
Shorter transcripts corresponding to the minimal terminal repeat
("panhandle") sequences or only the 3' end of segment 8 were
generated by in vitro transcription of the appropriate oligonucleotide
templates cloned into plasmid pNEB193 (New England Biolabs). For in
vivo RNA transcription assays, a synthetic influenza virus genome
segment containing an antisense chloramphenicol acetyltransferase (CAT)
gene was produced by in vitro transcription of plasmid pPB2CAT
(generous gift of Mark Krystal). Filter binding assays were performed
by incubating protein samples with 20 fmol of RNA (around 5,000 cpm) in
25 mM Tris-Cl (pH 7.6)-50 mM NaCl-5 mM MgCl2-0.5 mM
dithiothreitol-5% glycerol at room temperature for 20 min. The
reaction mixtures were passed through nitrocellulose filters
equilibrated in 20 mM Tris-Cl (pH 7.6)-50 mM NaCl and washed three
times with 200 µl of the same buffer. Bound radioactivity was
quantified by liquid scintillation counting.
Transfection of tissue culture cells, transient replication
assays, and indirect immunofluorescence.
BHK cells (in
35-mm-diameter dishes) were infected with recombinant vaccinia viruses
at a multiplicity of infection of 5 of each virus per cell for 2 h
at 37°C. The cells were washed three times with serum-free medium
before transfection with 1 µg of plasmid DNA encoding NP and 0.5 µg
of pPB2CAT9 in vitro-transcribed RNA and 10 µg of a cationic liposome
mixture (Lipofectin [GIBCO-BRL] or Escort [Sigma-Aldrich]),
according to the manufacturers' instructions. The cells were incubated
at 37°C for 20 h, washed three times with ice-cold PBS, and
solubilized in 1 ml of CAT ELISA lysis buffer (Boehringer Mannheim).
The lysate was clarified by centrifugation at 14,000 × g for 10 min at 4°C, and CAT expression was quantified relative to known standards by a commercial enzyme-linked immunosorbent assay (Boehringer Mannheim). Replication activities of mutants were
calculated as percentages of the CAT synthesis seen with the wild-type
(WT) gene after subtraction of the background obtained in the absence
of NP. Values were calculated from a minimum of three separate
experiments and two independent plasmid DNA preparations.
For immunofluorescence analysis, BHK or HeLa cells on coverslips were
infected and transfected with plasmid DNA as described
above. After
4 h of incubation at 37°C, the cells were washed
three times
with PBS containing 1% newborn calf serum and fixed
in PBS containing
4% formaldehyde for 20 min at room temperature
before being washed as
before. The cells were permeabilized with
0.2% TX-100 in PBS for 5 min
at room temperature, washed, and
incubated for 1 h at room
temperature with 200 µl of a 1-in-250
dilution of anti-RNP serum.
After cells had been washed, bound
immunoglobulin G was stained with
swine anti-rabbit immunoglobulin
G-fluorescein isothiocyanate
conjugate (DAKO). Coverslips were
applied in the presence of an
antiphotobleaching compound (Citifluor).
To preextract cells before
fixation, cells were washed with 60
mM PIPES (pH 6.8)-20 mM HEPES-1
mM MgSO
4-0.1 mM EGTA at 37°C,
incubated with the same
buffer supplemented with 0.1% TX-100 and
5 µM phallacidin for 2 min
at room temperature, washed twice more,
and then fixed and processed as
described above. F-actin was detected
by using 5 nM BODIPY-FL
phallacidin (Molecular Probes), and

-actin
was detected by using
monoclonal antibody clone AC-74 (Sigma)
at a dilution of 1:50.
Fluorescence was viewed with a Leitz Orthoplan
microscope or an MRC
1024 confocal microscope. Control experiments
in which cells including
untransfected cells were stained with
individual fluorescent reagents
confirmed that the labelling was
channel specific (data not
shown).
 |
RESULTS |
Binding of NP to F-actin.
We tested whether purified NP bound
F-actin in vitro by a cosedimentation assay, in which F-actin readily
separates from monomeric protein by centrifugation. As shown in Fig.
