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Journal of Bacteriology, September 2005, p. 6265-6272, Vol. 187, No. 18
0021-9193/05/$08.00+0 doi:10.1128/JB.187.18.6265-6272.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Differential Roles of the Universal Stress Proteins of Escherichia coli in Oxidative Stress Resistance, Adhesion, and Motility
Laurence Nachin,1
Ulf Nannmark,2 and
Thomas Nyström1*
Department of Cell and Molecular Biology,1
Institute of Anatomy and Cell Biology, Göteborg University, Medicinaregatan 9C, 413 90 Göteborg, Sweden2
Received 9 March 2005/
Accepted 10 June 2005

ABSTRACT
The universal stress protein (UspA) superfamily encompasses
a conserved group of proteins that are found in bacteria, archaea,
and eukaryotes.
Escherichia coli harbors six
usp genes
uspA,
-
C, -
D, -
E, -
F, and -
Gthe expression of which is triggered
by a large variety of environmental insults. The
uspA gene is
important for survival during cellular growth arrest, but the
exact physiological role of the Usp proteins is not known. In
this work we have performed phenotypic characterization of mutants
with deletions of the six different
usp genes. We report on
hitherto unknown functions of these genes linked to motility,
adhesion, and oxidative stress resistance, and we show that
usp functions are both overlapping and distinct. Both UspA and
UspD are required in the defense against superoxide-generating
agents, and UspD appears also important in controlling intracellular
levels of iron. In contrast, UspC is not involved in stress
resistance or iron metabolism but is essential, like UspE, for
cellular motility. Electron microscopy demonstrates that
uspC and
uspE mutants are devoid of flagella. In addition, the function
of the
uspC and
uspE genes is linked to cell adhesion, measured
as FimH-mediated agglutination of yeast cells. While the UspC
and UspE proteins promote motility at the expense of adhesion,
the UspF and UspG proteins exhibit the exact opposite effects.
We suggest that the Usp proteins have evolved different physiological
functions that reprogram the cell towards defense and escape
during cellular stress.

INTRODUCTION
The levels of the universal stress protein UspA of
Escherichia coli become elevated in response to a large variety of stress
conditions, including starvation for carbon, nitrogen, phosphate,
sulfate, and amino acids and exposure to heat, oxidants, metals,
uncouplers of the electron transport chain, polymyxin, cycloserine,
ethanol, and antibiotics (
9,
13,
17; T. Nyström, unpublished
data). The protein has given its name to the orthologous group
of proteins called the UspA superfamily of proteins (the COG0589
cluster in GenBank and the PF00582 protein family of alignments
at the Sanger Centre). This superfamily encompasses an ancient
group of proteins that are found in all the major branches of
the evolutionary tree (
1). Usp-containing organisms are usually
equipped with several
usp genes despite the fact that they exhibit
extensive similarity. They encode either a small Usp protein
(around 14 to 15 kDa) harboring one Usp domain, a larger version
(around 30 kDa) consisting of two Usp domains in tandem, or
large proteins in which the Usp domain is present together with
other functional domains (
13).
E. coli has five small Usp proteins
and one tandem-type Usp protein (UspE). Based on structure analysis
and their amino acid sequence, the Usp proteins have been divided
into four different classes. In
E. coli, UspA, UspC (
yecG),
and UspD (
yiiT) belong to class I, UspF (
ynaF) and UspG (
ybdQ)
belong to class II, and the two Usp domains of UspE (
ydaA) separate
into classes III and IV (
13,
23,
26; L. Brive, personal communication).
The Usp paradigm, UspA, is an autophosphorylating serine and threonine phosphoprotein (6). Phosphorylation occurs in response to stasis and is, in part, dependent on the tyrosine phosphoprotein TypA (7). Mutants devoid of UspA die prematurely during stasis (17), whereas overproduction blocks the cells in a growth-arrested state (18). In addition, deletion of class I or class III/IV usp genes results in sensitivity to DNA-damaging agents (9). In contrast, cells lacking the class II UspG (called UP12 in reference 2) are sensitive to uncouplers (e.g., carbonyl cyanide m-chlorophenylhydrazone) but not DNA-damaging agents (2), indicating that the functions of the class I and II Usps may be distinct. To approach this notion we created mutants of different classes, i.e., the
uspA
uspC
uspD triple mutant (class I), the
uspF
uspG double mutant (class II), and the
uspE mutant (class III/IV). Phenotypic analysis of these mutants revealed hitherto unknown Usp functions, including those related to iron scavenging, oxidative stress defense, cell adhesion, and motility. Moreover, the analysis of class I to IV and individual usp mutants demonstrates that functions may overlap between Usp classes and also that the function of Usps within a class is distinct.

