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Journal of Bacteriology, September 1999, p. 5790-5799, Vol. 181, No. 18
Department of Pediatrics, Children's
Hospital Regional Medical Center CH-31, University of Washington,
Seattle, Washington 98105,1 and
Department of Biochemistry, Wake Forest University Medical
Center, Winston-Salem, North Carolina 27157-10162
Received 30 March 1999/Accepted 7 June 1999
We have identified and characterized an Enterococcus
faecalis alkaline phosphatase (AP, encoded by phoZ).
The predicted gene product shows homology with alkaline phosphatases
from a variety of species; it has especially high similarity with two
alkaline phosphatases from Bacillus subtilis. Expression of
phoZ in Escherichia coli, E. faecalis, Streptococcus agalactiae (group B
streptococcus [GBS]), or Streptococcus pyogenes (group A
streptococcus [GAS]) produces a blue-colony phenotype on plates
containing a chromogenic substrate, 5-bromo-4-chloro-3-indolylphosphate
(XP or BCIP). Two tests were made to determine if the activity of the
enzyme is dependent upon the enzyme's subcellular location. First,
elimination of the signal sequence reduced AP activity to 3% of the
wild-type activity (or less) in three species of gram-positive
bacteria. Restoration of export, using the signal sequence from C5a
peptidase, restored AP activity to at least 50% of that of the wild
type. Second, we engineered two chimeric proteins in which AP was fused to either a periplasmic domain or a cytoplasmic domain of lactose permease (a membrane protein). In E. coli, the periplasmic
fusion had 17-fold-higher AP activity than the cytoplasmic fusion. We concluded that AP activity is export dependent. The signal sequence deletion mutant, phoZ Alkaline phosphatase is a
metalloenzyme that catalyzes the nonspecific hydrolysis of a wide
variety of phosphomonoesters (reviewed in reference
12). Alkaline phosphatases have been identified in a
wide variety of organisms, including Escherichia coli and humans (5, 22). A conserved set of amino acids has been
shown to be critical to catalysis, and both zinc and magnesium ions are
essential for function (23). The structure of the E. coli alkaline phosphatase has been refined to a resolution of 2.0 Å (24). Expression is induced in E. coli by
phosphate limitation, and control of expression has been extensively
investigated (reviewed in reference 39). E. coli alkaline phosphatase (encoded by phoA) is
synthesized as a precursor with a cleavable N-terminal signal sequence
(20). In E. coli, the cytoplasm is a reducing
environment while the periplasm has a disulfide bond-forming enzymatic
system. These contrasting redox environments are thought to limit the formation of essential disulfide bonds to the periplasm and may account
for the export-dependent activity of alkaline phosphatase (4).
Investigators working with gram-negative bacteria have exploited the
location-sensitive activity of E. coli alkaline phosphatase for many different tasks, including the identification of genes encoding secreted proteins and integral membrane proteins
(6), the analysis of membrane protein topology
(9), and the discovery of insertion-tolerant sites within a
membrane protein (28). The E. coli alkaline
phosphatase enzyme (encoded by phoA) exhibits reduced
activity in a gram-positive background, possibly due to the absence of
an extracytoplasmic enzyme with disulfide bond-forming activity
(30).
In contrast with the E. coli enzyme, much less is known
about the regulation, processing, structure, and activity of alkaline phosphatases from gram-positive bacteria. The most advanced studies have been performed in Bacillus subtilis, where a complex
pathway involving three two-component regulatory systems controls the phosphatase loci (reviewed in reference 19).
In this report we describe the identification and characterization of
the Enterococcus faecalis alkaline phosphatase protein (AP,
encoded by phoZ). Expression of phoZ conferred a
blue-colony phenotype in E. coli and three gram-positive
species on 5-bromo-4-chloro-3-indolylphosphate (XP or BCIP) agar.
Alkaline phosphatase activity was quantified, and in all strains the
activity per cell was shown to be minimal when AP was retained in the
cytoplasm. The activity per cell increased substantially when AP was
exported, suggesting that the activity of AP is export dependent. We
exploited these characteristics to identify random group B
streptococcus (GBS) chromosomal fragments that encoded signal
sequence-like peptides.