1, most of the actin sedimented after
centrifugation (lane 2) and only the expected critical actin monomer
concentration (0.1 to 0.2 µM) remained in the supernatant (lane 1).
Control assays showed that only trace amounts of the expressed proteins
pelleted in the absence of actin (Fig. 1, lanes 4, 8, and 12). However,
when GST, GST-NP, or MBP-NP was sedimented after mixing with F-actin,
the NP-containing polypeptides partitioned approximately evenly between
the supernatant and pellet fractions (Fig. 1, lanes 9, 10, 13, 14)
while GST did not (lanes 5 and 6), demonstrating association of NP with
actin filaments. To test the ability of nonfused NP to bind F-actin,
MBP-NP was cleaved into MBP and NP moieties by digestion with factor Xa
protease and sedimented with or without F-actin. Since MBP and actin
comigrate on SDS-PAGE, the samples were analyzed in parallel by Western blotting with an anti-MBP serum, confirming that MBP alone did not
pellet whether or not actin was present (Fig. 1, inset, lanes 15 to
18). However, the NP polypeptide pelleted only in the presence of actin
(Fig. 1, lanes 15 to 18). Thus, NP binds F-actin in vitro.

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FIG. 1.
F-actin-binding activities of GST, GST-NP, and MBP-NP.
The proteins (MBP/NP corresponds to MBP-NP digested with factor Xa
protease) were centrifuged in the presence (+) or absence ( ) of 3 µM F-actin. Supernatant (S) and pellet (P) fractions were analyzed by
SDS-PAGE and staining with Coomassie blue or by Western blotting with
anti-MBP serum (inset, lanes 15 to 18). Arrows indicate the named
polypeptides (right), and molecular mass markers (in kilodaltons) are
indicated on the left.
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|
To quantitate the interaction between NP and F-actin, we titrated
increasing concentrations of MBP-NP with a constant amount
of F-actin
in the sedimentation assay and determined the amount
bound. Figure
2 shows the molar ratio of MBP-NP bound
to F-actin
as a function of the free MBP-NP. Saturation occurred in
excess
of two NP molecules per actin subunit, indicating more than one
binding site for NP in the complex. The curve could best be described
(based on nonlinear least-squares fitting) as resulting from a
single
high-affinity site per actin subunit (approximate
Kd, 1
µM) and a lower-affinity site(s)
having a
Kd in excess of 40 µM.
While we
cannot exclude the possibility that a second NP binding
site is present
on F-actin, this weaker binding phase may be due
to self-association
with already bound NP.

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FIG. 2.
Titration binding curves of WT and R156-A MBP-NP for
F-actin. Sedimentation assays were performed by using 3 µM F-actin
and WT (open circles) or mutant R156-A (closed circles) MBP-NP. The
amount of bound MBP-NP (expressed as the molar ratio relative to actin)
is plotted against the concentration of free MBP-NP.
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The binding of NP to actin filaments was also visualized directly by
electron microscopy. Actin filaments incubated with an
equimolar amount
of MBP formed an essentially random distribution
of fibers (Fig.
3A). However, the addition of MBP-NP to
actin
in an equimolar ratio induced a predominantly pairwise
association
of filaments (Fig.
3B), with a regular alternation of
electron-dense
and transparent regions between the filaments suggestive
of cross-bridges
(Fig.
3D). Addition of higher ratios of NP to actin
induced the
bundling of fibers into arrays containing multiple strands
(Fig.
3C). The spacing between the cross-bridge arrangements at
equimolar
ratios of NP/actin was measured to be 332 ± 39.5 Å,
coincident
with every half-twist of the actin filament giving a ratio
of
1 cross-bridge to every 13 actins. The formation of ordered bundles
of fibers confirms that NP binds F-actin and is also consistent
with
the formation of NP-NP contacts.

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FIG. 3.
Electron microscopy of actin filaments mixed with
equimolar concentrations of MBP (A) and MBP-NP (B and D) and a
threefold excess of MBP-NP (C). Scale bars, 300 nm.
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RNA and the NP-actin interaction.