MATERIALS AND METHODS
Bacterial strains and culture conditions.
All strains used in this study are listed in Table
1. Strains
were cultivated at 37°C in Luria-Bertani (LB) medium. When
required, the medium was supplemented with antibiotics at the
following concentrations: ampicillin (50 µg ml
1),
kanamycin (50 µg ml
1), spectinomycin (100 µg
ml
1), and chloramphenicol (30 µg ml
1). The
strains LN81, LN32, and LN82 were obtained by P1 transduction
of the deletion mutation from the strains AD546, NGN183, and
AD547, respectively.
Construction of the uspA, uspF, and uspG deletion mutants.
The chromosomal deletion mutations were created stepwise. The
5'- and 3'-flanking regions of
uspA, -
F, and -
G were PCR amplified
using the 5F/5R and 3F/3R primers, respectively (Table
2). First,
the 5' regions were cloned into the pUC18 plasmid, generating
the p5 plasmid series (Table
1). In a second step, the 3'-flanking
regions were cloned into the p5 plasmids, generating the p5-3
plasmid series (Table
1). Third, the
aphA-3 gene (conferring
kanamycin resistance [Kan
r]) and the
cat gene (conferring chloramphenicol
resistance [Cam
r]) were cut out from plasmids pUC18K and pNGN27,
respectively, and ligated into the SmaI site of the p5-3 plasmids,
thus creating p

A (Kan
r), p

F (Kan
r), and p

G (Cam
r). The plasmids
were purified, and the cloned deletion constructs were excised
and introduced into the
E. coli strain KM354 by linear transformation.
This strain contains the plasmid pTP223 to promote gene replacement
by recombination (
16). The chromosomal deletion mutations were
then moved from the KM354 to the MG1655 background by transduction
using the phage P1.
Growth assays.
Overnight culture of
E. coli wild-type and
usp mutant strains
were used to inoculate fresh LB medium. During the exponential
growth phase (optical density at 600 nm [OD
600], 0.5) the precultures
were diluted 10 times and split into two cultures of equal volume.
To one, phenazine methosulfate (PMS; 15 µM) or streptonigrin
(1 µg ml
1) was added. Growth was monitored by measuring
OD
600.
t-BOOH sensitivity.
Aliquots of overnight cultures grown in LB medium were incubated with different concentrations of t-BOOH (tert-butyl hydroperoxide) for 1 h at 37°C without shaking. The viability of the cells after exposure was determined as the number of CFU ml1 on LB plates.
Autoaggregation assay.
Overnight cultures of the E. coli strains were adjusted to approximately the same OD600 (4.0), and 4 ml of each was placed in a sterile 15-ml tube at room temperature. At the beginning of each experiment, all cultures were vigorously shaken. Cell settlings were visually observed. Samples were also taken for observation using standard phase-contrast microscopy.
Ag43 immunodetection.
Cells grown overnight in LB were tested for the presence of the protein Ag43. For each culture, the equivalent of 0.2 OD600 units was analyzed by sodium dodecyl sulfate-12% polyacrylamide gel electrophoresis, followed by immunodetection using a 1:3,000 dilution of polyclonal rabbit antiserum raised against the
domain of Ag43 and a secondary goat anti-rabbit antibody conjugated to alkaline phosphatase.
Yeast cell agglutination assay.
Saccharomyces cerevisiae and E. coli cells from overnight culture were pelleted, washed, and resuspended in phosphate-buffered saline to OD600 of 5 and 3, respectively. Equal volumes of E. coli and yeast cell suspensions were mixed on a glass slide. Aggregation was monitored visually, and the titer was recorded as the last dilution of bacteria giving a positive agglutination reaction. To control that the agglutination observed was indeed due to the adhesion of bacterial fimbriae to mannose residues of the yeast cell surface, we also performed the experiments in the presence of D-mannose (25 mg ml1). In this condition, fimbria-dependent agglutination is abolished. All assays were performed at least three times and gave similar results.
Motility assay.
Bacterial cells were picked from colonies grown on LB agar plates and inoculated onto low-agar-concentration (0.3%) plates. The plates were incubated at room temperature for 48 h, and motility was assessed qualitatively by examining the circular halo formed by the growing motile bacterial cells.
Scanning electron microscopy (SEM).
Strains were grown overnight in LB medium at 37°C without shaking. From these cultures, 30 µl was taken, and cells were allowed to sediment and adhere to Au sputtered Thermanox plates for 15 min. The plates were then transferred to 2.5% glutaraldehyde for 15 min, rinsed with Na-cacodylate buffer, and postfixed in 1% OsO4 (15 min). Specimens were then dehydrated in graded series of ethanol and dried with hexamethyldisilazane for 2 x 5 min. All specimens were then sputter coated with Palladium and examined under a Zeiss DSM 982 Gemini scanning electron microscope.

