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Journal of Bacteriology, September 2002, p. 5194-5199, Vol. 184, No. 18
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.18.5194-5199.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Staphylococcus aureus Contains Two Low-Molecular-Mass Phosphotyrosine Protein Phosphatases
Didier Soulat,1 Elisabeth Vaganay,1 Bertrand Duclos,1 Anne-Laure Genestier,2 Jérôme Etienne,2 and Alain J. Cozzone1*
Institute of Biology and Chemistry of Proteins, University of Lyon, CNRS,1
Department of Medical and Molecular Microbiology, Faculty of Medicine Laënnec, Lyon, France2
Received 27 March 2002/
Accepted 13 June 2002

ABSTRACT
The analysis of the different amino acid sequences deduced from
the complete genome sequence of the gram-positive bacterium
Staphylococcus aureus suggested the presence of two eukaryotic-protein-like
low-molecular-mass phosphotyrosine protein phosphatases, which
are usually found in gram-negative bacteria. To check this prediction,
the corresponding genes were cloned and overexpressed in an
Escherichia coli system. Two distinct proteins with an apparent
molecular mass of 23 kDa each, PtpA and PtpB, were produced
and then purified by affinity chromatography and assayed for
enzymatic properties. As expected, they both exhibited phosphatase
activity in vitro, with a maximum value at a pH of around 6.2
and at a temperature of 40°C. In addition, their kinetic
constants, their specificity for phosphotyrosine residues, and
their sensitivity to two phosphatase inhibitors,
N-ethylmaleimide
and orthovanadate, matched those of acid low-molecular-mass
phosphotyrosine protein phosphatases.