Strains and media.
The gene encoding AP, phoZ,
was cloned from the E. faecalis strain 10C1 (ATCC 11700).
The E. coli strain DH5 DNA manipulation and transformation.
Cloning experiments
were performed as previously described (2, 32, 34).
Restriction enzymes were obtained from New England Biolabs (Beverly,
Mass.) or Promega. Sequencing reactions were carried out by using the
ABI PRISM dye terminator cycle sequencing kit (Perkin Elmer, Foster
City, Calif.). Sequencing products were separated from unincorporated
dyes by using Centri-Sep columns (Princeton Separations, Inc.,
Adelphia, N.J.). Automated sequencing was performed at the Fred
Hutchinson Cancer Research Center (Seattle, Wash.). Plasmid
preparations were performed by using Qiagen Mini or Maxi preparation
kits (Qiagen, Chatsworth, Calif.). GBS and GAS were electroporated as
described in references 17 and
35, respectively. E. faecalis was
transformed as described in reference 13 except that
the SGM17 media contained 3.5% glycine and 0.4% sucrose.
Electroporated cells were recovered in a THB-0.25 M sucrose solution.
PCR of large segments of DNA (up to 6 kb) was performed by using the
Expand High Fidelity system (Boehringer Mannheim, Indianapolis, Ind.).
Plasmids and
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Characterization of Enterococcus
faecalis Alkaline Phosphatase and Use in Identifying
Streptococcus agalactiae Secreted Proteins

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ABSTRACT
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
ss, was used to identify random
genomic fragments from GBS that encode exported proteins or integral
membrane proteins. Included in this set of fragments were genes that
exhibited homology with the Rib protein (a cell wall protein from GBS)
or with DppB (an integral membrane protein from GAS). AP acts as a
reporter enzyme in GBS, GAS, and E. faecalis and is
expected to be useful in a variety of gram-positive bacteria.
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INTRODUCTION
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
![]()
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
F' (Promega, Madison, Wis.) was
used for the cloning experiments. The E. coli strain CC873
is CC118 (29) with F' lacIq
lacY::cat (2a). Note that
CC118 carries
phoA. The GBS strain COH31r/s
(33), the group A streptococcus (GAS) strain CS101 (21), and E. faecalis OG1SSp (15) were
used for colony morphology studies and quantitative AP assays. E. coli strains were grown either in Luria broth (LB) or M9 medium
(Difco, Detroit, Mich.) supplemented with 15 g of agar/liter, 100 µg of ampicillin/ml, 10 µg of chloramphenicol/ml, 50 µg of XP
(Sigma, St. Louis, Mo.)/ml, or 2 mM
isopropyl-
-D-thiogalactopyranoside (IPTG)
(5-Prime-3-Prime Inc., West Chester, Pa.) as required. COH31 r/s was
grown in Todd-Hewitt broth (THB) (Difco) supplemented with 10 µg of
chloramphenicol/ml as required. Both CS101 and OG1SSp strains were
grown in THB supplemented with 0.2% yeast extract (Difco) and 5 µg
of chloramphenicol/ml. E. coli and GBS cultures were grown
with shaking at 200 rpm. Strains carrying derivatives of the
temperature-sensitive vector pVE6007 were grown at 30°C; all others
were grown at 37°C.
libraries.
The construction of plasmids is
diagrammed in Fig. 1. E. faecalis chromosomal DNA was sheared by repeated passage through a
narrow-gauge needle, size selected (3 to 8 kb), and joined with EcoRI linkers before ligating the fragments into
phosphatase-treated
gt11 arms. After in vitro packaging,
recombinants were isolated at a frequency of 8 × 105
per µg of streptococcal DNA. An isolate exhibiting APase activity was
purified, and the gene was subcloned, initially into pUC13.

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FIG. 1.