RESULTS
The class I proteins UspA and UspD and class II proteins UspF and UspG confer resistance against oxidative stress.
Production of UspA has been shown to drastically increase when
exponentially growing
E. coli cells are challenged with hydrogen
peroxide (H
2O
2) (
9,
17). Moreover, the viability of growing
uspA mutant cells was found to be markedly more reduced than
that of the wild-type strain after H
2O
2 exposure (
17). Thus,
we assayed the sensitivity of the different
usp mutants toward
the superoxide-generating agent, PMS, added during exponential
growth of cells. Cells lacking all class I (
uspACD) genes were
drastically more sensitive than the wild-type strain to such
oxidative stress (Fig.
1). When analyzing the single-mutant
strains of this class, it appeared that the sensitivity of the
triple mutant was due to the additive effect of the two deletions
of
uspA and
uspD; both single mutants were more sensitive than
the wild-type strain but less so than the triple mutant (Fig.
1). In contrast, the lack of
uspC did not affect the sensitivity
of cells towards PMS. The class II genes,
uspF and
uspG, seemed
to play a minor role in oxidative stress resistance. Cells lacking
both these genes displayed a slightly increased sensitivity
toward PMS. The sensitivity of this double mutant appears to
be due to the simultaneous absence of
uspF and
uspG since the
single mutants exhibited no significant sensitivity to PMS.
The class III/IV mutant,
uspE, was indistinguishable from the
wild-type strain with respect to PMS sensitivity.
The class I protein UspD and class II proteins UspF and UspG confer resistance against streptonigrin.
In many cases oxidative stress and iron homoeostasis are intimately
linked. The iron exacerbates the effects of the reactive oxygen
species through the Fenton reaction producing hydroxyl radicals
in the presence of oxygen (
11). Overproduction of the UspA protein
has been demonstrated to reduce the synthesis of iron siderophore
uptake proteins (
18). Thus, it is possible that the lack of
Usp proteins could cause a decontrolled influx of iron, leading
to an excess in the cell. We tested this hypothesis by analyzing
the effects of streptonigrin on cell growth. Streptonigrin is
an antibiotic whose toxicity is dependent on intracellular iron
concentrations; increased sensitivity to this drug is a sign
of increased availability of intracellular free iron (
25). Based
on PMS sensitivity data, we expected the class I
uspACD and
class II
uspFG mutants to be more sensitive to streptonigrin.
This was indeed the case, and the class III/IV
uspE mutant,
again, showed no sensitivity (Fig.
2). We also found a good
correlation between the degree of streptonigrin and PMS sensitivity:
in both cases the lack of UspFG is less dramatic than the lack
of class I Usps. When testing the single deletion mutants we
observed, again, an additive effect of the lack of UspF and
UspG (Fig.
2). As expected, the lack of the class I protein
UspC did not affect sensitivity towards streptonigrin. However,
somewhat surprisingly, the lack of only
uspD and not
uspA resulted
in an increased streptonigrin sensitivity (Fig.
2). Thus, the
sensitivity of
uspD and
uspFG but not
uspA mutants to oxidative
agents is associated with streptonigrin sensitivity, i.e., increased
intracellular iron availability.
Deficiencies in the class I protein UspC, the class II protein UspG, and the class III/IV protein UspE affect cell-to-cell aggregation.
In the course of characterizing the
E. coli usp mutants, we
made the serendipitous observation that
uspE mutant cells failed
to sediment in liquid medium after letting the culture stand
still for hours. A similar phenotype has been described previously
for
Azospirillum brasilense carrying a mutation in a
usp-like
gene (
8). Microscopic observations of overnight cultures of
the different
E. coli usp mutants revealed differences in the
strains' capacities to form cell aggregates (Fig.
3A, upper
panel). In parallel, the cell settlings of the
usp mutants were
assayed by observing the formation of a cell pellet in the overnight
cultures (Fig.
3A, lower panel). The
uspE mutant was completely
unable to aggregate, and only single cells were observed in
all the
uspE cultures assayed. Also, even after prolonged incubation
(several hours) no cell pellet was visible in the
uspE culture.
The
uspC,
uspACD, and
uspG mutants were also impaired in their
ability to form aggregates, but a few could be observed, albeit
smaller than those formed by the wild-type cells. After 1 h,
the cells of these mutants had not settled, but they eventually
did so after prolonged static incubation (Fig.
3A and data not
shown). Ectopic expression of the
uspC gene complemented the
aggregation defect of the
uspC mutant (data not shown). No other
usp gene significantly affected cell flocculation (Fig.
3A).
In
E. coli, cell-to-cell aggregation (as described above) can
be mediated by the outer membrane protein Ag43 encoded by the
flu gene. Using antibody raised against the