TEXT
Protein phosphorylation on tyrosine has long been considered
a posttranslational modification specific to eukaryotes. In
these organisms, it has been shown to play a key role in a series
of fundamental biological functions, including signal transduction,
growth control, metabolism, and malignant transformation (
10,
12). In recent years, this modification has been demonstrated
to occur also in bacteria, both gram-negative and gram-positive
species (for a review, see reference
7). However, its biological
significance remains unclear even if, in a few cases, a possible
functional role has been proposed. Thus, it has been reported
that protein tyrosine phosphorylation could be involved in the
mechanism of pigment production in
Streptomyces coelicolor (
29).
Alternatively, it could participate in the control of biosynthesis
and/or transport of exopolysaccharides in
Escherichia coli (
13,
30,
31),
Streptococcus pneumoniae (
3,
18), and
Sinorhizobium meliloti (
21). Since exopolysaccharides have an important part
in the interactions of bacteria with their environment, namely,
with host cells, as well as in the process of adherence and
in the resistance to host immunity, they are commonly considered
essential virulence factors in many pathogens (
24). On this
basis, it has been suggested that protein tyrosine phosphorylation
might be connected to bacterial pathogenicity (
3,
13).
A major characteristic of protein phosphorylation in general is the fact that it is a reversible reaction. Indeed, the extent of phosphorylation of proteins results from the relative activity of two types of opposing enzymes, protein kinases and protein phosphatases. The differential functioning of these enzymes thus constitutes a regulatory device that the cell may utilize for controlling its metabolism and physiology. To discover the biological role(s) of protein tyrosine phosphorylation, it is therefore important to study not only the protein tyrosine kinases responsible for phosphorylation on tyrosine but also the phosphotyrosine protein phosphatases that catalyze dephosphorylation.
Two main classes of phosphotyrosine protein phosphatases have been characterized so far based on the type of bacteria in which they are found (14). First, in gram-negative species, phosphatase activity is borne by eukaryotic-protein-like enzymes of low molecular mass which all contain two conserved active-site sequence motifs, D-P-Y and C-X4-C-R (9, 26, 27). Second, in gram-positive bacteria, phosphatase activity is generally harbored by phosphoesterases of the PHP (polymerase and histidinol phosphatase) family, which have in common four conserved motifs, termed domains I to IV, essential for metal binding and dephosphorylating activity (2, 19). In particular, the presence of an enzyme of the latter type, called phosphatase CapC, has been predicted in Staphylococcus aureus (19), a bacterium that represents one of the main causes of community-acquired and hospital-acquired infections and that has become resistant to practically all antibiotics. This phosphatase is a homologue of protein CpsB, which has been demonstrated to possess PHP activity in Streptococcus pneumoniae (19).
In this work, we took advantage of the recent availability of the complete genome sequence of S. aureus to perform an exhaustive analysis of its phosphotyrosine protein phosphatase content. We present for the first time evidence that S. aureus contains two other phosphotyrosine protein phosphatases besides CapC. Interestingly, these two enzymes exhibit the structural and biochemical features specific to the low-molecular-mass phosphatases usually found in gram-negative bacteria rather than in gram-positive species.
Prediction of two low-molecular-mass phosphatases.
The starting point of this study was the comparative analysis of the different amino acid sequences deduced from the complete genome sequence of serotype 5 S. aureus available in The Institute for Genomic Research database (www.tigr.org) and the amino acid sequences of certain phosphotyrosine protein phosphatases previously characterized in other organisms. Besides the occurrence of CapC, a phosphotyrosine protein phosphatase of the PHP type, which was previously suggested by other authors (19), we detected a striking sequence similarity between two putative proteins of S. aureus (Reynolds strain) and various prokaryotic and eukaryotic phosphotyrosine protein phosphatases of low molecular mass (around 20 kDa), including Wzb from E. coli (30), EpsP from Pseudomonas solanacearum (11), AmsI from Erwinia amylovora (4), SA-PTPase from Schizosaccharomyces pombe (17), and BLACP1 from bovine heart (32) (Fig. 1). In particular, these two proteins appeared to contain the essential catalytic-site residue D within the conserved motif D-P-Y (amino acids 120 to 122) as well as the essential active-site residues C-X4-C-R (amino acids 8 to 14) in the phosphate binding loop, which are considered two signatures specific to this class of protein phosphatases (9, 27). These two proteins were termed PtpA and PtpB to recall their homology with phosphotyrosine phosphatases. The molecular masses calculated from the nucleotide sequences of the relevant genes were 17,493 Da for PtpA and 15,790 Da for PtpB. Further analysis using The Institute for Genomic Research database showed that the ptpA and ptpB genes are distant from each other (separated by 221,093 nucleotides), which suggested that they are not located on the same operon, even though no information on the nature of the surrounding genes is currently available. Interestingly, the presence of a pair of genes that were 100% identical in sequence to ptpA and ptpB was also observed in each of several different strains of S. aureus, including N315, COL, EMRSA, NTC 8325, Mu50, and MSSA, and even in Staphylococcus epidermidis. It therefore appeared that these two genes are widely conserved across the Staphylococcus species.
Cloning and overproduction of phosphatases.
Based on this predictive analysis, a series of experiments was
undertaken to demonstrate the presence of proteins PtpA and
PtpB in
S. aureus cells and then to study their biochemical
properties. First, the
ptpA and
ptpB genes, with appropriate
restriction sites at both ends, were prepared by using total
DNA from
S. aureus (
25) as a template in PCR amplification and
specific oligonucleotide primers. The locations, directions,
and DNA sequences of the various primers used are available
from the authors on request. Amplified fragments were digested
with appropriate restriction enzymes and inserted separately
into the pET15b vector previously opened with the same enzymes
to yield the expression plasmids pET15b-
ptpA and pET15b-
ptpB.
Each plasmid could thus synthesize a fusion protein with a six-histidine
tag at its N terminus. After transformation of competent cells
from the BL21(DE3) strain of
E. coli at 37°C (
1,
8), the
pET15b-
ptpA construct could efficiently overproduce, in the
soluble fraction of cells, a 23-kDa protein, PtpA, upon induction
by isopropyl-ß-
D-thiogalactopyranoside (IPTG) (Fig.
2, lane 2). By contrast, the pET15b-
ptpB plasmid was unable
to direct high-yield production of soluble protein PtpB in the
same BL21(DE3) strain of
E. coli. In fact, a significant amount
of total protein was produced, but most of it was found in inclusion
bodies, i.e., in insoluble form. Therefore, a different strain
of
E. coli, BL21(DE3) (pREP4-
groESL), was used. This strain
overproduces the two chaperone proteins GroES and GroEL and
is suitable for obtaining proteins in a soluble form when they
possess a high degree of hydrophobicity and, consequently, a
tendency to aggregate. In these conditions, pET15b-
ptpB could
then overproduce a relatively large amount of a 23-kDa soluble
protein, His-tagged PtpB, upon induction by IPTG (Fig.
2, lane
5). Still, PtpB appeared to be essentially soluble in cells
grown at around 20°C and became insoluble when the temperature
was raised to 37°C, even in the presence of chaperones GroES
and GroEL.
Purification of proteins PtpA and PtpB.
E. coli DH5