Construction of plasmids used to characterize AP
activity. The phoZ gene was subcloned from a
library on
a 3.2-kb EcoRI fragment into pUC13 to form pAP01 (not
depicted). A 1.9-kb EcoRI-SalI fragment
containing phoZ was subcloned from pAP01 into pBluescript to
make pAP03. To characterize phoZ activity in E. faecalis, the phoZ gene was joined to a constitutive
promoter from the NADH peroxidase gene (Pnpr)
(unpublished data) and carried on the pAM401 vector in a three-part
ligation producing pAP09. We planned to fuse the mature region of AP
('AP, encoded by 'phoZ) to the integral membrane protein
lac permease (encoded by lacY) as part of our
characterization of AP activity. Consequently, the phoZ gene
on pAP09 was moved on an XbaI-SalI fragment into
the broad-host-range vector pGBS1 to make pGBS1phoZ (not
depicted). Two BamHI sites found in pJS3phoZ were
eliminated by digestion, Klenow filling, and ligase treatment of the
blunt-ended fragment to produce pMHL101. Inside-out PCR was used to
amplify the entire pJS3phoZ plasmid except the signal
sequence codons. (The primers used in the amplification, oML101B and
oML107, had 5' noncomplementary sequences that included a
BamHI site [Table 2].) The linear PCR product was digested
with BamHI and then ligase treated to form pMHL102, in which
the codons encoding the signal sequence were replaced with two codons
containing a BamHI site (phoZ
ss). The
BamHI-AflII fragment from pMHL102 encodes 'AP.
Plasmid pCM701 has an insertion carrying a BamHI site within
the region of lacY encoding the first periplasmic domain,
lacY(P1) (28). Fusion of 'AP to lactose permease
was created by introducing the BamHI-AflII
fragment from pMHL102 into BamHI-AflII-digested
pCM701 to produce pMHL103. To enhance the utility of phoZ
(see the Materials and Methods section) the recognition site for
PstI was removed by site-directed mutagenesis from pAP03 to
form pAP010, while the HindIII site was removed from
pAP09 to produce pAP011 (product plasmids not depicted). A
HincII fragment from pAP011, bearing the
HindIII site point mutation, was cloned into
HincII-digested pAP010 to produce the (neither
HindIII nor PstI site) double mutant termed
phoZ1, on pAP12. An SphI linker was inserted at
the unique Eco57I site in phoZ1 on pAP12 to
create an allele with wild-type activity, termed phoZ2, on
pDC110 (not depicted). The phoZ2 gene was isolated from
pDC110 on a HaeII-XmnI fragment and cloned into
pDC111 (a pJS3 derivative) to produce pDC113 (10). The
codons encoding the hydrophobic core of AP were eliminated from pDC113
by using inside-out PCR with the primers used to create pMHL102.
However, the resulting plasmid, pMHL108, was shown to contain a number
of PCR-induced mutations. These mutations were reversed by cloning in
the BamHI-AflII fragment from pMHL102 to create
pMHL109, encoding phoZ
ss. Restoring the original signal
sequence by inserting a PCR fragment in the BamHI site
failed to restore full activity (not shown). Consequently, a PCR
fragment placing the BamHI site further upstream and
containing all the sequence differences, termed `phoZ',
was amplified from pDC113 and cloned into pMHL109 to form pAN200 (see
the Materials and Methods section and Table 2).
10 promoter sequences, but the sequences at the
35
position were not included on the cloned chromosomal fragment. Several promoter and broad-host-range vector combinations were constructed in
the course of optimizing expression. Plasmid pAP09 contains a 241-bp
fragment in which the npr promoter is fused to
phoZ and exhibits high AP activity in E. faecalis
but not in GBS. Plasmid pGBS1 is composed of the broad-host-range
plasmid pJS3 (3) with the multiple cloning site from pUC19
(40) inserted at the HindIII site. When the
Pnpr-phoZ construct was cloned into pGBS1, the
resulting vector (pMHL101) also failed to produce high levels of AP
expression in GBS. When phoZ was cloned in front of the
cat promoter in pDC111, the resulting plasmid (pDC113) caused GBS transformant colonies to exhibit a striking blue color on XP
media (10).