Since NP is a
single-stranded-RNA-binding protein, we investigated the relationship
between actin binding and RNA binding. First, we examined the effect of
actin on the ability of NP to bind RNA in solution by titrating a
radiolabelled 178-nucleotide RNA corresponding to the 5' and 3'
noncoding sequences from vRNA segment 8 with increasing concentrations
of MBP, MBP-NP, and MBP-NP plus 3 µM actin. Addition of MBP up to a
concentration of 300 nM did not result in significant retention of the
labelled probe, indicating that MBP itself does not bind RNA (Fig.
4a). However, titration with increasing
amounts of MBP-NP resulted in the retention of 50% of the input RNA
with around 20 nM protein (Fig. 4a). In replicate experiments, the
affinity of MBP-NP for RNA was determined to be 16.3 ± 3.8 nM
1 (n = 5), which is in good agreement
with that estimated for NP purified from influenza virus virions (20 nM
1 [4]). Therefore, the bacterially
expressed NP behaved similarly to native NP and was fully competent to
bind RNA. Moreover, addition of F-actin to the reaction mixtures had no
significant effect on this RNA-binding activity (Fig. 4a).

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FIG. 4.
RNA and the interaction between NP and F-actin. (a)
Effect of actin on the RNA-binding activity of NP. The amounts of
radiolabelled RNA (1 nM) bound by MBP (circles), MBP-NP (squares), and
MBP-NP plus 3 µM F-actin (triangles) were determined by a filter
assay. (b) Effect of RNA on actin binding by NP. MBP-NP (0.75 µM) was
cosedimented in the presence (+) or absence ( ) of 3 µM F-actin with
the indicated molar ratio of a 34-mer RNA. S, supernatant; P, pellet.
(c) Cosedimentation of RNA with actin and NP. Radiolabelled 34-mer (100 nM in 100 µl; open bars) or 54-mer (50 nM; shaded bars) was
cosedimented in the presence of 3 µM MBP-NP with or without 3 µM
F-actin.
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Since NP binds to RNA with higher affinity than it does to actin
(
Kd ~16 nM versus 1 µM [Fig.
2 and
3]), we
examined the effect
of a molar excess of RNA on actin binding by NP. We
used a 34-mer
transcript corresponding to the 3' end of segment 8, which is
long enough to bind efficiently to NP (
47) but is
not sufficiently
large to bind multiple copies of NP and thus form RNP
structures
which would sediment irrespective of any association with
actin
fibers. In control reactions, this RNA did not cause a
significant
increase in the quantity of MBP-NP that pelleted in the
absence
of actin (Fig.
4b, lanes 5 to 8). However, the extent of
sedimentation
of MBP-NP with F-actin was unaffected by the presence of
a twofold
molar excess of RNA transcript relative to NP (Fig.
4b,
compare
lanes 1 and 2 with lanes 3 and
4).
To test whether NP was capable of binding both actin and RNA
simultaneously, we assayed the sedimentation of radiolabelled
RNAs
(either the 3' end [34-mer] or the 5' and 3' panhandle sequences
[56-mer] of segment 8) with actin and MBP-NP. Mixtures of RNA,
actin,
and MBP-NP were subjected to centrifugation, and the pellet
fractions
were examined for their RNA content. Figure
4c shows
that substantial
quantities of both radiolabelled RNAs associated
with the MBP-NP and
the actin pellet (Fig.
4c). By contrast, there
was no binding to actin
alone (Fig.
4a) and minimal binding to
MBP-NP alone (Fig.
4c),
presumably reflecting the presence of
oligomerized MBP-NP. Thus, NP,
RNA, and F-actin can exist in termolecular
complexes.
Mutational analysis of actin binding.
To further delineate the
NP-F-actin interaction, we performed a mutational analysis of NP. On
the grounds that an interaction with a relatively invariant protein
such as actin might be reflected by sequence conservation within NP, we
altered residues in regions conserved among the NPs of influenza A, B,
C, and Dhori viruses (12) (summarized in Fig.