domain of Ag43,
we could detect this protein in the wild type and all the single
usp mutants (Fig.
3B). However, we noticed that Ag43 levels
were lower in the mutants lacking
uspE or
uspC (Fig.
3B). Thus,
the failure of the
uspE and
uspC mutants to aggregate can, in
part, be explained by a lower production of Ag43. An
E. coli flu mutant is devoid of the capacity to aggregate and has also
been shown to be more sensitive to H
2O
2 killing (
5,
21). Therefore,
we decided to test the capacity of the
uspE mutant, which is
totally unable to aggregate in stationary phase, to cope with
lethal doses of oxidative stress, and we determined the rate
of die-off during such conditions. Overnight cultures were challenged
with t-BOOH, and the number of CFU was determined after exposure
to the oxidant (Fig.
4). After exposure to 0.5% t-BOOH the viability
of the mutant strain was significantly reduced compared to that
of the wild-type strain. An even more drastic difference was
obtained when the cells were exposed to 1% t-BOOH: only 0.003%
of the
uspE cells survived compared to 15% of the wild-type
cells (Fig.
4). When we assayed the sensitivity of the
uspE mutant toward PMS during growth, we did not observe any difference
compared to the wild-type strain (Fig.
1). We wondered then
if this was due to a specific sensitivity of the
uspE mutant
to peroxide agents (t-BOOH) rather than superoxide-generating
agents (PMS). Therefore, we challenged the
uspE mutant with
t-BOOH during growth, the same way we did with PMS, but could
not see any significant sensitivity (data not shown). Thus,
we detected an oxidative stress sensitivity of the
uspE mutant
only when growth-arrested cells were exposed to lethal doses
of t-BOOH.
Fimbria-mediated adhesion is increased by the class II UspF and UspG proteins and decreased by the class I UspC and class III/IV UspE proteins.
The Ag43-dependent aggregation of
E. coli has been shown to
be antagonized by the presence of type 1 fimbriae on the bacterial
cell surface (
10). Thus, we tested the fimbriation of the
usp mutants by their ability to agglutinate yeast cells, a fimbria-dependent
process (the FimH subunit binds to mannose residues on the yeast
cell surface [
12]). To confirm that the formation of yeast aggregates
was indeed due to the presence of bacterial fimbriae, we verified
that the agglutination observed was abolished in the presence
of
D-mannose (see Materials and Methods) (data not shown). We
found that the
E. coli cells' efficiency of yeast cell agglutination
was markedly enhanced when either
uspC or
uspE was inactivated
(Table
3), consistent with the fact that cell-cell aggregation
was markedly reduced in these mutants (Fig.
3A). On the other
hand, although the double mutant
uspFG exhibits the same ability
as the wild-type strain to agglutinate yeast, cells lacking
one or the other of these two class II Usps were greatly impaired
(Table
3). Thus, the single deletion of
uspF or
uspG displayed
a negative dominant effect on fimbria-dependent adhesion.
Inactivation of the class I uspC or the class III/IV uspE inhibits motility.
Adhesion and motility represent two dynamic aspects of the bacterial
life cycle. These two fundamental properties have been found
to exhibit reciprocal regulation to avoid simultaneous expression
of counterproductive functions/organelles, i.e., adhesion/fimbriae
and motility/flagella (
4,
24). Such coordinated regulation may
occur through two-component systems (
22), direct cross talk
between fimbrial gene products and bacterial motility genes
(
4), and small signaling molecules, such as acetyl phosphate
(
22,
24). We wondered whether the increased ability of
uspC and
uspE mutants to perform fimbria-dependent adhesion was associated
with a decreased motility and whether the opposite was true
for the
uspF and
uspG mutants. This was indeed the case. As
seen in Fig.
5A,
uspE mutant cells are severely restricted in
their ability to swim and the
uspC mutant (as well as the triple
uspACD mutant) is completely nonmotile, whereas the
uspF and
uspG mutants displayed an enhanced swimming capacity. Ectopic
expression of
uspC caused an enhanced motility exceeding that
of the wild-type cells (data not shown). The
uspA and
uspD mutants
displayed no apparent defects in swimming ability (Fig.
5A).
The nonmotile phenotype of
uspC and
uspE mutants could be a
consequence of a failure in making flagella or an inability
to properly use these organelles. SEM revealed the first possibility
to be true (Fig.
5B). Quantitative analysis of SEM data demonstrated
that, while 4% of the wild-type cells had visible flagella,
under the conditions used, no
uspC cell (in 10,000) and only
one
uspE cell (in 10,000) displayed flagella. Although the
uspF and
uspG mutants displayed an enhanced motility we did not observe
an increased number of flagella on the cells by SEM (data not
shown).