In the course of cloning phoZ and evaluating expression
schemes, we also made a number of alterations to its primary structure. We anticipated that phoZ could be used in cloning vectors
that have a multiple cloning site within phoZ. Insertions of
cloned DNA should disrupt phoZ and could be identified on
the basis of whether colonies were blue or white. Consequently, the
sites for the commonly used enzymes HindIII and
PstI were removed from phoZ by site-directed
mutagenesis to form phoZ1 on pAP12 (see Table 2 for complete
definitions for oligonucleotides PX and HX). Linkers carrying
SphI were inserted at a number of restriction sites in phoZ1 as a means of detecting insertion-tolerant sites. One
such mutation introduced a linker into the unique Eco57I
site to form phoZ2, which proved to be phenotypically silent
(plasmid pDC113 [10]). All three alterations are
detailed in Table 1.
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ss (AP lacking its signal sequence) are shown in Table
2. The PCR that produced
phoZ
ss on pMHL108 also introduced several mutations 3' to
the new BamHI site. To remove these mutations the
BamHI-AflII fragment from pMHL102 carrying
'phoZ (encoding 'AP) was inserted into pMHL108 to create
pMHL109. This construct exhibited decreased AP activity. However,
activity was not fully rescued when the deleted signal sequence codons
were PCR amplified (with flanking BamHI sites) and inserted
into the BamHI site in phoZ
ss (data not
shown). We speculated that the codons encompassing the BamHI
sites were distorting the polar region of the signal sequence.
Consequently, oligonucleotides ANML121 and ANML122 were used to amplify
a region of phoZ that did not include putative polar region
codons (Table 2 includes exact descriptions of the oligonucleotides and
the changes to AP). The PCR product, termed `phoZ' (Fig.
1), was cloned into pMHL109 to produce pAN200. The phoZ2
ss construct on pAN200 could be fully rescued by
exogenous signal sequences (see the Results section).
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AP assays. AP assays in E. coli were performed as described in reference 8 except that iodoacetamide was added to lysed cells (14). Experiments with and without 1 mM iodoacetamide revealed that the reagent had no effect on wild-type AP (data not shown). The AP assay for gram-positive species was very similar to the E. coli assay, but no cell lysis step was performed (there is no outer membrane to slow substrate diffusion) and iodoacetamide was omitted. Briefly, overnight cultures were grown in rich media (see "Strains and media," above). The cultures were diluted and allowed to grow to mid-log phase (an optical density at 600 nm [OD600] of ~0.6 for GBS), and the cells were pelleted, washed, and resuspended to their original volume in MOPS (morpholinepropane sulfonic acid) salts (14). Cell density was determined by optical absorbance (OD600 for GBS and E. faecalis and OD680 for GAS). A small volume of cells (5 to 100 µl, depending on the activity per cell) was added to AP buffer (1 M Tris [pH 8.0]-0.1 mM ZnCl2) to a final volume of 0.9 ml, 100 µl of 0.4% p-nitrophenyl phosphate (pNPP) was added, and the reaction was started by incubation at 37°C. Reactions were stopped by adding 120 µl of stop solution (a 1:5 mix of 0.5 M EDTA:1 M KH2PO4). The activity per cell was calculated in Miller units. The numbers of CFU per absorbance unit vary from species to species, so only relative changes can be compared across species. Experiments were run to verify that the measured activity per milliliter was proportional to the number of cells per milliliter (data not shown), to control against saturation of the assay.
Nucleotide sequence accession number and sequence analysis. The sequence for phoZ has been submitted to GenBank and deposited under accession no. AF154110. Homologs were identified by using a FASTA search on Biology Workbench (38). Alignments were established with the PILEUP or Gap modules of the Genetics Computer Group's Wisconsin Package (18).
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RESULTS |
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A
gt11 library carrying E. faecalis inserts was
constructed with the intention of isolating various enterococcal genes
by immunological techniques. Plaques were screened by hybridizing with
a secondary antibody conjugated with alkaline phosphatase and
incubating the blot in the presence of a chromogenic alkaline phosphatase substrate. Unexpectedly, certain plaques were able to
cleave the substrate even in the absence of this conjugated antibody,
indicating that the recombinant phage encoded an alkaline phosphatase.