cells were transformed with plasmid pET15b-
ptpA or plasmid pET15b-
ptpB. Then, plasmid pET15b-
ptpA was transferred
from
E. coli DH5

cells to
E. coli BL21(DE3) cells. Cells from
this strain were used to inoculate 100 ml of Luria-Bertani medium
supplemented with ampicillin (100 µg ml
-1) and were incubated
at 37°C with shaking until the
A600 reached 0.5. IPTG was
added at a final concentration of 1 mM. Growth was continued
for 2 h at 37°C with shaking. Plasmid pET15-
ptpB was transferred
from
E. coli DH5

cells to
E. coli BL21(DE3) (pREP4-
groESL) cells.
Cells from this strain were used to inoculate 200 ml of Luria-Bertani
medium supplemented with ampicillin (100 µg ml
-1) and
kanamycin (25 µg ml
-1) and were incubated at 37°C
with shaking until the
A600 reached 0.5. Ampicillin and IPTG
were then added at final concentrations of 100 µg ml
-1 and 1 mM, respectively. Growth was continued for 3 h at 20°C
with shaking.
Both types of cells were further treated under the same conditions. Cells were harvested by centrifugation at 3,000 x g for 10 min and suspended in 5 ml of buffer A (50 mM Tris-HCl [pH 7.4], 300 mM NaCl, 10% [vol/vol] glycerol) containing DNase I and RNase A at a final concentration of 2 µg ml-1 each. Cells were disrupted in a French pressure cell at 16,000 lb/in2. The resulting suspension was centrifuged at 4°C for 30 min at 30,000 x g. The supernatant was incubated for 1 h at 4°C with 750 µl of Ni-nitrilotriacetic acid (NTA) agarose (Qiagen) suitable for purification of fusion protein carrying a polyhistidine tag. The matrix was then packed and washed with 100 ml of buffer A containing 10 mM imidazole. Protein elution was monitored at 280 nm, and eluted fractions were analyzed by electrophoresis (15). His-tagged PtpA and PtpB were eluted at a concentration of 200 mM imidazole. Fractions containing purified PtpA or PtpB were dialyzed against buffer B (50 mM Tris-HCl [pH 7.4], 100 mM NaCl, 1 mM EDTA, 1 mM dithiothreitol, 10% [vol/vol] glycerol) and stored at -20°C. A typical electrophoretic pattern of each purified phosphatase is shown in Fig. 2 (lanes 3 and 6). In each case, besides the major band corresponding to the phosphotyrosine protein phosphatase, a few contaminating proteins could also be detected in the upper part of the gel in the form of two to three minor bands. It was unlikely, however, that these proteins could harbor a phosphatase activity, namely, one arising from the E. coli host in which PtpA and PtpB were produced. Indeed, they had molecular masses ranging from 45 to 75 kDa, whereas the two phosphotyrosine protein phosphatases present in E. coli, Wzb and Etp, are known to have masses of only 16,709 and 16,386 Da, respectively (30). In addition, these two E. coli phosphatases could hardly copurify, and consequently comigrate, with PtpA and PtpB since only the latter enzymes were His tagged and could be adsorbed on a Ni2+-agarose column.
Phosphatase activity of PtpA and PtpB.
The phosphatase activity of these two proteins was assayed in vitro by using a method based on the detection of p-nitrophenol (PNP) formed from p-nitrophenyl phosphate (PNPP) cleavage. Tests were performed in a 1-ml reaction volume containing 100 mM sodium citrate, 1 mM EDTA, and PNPP at various concentrations from 1 to 40 mM. The amount of PNP produced was determined by the addition of 500 µl of 4 M NaOH to the reaction mixture. Phosphatase activity was estimated at 405 nm by using a PNP concentration range (22). The assay was optimized with respect to protein concentration, time, and pH. Two series of assays were performed to evaluate the effects of pH and temperature. Maximum activity was observed at pH 6.2 for PtpA and at a pH value ranging from 5.7 to 6.5 for PtpB (Fig. 3A), i.e., at acidic pH for both enzymes. Measurement of the phosphatase activity as a function of temperature showed that, for each enzyme, maximum activity was obtained at around 40°C (Fig. 3B). All subsequent enzyme assays were carried out at pH 6.2 and 37°C, which is a more physiological temperature. In these conditions, the kinetic constants were measured. The Km values for PNPP were found to be similar for both enzymes (1.2 mM for PtpA and 1.5 mM for PtpB), whereas the specific activity of PtpA was much higher than that of PtpB (33.6 and 1.4 µmol min-1 mg-1, respectively). These values were consistent with those previously reported for other acid low-molecular-mass protein phosphatases (23, 33).