DISCUSSION
The large number of
usp genes in many bacteria and the coordinated
induction of
usp genes upon cellular stress (
9) has previously
appeared somewhat redundant in view of the sequence similarity
of Usp proteins, especially within a class (
13). However, the
phenotypes of the different
usp mutants reported here provide
new insights into the role of universal stress proteins in the
life cycle of bacteria. It is now clear that the function of
Usps in
E. coli is multifaceted (Fig.
6). Class I UspA and UspD
appear involved in regulating the cells' capacity to withstand
oxidative agents and, in the case of UspD, intracellular iron
availability. The functions of other Usps, i.e., class I UspC
and class II UspF and UspG, are instead mainly related to adhesion
and motility. In addition, the role of the unique Usp protein
of class III/IV, UspE, overlaps the functions of all the other
classes (Fig.
6).
With respect to oxidative stress resistance, UspA has previously
been shown to be important for H
2O
2 resistance during growth
(
17). Here, we tested the resistance of all
usp mutants of
E. coli to oxidative agent exposure during growth. The results
suggest a major role for the class I proteins, UspA and UspD,
in the PMS (superoxide) resistance of growing cells (Fig.
1).
The contribution of UspD to PMS resistance may be associated
with a role in iron scavenging, i.e., the effect of reactive
oxygen species in the
uspD mutant could be exacerbated by an
excess of free intracellular iron, as indicated by the elevated
sensitivity towards streptonigrin (Fig.
2). The PMS sensitivity
of the
uspA mutant, in contrast, was not associated with elevated
sensitivity to streptonigrin. Thus, the functions of UspA and
UspD in PMS resistance are probably not identical or entirely
overlapping. This notion is supported also by the fact that
the
uspA and
uspD mutants acted in an additive manner (Fig.
1). A minor role in oxidative stress resistance can be attributed
to the class II proteins UspF and UspG (Fig.
1). Like for
uspD,
the minor sensitivity of the double mutant
uspFG was associated
with signs of elevated levels of free iron in the cell (streptonigrin
sensitivity) (Fig.
2). In addition, UspE appears to play a crucial
role in oxidative stress resistance, but this role was restricted
to defense against high concentrations of oxidative agent (Fig.
4). The exact function of the tandem UspE protein is not known,
but one interesting and unique phenotype of the
uspE mutant
is its total inability to form cell-cell interactions and cell
aggregates in stationary phase (Fig.
3A). The outer membrane
protein Ag43 has been identified as responsible for cell aggregation
in
E. coli, and such aggregation had been shown to confer protection
against H
2O
2 killing (
5,
21). This has been mechanistically
explained by the fact that cells in direct contact with the
oxidative agent will be more affected than cells located inside
an aggregate. Thus, the elevated sensitivity of the
uspE mutant
to oxidative agents might be related to its failure to form
aggregates under these conditions. The aggregation defect of
the
uspE mutant could be linked to a lower production of the
Ag43 protein (Fig.
3B) and an enhanced capacity of adhesion
promoted by the FimH protein (Table
3); indeed, the Ag43-mediated
aggregation of
E. coli cells has previously been shown to be
blocked by type 1 fimbriation (
10).