These plaques were isolated, and subsequent cloning experiments
identified a 1.9-kb EcoRI-SalI fragment with a
471-codon open reading frame that encodes a predicted protein of 51 kDa. A ribosome-binding site (GGAGG) was found 10 bp upstream of the
initiator methionine codon. The
10 sequence (TATAGT)
typical of
70-controlled transcription was found further
upstream, but the corresponding
35 sequences were not included on the
fragment cloned from E. faecalis.
Database searches revealed significant homology to alkaline phosphatases from a variety of organisms. One-on-one Gap sequence analysis indicated that AP residues were identical to 56% of the residues in B. subtilis alkaline phosphatase A and to 63% of the residues in B. subtilis alkaline phosphatase B. In contrast, there were 30 to 40% identities between residues when AP was compared to phosphatases from gram-negative bacteria or eukaryotes. The catalytic core of the E. coli alkaline phosphatase is composed of residues Asp 101, Ser 102, Ala 103, and Arg 166 (of the mature E. coli sequence). These residues are well conserved in an alignment of phoZ with the phosphatase genes from B. subtilis, Bacillus licheniformis, Saccharomyces cerevisiae, Thermus sp. FD3041, and Halocynthia roretzi (not shown). The Thermus alkaline phosphatase has a similar Glu-Ser-Ser sequence in place of the canonical Asp-Ser-Ala. The eight metal-ion-coordinating residues are almost perfectly conserved in this alignment (a histidine expected at position 419 of the Halocynthia sequence appears at position 417 instead).
The full-length AP protein includes a signal sequence composed of an N-terminal region containing three positively charged residues and a core region with 14 hydrophobic residues. The protein appears be exceptionally stable, as it retains phosphatase activity after sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electroblotting onto nitrocellulose (data not shown).
Signal sequence deletions.
A strategy of removing and
replacing the signal sequence was adopted to compare the activities of
AP in different subcellular locations. The codons encoding the
hydrophobic core and putative polar region (underlined),
MKKRALLGVTLLTFTTLAGCTNLSEQKS, were replaced with two new
codons containing a BamHI site. The predicted N-terminal
sequence expressed from the phoZ
ss mutant was
MKKRDPEQKS. E. coli MC1061 was transformed with
pJS3 (does not express AP), pDC113 (expresses AP), or pAN200 (expresses
AP
ss), and the transformants were subjected to quantitative alkaline
phosphatase assays. The negative control, MC1061(pJS3), exhibited AP
activity of 2 Miller units. The phoZ+ strain,
MC1061(pDC113), exhibited activity of 770 units. In contrast, the
phoZ
ss strain, MC1061(pAN200), exhibited activity of only 54 units. The 14-fold difference in AP activity between strains expressing phoZ and phoZ
ss supports the
hypothesis that AP activity is export dependent in E. coli.
Although the AP
ss strain had relatively low activity, it is notable
that it exhibited significantly greater activity than that associated
with the AP
strain, MC1061(pJS3). It is possible that
AP
ss was released from the cytoplasm through a slow process of cell
lysis, where it acquired an active conformation.
Restoring signal sequence activity.
Deletion of the signal
sequence decreased AP activity. This may be due to the altered
subcellular location of the mutant enzyme. However, it is also possible
that the mutation may have disrupted the enzyme's catalytic mechanism.
To distinguish between these hypotheses, a PCR fragment encoding the
signal sequence from the GBS C5a peptidase (scpB) was
inserted at the BamHI site of phoZ
ss. The new
plasmid was designated pAN202 and encodes phoZsss
(scpB signal-sequence). The predicted N-terminal sequence of
APsss was MKKR
QKLPFDKLAIALMSTSILLNAQS
EQKS.
Both of the aspartic acid-proline peptide sequences (double underlined)
are encoded by the DNA sequences that contain the BamHI
sites. The underlined amino acids are native to C5a peptidase.
Test of export-dependent activity in gram-positive bacteria.