5b) and tested the effects of the
mutations on actin-binding activity. Many of the mutations had no
effect on the interaction. Quantitative analysis of the R156-A mutant produced a binding curve indistinguishable from that of the WT polypeptide (Fig. 2). Similarly, when tested at concentrations in the
low micromolar range, the W104-F and R391-A mutants bound efficiently
to F-actin (Fig. 5a, panels ii and vi, respectively; cf. panel i
[WT]). The binding affinities for F-actin of these and the R8-A,
W120-A, R199-A, K236-A, and R267-A mutants were found to vary from that
of the WT protein by less than threefold (Fig. 5b). However, the
F338-A, E339/D340-AA, R342-A, and Q405-A polypeptides showed markedly
different behavior, with the majority of each protein remaining in the
supernatant fractions at each concentration tested (Fig. 5a, panels
iii, iv, v, and vii). Quantification produced estimated binding
constants for F-actin some 10- to 35-fold lower than for the WT protein
(Fig. 5b). Thus, four mutations that disrupted the ability of the
protein to bind F-actin were identified in the C-terminal one-third of
NP.

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FIG. 5.
Identification of NP point mutations which disrupt actin
binding. (a) WT or mutant MBP-NP polypeptides were cosedimented in the
absence ( ) or presence (+) of 3 µM F-actin, and supernatant (S) and
pellet (P) fractions were examined by SDS-PAGE. (b) Summary of point
mutations and cellular localization signals in NP. Arrows indicate the
positions of amino acid changes introduced into NP. White arrows
indicate mutations with no major effect on F-actin binding and black
arrows indicate those that substantially reduced binding. Tabulated
values are the fold decrease in binding affinity for F-actin relative
to values for the WT protein. Also shown are the positions of the three
postulated cellular localization signals that have been identified in
NP.
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Ability of actin-binding mutants to support viral
transcription.
Although we had identified mutations that reduced
the ability of NP to bind actin, it was necessary to examine whether
the mutations affected other functional properties of NP. Many lines of
evidence indicate that NP is essential for virus RNA synthesis (18). This has been confirmed in a recombinant system where NP and the three subunits of the influenza virus RNA polymerase are
necessary and sufficient to drive transcription and replication of a
synthetic influenza virus genome segment containing an antisense CAT
(flu-CAT) reporter gene (16). We used an adaptation of this assay to apply the stringent test of whether the mutants defective in
actin binding could support virus RNA synthesis.
The WT and mutant NP genes were subcloned into plasmid pKT0 (as
described in Materials and Methods) to allow T7 RNA polymerase-driven
expression of native NP. BHK cells were multiply infected with
vaccinia
viruses expressing the influenza virus RNA polymerase
and bacteriophage
T7 RNA polymerase (
11,
37) and transfected
with flu-CAT RNA
and plasmids encoding WT or mutant NP, and the
accumulated CAT
polypeptide levels were measured 20 h later. Control
experiments
established that, as expected, the flu-CAT gene was
transcribed and
replicated to produce CAT polypeptide in the presence
of the influenza
virus RNA polymerase and NP and that NP was essential
for this process
(data not shown). The activities of the mutants
were then quantified
relative to that of the WT gene. The E339/D340-AA
mutant failed to
support the accumulation of CAT polypeptide (0.1%
± 0.3%). However,
the Q405-A mutant supported CAT synthesis to
a degree indistinguishable
from that of the WT protein (98.2%
± 10.1%), while the F338-A and
R342-A mutants possessed somewhat
diminished (61.0% ± 20.3% and
23.9% ± 6.5%, respectively) activity.
Hence, the last three mutants
are capable of successfully participating
in the multiple
protein-protein and protein-RNA interactions necessary
for the
formation of a transcriptionally active influenza virus
RNP
core.
Actin and the intracellular localization of NP.
Since F-actin
is cytoplasmic and NP can also accumulate in the cytoplasm, we examined
the relevance of actin binding to the localization of NP. Because
exogenously expressed NP shuttles between nucleus and cytoplasm and has
been shown to accumulate in the cytoplasm under certain circumstances
(27, 43), we first established the localization parameters
of the WT polypeptide in our expression system by testing the effect of
expression levels on the compartmentalization of NP. BHK cells were
infected with a recombinant vaccinia virus expressing T7 RNA polymerase
and transfected with various amounts of plasmid pKT5, and the
subsequent expression and cellular localization of NP were examined by
indirect immunofluorescence at 4 h posttransfection.