Substrate specificity of phosphatases.
To gain more information on the substrate specificity of PtpA
and PtpB, their in vitro activity on individual phosphorylated
amino acids was assayed at 37°C in a 50-µl reaction
volume containing 10 mM
O-phosphoserine,
O-phosphothreonine,
or
O-phosphotyrosine as a substrate, 100 mM sodium citrate (pH
6.25), 1 mM EDTA, and 0.4 µg of purified PtpA or PtpB.
After 15 min of incubation, the reaction was stopped by adding
150 µl of 25% (wt/vol) trichloroacetic acid and then 50
µl of bovine serum albumin (10 mg ml
-1). The precipitated
protein was removed by centrifugation, and the supernatant was
used for measuring released inorganic phosphate by using 1 volume
of a mixture containing 1.2 M sulfuric acid, 0.5% ammonium molybdate,
and 2% ascorbic acid. Samples were heated at 56°C for 15
min, and the absorbance was measured at 750 nm (
5,
20). It was
found that PtpA and PtpB released 140 and 40 µmol, respectively,
of inorganic phosphate from phosphotyrosine but had no effect
on either phosphoserine or phosphothreonine. The specificity
of PtpA and PtpB for phosphotyrosine was confirmed by studying
the effect of two different molecules known to inhibit phosphotyrosine
protein phosphatases,
N-ethylmaleimide and sodium orthovanadate
(
6,
34). Assays were carried out by using the same method as
that described above for the phosphatase assay, with a buffer
containing 100 mM sodium citrate (pH 6.25), 1 mM EDTA, 40 mM
PNPP, purified PtpA or PtpB, and various concentrations of inhibitors.
Both
N-ethylmaleimide and sodium orthovanadate were found to
strongly inhibit the phosphatase activity of PtpA and PtpB (Fig.
4). More precisely, the concentrations required for blocking
the enzyme activity by 50% were around 7 mM for
N-ethylmaleimide
and 3 mM for sodium orthovanadate, with, in general, PtpA having
a slightly higher sensitivity to inhibitors than PtpB.
Conclusion.
Together, these data concurred in showing that
S. aureus harbors
two distinct enzymes, PtpA and PtpB, which have similar structural
and functional properties and which belong to the family of
acid low-molecular-mass phosphotyrosine protein phosphatases.
A series of previous observations (
26) has shown that, in general,
this type of phosphatase is found in gram-negative bacteria
rather than in gram-positive species. The present results provide
evidence that low-molecular-mass phosphatases are also present
in gram-positive bacteria and thus confirm a similar observation
made with another gram-positive bacterium,
Streptomyces coelicolor (
16), which had been considered an exception until now. Given
the previous suggestion that
S. aureus also contains a phosphotyrosine
phosphatase, CapC, of the PHP family that is homologous to the
CpsB protein from
Streptococcus pneumoniae (
19), it would therefore
appear, for the first time, that one bacterial species can simultaneously
harbor two different classes of phosphotyrosine protein phosphatases.
Further experiments are now needed to characterize the protein
substrates of these various phosphatases and to assess their
differential roles in the physiology, and possibly in the pathogenicity,
of bacteria.

ACKNOWLEDGMENTS
We thank I. Martin-Verstraete (Pasteur Institute, Paris, France)
for providing
E. coli strain BL21(DE3) (pREP4-
groESL).
This work was supported by grants from the Ministère de la Recherche (contract FNS 2000 Microbiologie), the Société Ezus-Lyon (contract 482.022), and the Institut Universitaire de France.

FOOTNOTES
* Corresponding author. Mailing address: Institute of Biology and Chemistry of Proteins, 7 Passage du Vercors, 69367 Lyon Cedex 07, France. Phone: 33 (0)4.72.72.26.72. Fax: 33 (0)4.72.72.26.01. E-mail:
aj.cozzone{at}ibcp.fr.


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Journal of Bacteriology, September 2002, p. 5194-5199, Vol. 184, No. 18
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.18.5194-5199.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
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