We compared AP activities in strains expressing either no
phoZ (negative control) or phoZ2 (positive
control), phoZ
ss, and phoZsss. The plasmids
carrying these genes are pJS3, pDC113, pAN200, and pAN202,
respectively. The four plasmids were electroporated into the GBS strain
COH31r/s, the GAS strain CS101, and E. faecalis OG1SSp. The
colony phenotypes on XP media are shown in Fig.
2 (bottom). In all three species, the
control strain without phoZ produced white colonies. The
strains that expressed phoZ
ss were white or very pale
blue. In all three species, however, the strains that expressed either
phoZ or phoZsss were blue.
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ss
could be rescued by insertion of a heterologous signal sequence. Unfortunately, it is difficult to distinguish a partial rescue of AP
activity from a complete rescue of AP activity by using plate assays.
These two types of rescue can be distinguished with a colorimetric
liquid AP assay. The results of such an assay are shown in Fig.
3. In GBS, GAS, and E. faecalis, strains deficient for AP exhibited activity of 7 Miller
units or less. Strains expressing wild-type AP exhibited activity of at
least 1,500 Miller units. Strains expressing the signal sequence
deletion, AP
ss, exhibited less than 3% of the wild-type AP
activity. Strains expressing the chimeric protein, APsss, exhibited
more than 50% of the wild-type AP activity. The substantial
restoration of AP activity by the heterologous signal sequence in APsss
supports the hypothesis that AP activity is export dependent.
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Membrane-protein fusions. The hypothesis that AP functions with different levels of efficiency in different subcellular locations was further tested by fusing 'phoZ at different sites along a gene encoding an integral membrane protein. AP fused to a cytoplasmic site should be retained in the cytoplasm, while a fusion to an extracytoplasmic site should cause AP to be exported.
Lactose permease is an E. coli integral membrane protein encoded by lacY. ISlacZ/in mutagenesis has previously been used to introduce BamHI sites at various points along the length of lacY (28). Mutant lacY(P1) has an insertion just after the codon for asparagine 38, in the region of lacY encoding the first periplasmic domain (Fig. 4A). A 'phoZ cassette was cloned into the BamHI site in lacY(P1), producing lacY(P1)::phoZ on pMHL103 (Fig. 1). This fusion encodes a protein in which the mature region of AP is fused to the first periplasmic domain in lactose permease (Fig. 4B). Similarly, mutant lacY(C2) has a BamHI site inserted after the codon for glycine 71, in the region of lacY encoding the second cytoplasmic domain of lactose permease (Fig. 4C). The 'phoZ cassette was cloned into the BamHI site in lacY(C2), producing lacY(C2)::phoZ on pMHL104. This fusion encodes a protein in which the mature region of AP is fused to the second cytoplasmic domain in lactose permease (Fig. 4D).
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Transformation of fusions into GBS. The fusion studies showed that AP exhibits higher phosphatase activity when exported in E. coli. However, ultrastructural differences between gram-negative and gram-positive organisms may cause fusions to behave differently in gram-positive bacteria. Both lacY::phoZ fusion genes were cloned into a shuttle vector, pVE6007. Both of the new constructs exhibited the expected AP activities when transformed into E. coli (data not shown). Three attempts were made to electroporate the plasmids into GBS. The control plasmid pVE6007 transformed GBS at approximately 103 transformants per µg; however, no colonies were isolated when plasmids encoding the fusion proteins were used. The reason for our inability to transform GBS with these plasmids remains unclear. Plasmids encoding wild-type AP have been transformed into GBS previously (here, and see reference 10), and functional lactose permease has been expressed in the gram-positive organism Corynebacterium glutamicum (7). It is possible that transcription from the fusion gene interfered with plasmid maintenance functions or that the fusion unexpectedly produced a toxic protein in GBS.
Cloning genes encoding exported proteins.
The phoA
gene from E. coli is widely used in gram-negative bacteria
to identify genes that encode secreted proteins or to characterize the
topology of integral membrane proteins. We hypothesized that
phoZ could be used for the same purpose in GBS. COH1
chromosomal DNA was partially digested with Sau3A, and
fragments in the range from 0.5 to 4 kb were cloned into the
BamHI site of the phoZ
ss construct (pAN200).