Nontransfected cells revealed only a diffuse, low-level fluorescence
(data not shown). In contrast, cells transfected with a plasmid
containing the WT NP gene exhibited strong fluorescence, the location
of which depended on the amount of plasmid transfected. In cells
transfected with a high dose of plasmid (0.3 µg/105
cells), virtually all the fluorescence was cytoplasmic, often with
apparent sparing of the nucleus (Fig.
6a). However, cells transfected with a
low dose of plasmid (3 ng/106 cells) showed almost
exclusively nuclear fluorescence (Fig. 6c). Cells transfected with an
intermediate amount of plasmid (30 ng/105 cells) showed an
intermediate pattern, with many cells containing substantial amounts of
cytoplasmic NP but with nuclear accumulation as well (Fig. 6b). When
lysates from cells transfected in parallel were subjected to SDS-PAGE
and Western blot analysis to assess the quantity of NP expressed, the
amount correlated with the plasmid dose (data not shown). The
transfection efficiency varied by less than twofold (generally ranging
between 20 and 40%; data not shown) over the range of plasmid
concentrations tested. This indicates that the expression levels
depended primarily on the amount of plasmid received per cell and not
the number of cells transfected. Thus, the cellular distribution of NP
depended on the amount (or rate) of synthesis of protein within any one
cell.

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|
FIG. 6.
Cellular localization of WT and mutant NP polypeptides.
BHK cells (105) were infected with a recombinant vaccinia
virus expressing T7 RNA polymerase, transfected with the indicated
amounts of plasmids, and examined 4 h later by indirect
immunofluorescence with anti-NP serum.
|
|
We next tested whether cytoplasmic NP associated with F-actin in vivo.
The perinuclear actin network in cells was visualized
by staining with
anti-

-actin as an irregular ring structure that
at most but not all
points coincided with anti-NP fluorescence
(Fig.
7a to
c). Striking colocalization of NP and

-actin was
also observed at the periphery of cells, particularly at
the leading
edges of lamellipodia (Fig.
7d to f). We also saw
colocalization
of NP with

-actin that had been incorporated into
stress fibers
(data not shown). To examine this further, we extracted
cells
with nonionic detergent before fixation, to remove soluble
cytosolic
proteins, and stained them with anti-NP and fluorescent
phallacidin,
a reagent that preferentially binds to actin in the form
of stress
fibers. Under these conditions, substantial quantities of NP
remained
cell associated, but in a granular pattern, often denser in
the
perinuclear area (data not shown). Moreover, many of the granules
were arranged in linear arrays coincident with the phallacidin-stained
F-actin stress fibers (Fig.
7g to i). In addition, colocalization
between NP and actin was observed in a variety of cell types,
including
HeLa (Fig.
7a to f), BHK (Fig.
7g to i), and CV1 cells
(data not
shown). Therefore, exogenously expressed NP interacts
with actin in
vivo.

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|
FIG. 7.
Colocalization of NP and F-actin. Cells were transfected
with 0.3 µg of pKT5 and examined 4 h later by confocal laser
microscopy after staining for NP (red) or actin (green). Panels b, e,
and h are images resulting from the merger of the red and green
channels. Panels a through f are from HeLa cells fixed before detergent
extraction. Panels g through i are from a BHK cell extracted with
detergent before fixation.
|
|
We next examined the intracellular localization of mutant NP molecules
defective for actin binding. Significantly, even when
cells were
transfected with high doses of plasmids encoding these
mutants, the
fluorescence was predominantly nuclear (Fig.
6d and
e). This increased
nuclear accumulation was not simply the result
of lower expression of
the mutants, since the amounts of polypeptide
detected by SDS-PAGE and
Western blot analysis of parallel transfections
were comparable with
those of the WT polypeptide (relative densitometric
scores of 1.1 ± 0.1 and 1.0 ± 0.2 for F338-A and Q405-A, respectively;
data
not shown). This suggests that the F338-A and Q405 polypeptides
are
more karyophilic than the WT
protein.
To examine further the effect of mutations affecting actin binding on
the cellular localization of NP, we tested the effects
of combining
them with a mutation (R8-A [Fig.