Despite the fact that the UspC protein clearly belongs to the class I subfamily of Usp proteins based on sequence analysis, it is functionally distinct from its family members, UspA and UspD. In fact, the function of UspC appears closer to that of the class III/IV protein UspE (Fig. 6). For example, both uspC and uspE mutants are nonmotile due to the lack of flagella (Fig. 5); the residual motility of the uspE mutant could be due to the few cells possessing flagella (1 out of 10,000) or may be accomplished by a sliding phenomenon, which is linked to lipopeptide, lipopolysaccharide, and glycolipid production (3). In addition, both the uspC and uspE mutants display an enhanced capacity for adhesion, linked to the presence of fimbriae (Table 3). Intriguingly, the class II proteins, UspF and UspG, appear to have the exact opposite effects, i.e., both deletion mutations enhanced motility (Fig. 5A) and resulted in poor fimbriation (yeast agglutination data are shown in Table 3). Using DNA microarray analysis, the expression of uspG was reported as being induced 21 times in a fimH mutant (20). In the same study, the authors observed only a twofold induction of uspG expression when using a mutant deleted of the entire fim operon. FimH is the protein responsible for the initiation of the fimbria formation. In a fimH mutant, the major fimbrial subunit protein FimA accumulates in the periplasm, but this will, of course, not occur when the entire fim operon is deleted. Thus, it is possible that the gene encoding UspG (and perhaps also the gene encoding UspF) responds to the accumulation of surface-destined proteins in the periplasm and that this class of Usps is involved in the export of such proteins.
In light of the data presented in this paper, the coordinated induction of Usps can now be partly explained: elevated levels of Usp proteins during a shift from feast to famine conditions are expected to enhance the cell's capacity to withstand different stresses and modulate activities related to motility and adhesion. Thus, the Usps are reprogramming the cell towards defense and escape. Notably, the functions provided by the Usp proteins, oxidative stress defense, iron homeostasis, and motility/adhesion, are known to be essential in bacterial pathogenesis, and it would therefore not be surprising if usp mutants of different pathogens displayed a reduced virulence. However, we suggest that creating cells lacking the whole complement of their Usp repertoire may be the only means of revealing the true importance of Usp proteins in the bacterial life cycle and virulence.

ACKNOWLEDGMENTS
This work was sponsored by grants from the Swedish Natural Research
Council, the Inga-Britt and Arne Lundberg Research Foundation,
and an award from the Göran Gustafsson Foundation for Scientific
Research in Molecular Biology.
We thank all members, past and present, of the Thomas Nyström group for fruitful discussions, Laurent Loiseau for providing plasmids, Peter Owen for antibodies against Ag43, and Karen Otto for help with the yeast agglutination assays.

FOOTNOTES
* Corresponding author. Mailing address: Department of Cell and Molecular Biology, Göteborg University, Medicinaregatan 9C, 413 90 Göteborg, Sweden. Phone: 46 31 7732582. Fax: 46 31 7732599. E-mail:
thomas.nystrom{at}gmm.gu.se.


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Journal of Bacteriology, September 2005, p. 6265-6272, Vol. 187, No. 18
0021-9193/05/$08.00+0 doi:10.1128/JB.187.18.6265-6272.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
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