5b]) that disrupted
the N-terminal
mammalian NLS (
41). In BHK cells, the R8-A mutation
rendered
NP almost exclusively cytoplasmic at 4 h posttransfection
regardless of the amount of plasmid transfected (Fig.
8a and
b).
In contrast to the situation for WT
NP, even levels of R8-A expression
that were barely detectable by
immunofluorescence resulted in
cytoplasmic staining and apparent
sparing of the nucleus (Fig.
8b; cf Fig.
6c). This is consistent with
the importance of the
N-terminal NLS for nuclear import in mammalian
cells (Fig.
5,
NLS-1) (
41). Combining the R8-A mutation with
others that did
not affect actin binding also resulted in a staining
pattern where
the nuclei emitted lower-intensity fluorescence than did
the cytoplasm
(Fig.
8c [R8-R391] and data not shown [R8-K236]).
However, when
either of the F338-A, E339/D340-AA, or R342-A mutations
(which
disrupt actin binding) were introduced into R8-A, the ability
of
the polypeptide to accumulate in the nuclei of cells was partially
restored (Fig.
8d to f). Therefore, mutations which weaken the
affinity
of NP for actin can compensate for a mutation which disrupts
a nuclear
import signal. Thus, the NP-actin interaction causes
cytoplasmic
retention of NP.

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|
FIG. 8.
Cellular location of NP mutants bearing amino acid
substitutions in NLS I. Cells transfected with 0.3 µg (except for
those shown in panel b, which were transfected with 3 ng) of plasmids
encoding the indicated mutants were examined by indirect
immunofluorescence with anti-NP serum.
|
|
 |
DISCUSSION |
Two recent studies suggested that influenza virus NP interacts
with microfilaments of the host cell cytoskeleton late in infection (3, 17). Both reports found that NP partitioned into
cytoskeleton-containing pools during biochemical fractionation of
infected cells; that NP colocalized with microfilaments, especially at
the cell periphery; and that disruption of microfilaments with
cytochalasins altered the distribution of NP. Here, we confirm and
extend these observations by using two methods to show that NP binds
directly to F-actin in vitro (Fig. 1 to 3) with an affinity comparable
to that of many cellular F-actin-binding proteins (35). We
also show that NP associates with actin filaments in vivo in the
absence of other influenza virus proteins (Fig. 7). Furthermore,
complexes containing F-actin, NP, and RNA could be formed (Fig. 4). As
the in vitro actin-binding assay employed high-speed centrifugation, we
could not directly test whether authentic RNP particles bound F-actin because they sediment under these conditions, but we predict that RNP
structures bind F-actin.
We have identified point mutations in NP which weaken its affinity for
actin in vitro (Fig. 5) and decrease the extent of colocalization of
the proteins in vivo (Fig. 6 and 8). These mutations were largely
localized to a region of NP previously identified as important for the
accumulation of the protein in the nuclei of Xenopus oocytes
(9). The signal mapped by Davey and colleagues was one of
the first NLSs proposed, but as subsequent NLSs are identified, it
appears increasingly atypical. In sequence composition, it does not
possess the small stretch of basic amino acids found in other viral
proteins such as simian virus 40 large T antigen, or the bipartite
basic NLS contained in many cellular proteins (10). In
oocytes it acts as a sequence which causes the retention of NP that has
diffused into the nucleus, rather than as a signal for the active
uptake of the protein; hence it was called a "nuclear accumulation"
signal (NAS) (9). Subsequently, the study of Wang et al.
(41) found that this NAS was not essential for nuclear localization of NP in mammalian cells. Here we show that mutation of
residues within the NAS actually increases the ability of NP to
localize to the nuclei of mammalian cells (Fig. 6 and 8). The reason
for the discrepancy between the activities of the NAS in mammalian and
amphibian cells is not clear, but the fact that, unlike most somatic
cells, the nuclei of amphibian oocytes have been shown to contain actin
may be relevant (8, 34). Nevertheless, the region of NP
defined as the NAS, which we find important for actin binding, is one
of the most highly conserved blocks of amino acids between influenza A,
B, C, and Dhori virus NPs (12), suggesting that it is
functionally important.
The most plausible role for the NP-actin interaction is during the late
stages of viral infection, when NP is also found in the cytoplasm. In
this study, we show that the cellular localization of exogenously
expressed NP depends on the amount of protein synthesized. Low levels
of NP were targeted efficiently to the nucleus, but in a dramatic
switch, large amounts localized almost exclusively to the cytoplasm
(Fig. 6), where in part NP associated with actin (Fig. 7). These
phenomena could perhaps be explained by saturation of the nuclear
import machinery leading to cytoplasmic accumulation of NP and
subsequent F-actin binding. However, the fact that all the mutations
that weakened F-actin binding restored nuclear import, even under
conditions of high-level expression (Fig. 6) or in the absence of a
functional N-terminal NLS (Fig. 8), strongly implies a causative link
between F-actin binding and cytoplasmic retention of NP. We propose
that the interaction between NP and actin plays a role in regulating
the localization of RNPs by causing their cytoplasmic retention late in
infection. Previous work has shown that nuclear import of NP and RNPs
is driven by NLSs in NP and that export of RNPs depends at least in
part on the subsequent expression of M1 and NS2. Mechanistically,
retention of RNPs on cytosolic actin filaments would act in opposition
to the import pathway, but in concert with the export pathway, to
prevent reimport of exported RNPs destined for packaging into progeny virions.
Cytosolic anchoring as a means of regulating nuclear localization is
well established for several cellular proteins, such as the
transcription factors of the NF-
B family, or Xenopus xnf7 (29, 40). In the case of NF-
B, retention is thought to
result from masking of the NLS by the cytoplasmic anchor, since the
addition of an extra NLS overrides the retention mechanism
(5). In contrast, Xenopus xnf7 remains
cytoplasmic even after addition of another NLS, leading to the proposal
that cytoplasmic retention results from a physical interaction with a
fixed anchor, possibly the cytoskeleton (20). Here we show
that direct interaction with actin microfilaments mediates cytoplasmic
retention of an NLS-containing protein. This represents a novel
mechanism for controlling the cellular location of a ribonucleoprotein
complex and may be applicable to a wider range of cellular proteins and RNAs.
It seems likely that the interaction between NP and actin is subject to
regulation. The quantity of actin in the cell is such that the switch
in NP localization between low- and high-dose transfections cannot be
explained purely in terms of the protein's affinity for actin. In
addition, the nonuniform colocalization of NP with actin (Fig. 7) also
suggests a regulated process. Since the microfilament network in cells
consists of a polarized distribution of the various actin isoforms in
complex with many different cellular actin-binding proteins
(14), this could reflect a largely passive process,
resulting from the occlusion of potential actin-binding sites and/or
preferential binding to others. However, influenza virus may also have
evolved positive mechanisms for regulating the NP-actin interaction, a
likely candidate being phosphorylation of NP (2, 27). This
is consistent with the effect of protein kinase inhibitors on NP
localization noted by Neumann et al. (27), while
phosphorylation is a well-documented mechanism for the control of the
subcellular localization of cellular proteins, by modulation of both
nuclear import (19, 21, 23) and actin binding (1, 24).
 |
ACKNOWLEDGMENTS |
We thank Mark Krystal for the gift of plasmid pPB2CAT, Geoff
Smith for the gift of recombinant vaccinia viruses, Keff Tibbles for
the gift of plasmids pKT8-
3'5' and pKT0, and Sabine Gonsior for help
with confocal microscopy. We also thank Ian Brierley, John McCauley,
and Laurence Tiley for helpful criticism.
This work was supported by grants from the Royal Society, the Medical
Research Council (grant G9232370), and the Wellcome Trust (grant
048911) to P.D. P.D. is a Royal Society University research fellow.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Division of
Virology, Department of Pathology, University of Cambridge, Tennis
Court Rd., Cambridge CB2 1QP, United Kingdom. Phone: 44 1223 336921. Fax: 44 1223 336926. E-mail:
pd1{at}mole.bio.cam.ac.uk.
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Journal of Virology, March 1999, p. 2222-2231, Vol. 73, No. 3
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