The library was electroporated into E. coli ER2566 and
plated on media containing XP. After 24 h of growth, 0.6% of the
transformed colonies were blue. Electroporation of the ligation
products into the GBS strain COH31 r/s did not produce transformants,
presumably due to the low efficiency of electroporation in GBS.
Instead, the library established in E. coli was recovered, and the amplified library was electroporated into GBS. After 24 h
of growth, 0.5% of the transformed GBS colonies were blue. The number
of blue colonies increased with longer incubation, although the
background levels of alkaline phosphatase activity made it difficult to
distinguish low-activity fusions after growth for three days.
ss strain
exhibited activity of 1 Miller unit, and the strain expressing
wild-type AP exhibited activity of 70 Miller units. All eight of the
chimeric proteins produced higher activity than the strain expressing
wild-type XP. However, there was no support for the hypothesis that
fusions identified in GBS exhibit activity significantly different from that of fusions identified in E. coli (P > 0.20, t test for two groups of unpaired observations). The high activity
of the fusions was not surprising, as we had screened the library of
phoZ fusions for those that conferred a dark-blue-colony
phenotype within the first 24 h of growth. Variations in activity
could be attributed to changes in plasmid copy number, increases in
levels of expression due to the introduction of new promoters or
ribosome-binding sites, or improved export due to fusion of AP with a
more efficient export signal.
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23
kcal/mol or less (26). In this analysis, each residue in a
signal sequence is assigned a hydrophobicity value by using the GES
scale (16). The peptide sequence is broken into contiguous
segments delimited by charged residues, and the hydrophobicities of all
residues within a segment are summed. Export in gram-positive bacteria is less well characterized than export in gram-negative bacteria, and
we were interested in determining if the phoZ fusions
identified in GBS had segments with summed hydrophobicities exceeding
the E. coli threshold.
All eight phoZ fusions were sequenced to determine if the
chimeric proteins had segments of uncharged residues that met the summed-hydrophobicity criteria. The results are summarized in Table
3. All five chimeras identified in
E. coli contained nonpolar peptide segments with summed
hydrophobicities ranging from
33 to
52 kcal/mol. Similarly, the
inserts identified in GBS all had hydrophobic segments with summed
hydrophobicities ranging between
39 and
43 kcal/mol. Thus, all of
the chimeric proteins characterized in this study conformed to the
hydrophobicity threshold established for efficient export in E. coli. A similar threshold may exist for efficient export in GBS.
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DISCUSSION |
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We have identified and characterized phoZ, an E. faecalis gene that encodes AP. AP activity is reduced when the peptide is retained in the cytoplasm of gram-positive bacteria, and changes in activity can be easily screened by using plate assays based on the cleavage of a chromogenic substrate. These features were exploited to identify GBS genes that encode exported proteins.
An active phosphatase with low specificity could be deleterious if retained in the cytoplasm. Indeed, when E. coli alkaline phosphatase is retained in the cytoplasm the enzyme is inactive, possibly due to slow rates of disulfide bond formation in the cytoplasm (4). E. faecalis AP activity was expected to be similarly export dependent. In GAS, GBS, and E. faecalis, the signal sequence deletion mutant exhibited reduced activity. When export was restored by using an exogenous signal sequence, however, AP activity was restored. The exogenous signal sequence was unlikely to have the conformation and side chains needed to restore a disrupted catalytic site, so mutational inactivation is an implausible cause for low AP functionality in the cytoplasm. It is interesting that the deletion removed the only cysteine codon found on the phoZ open reading frame. Thus, unlike the E. coli alkaline phosphatase, disulfide bond formation cannot be essential for AP activity and cannot contribute to the different activities of the enzyme in different subcellular locations.
In an independent test, AP was placed in opposing subcellular locations by fusing the enzyme to a cytoplasmic domain or to a periplasmic domain in lactose permease. We could predict the subcellular location of AP for both of these chimeras, because E. coli alkaline phosphatase has been fused to the same two lactose permease domains and those chimeras placed alkaline phosphatase in opposing locations (9). The periplasmic AP chimera produced 17-fold-greater activity than the cytoplasmic chimera. In this test the native AP signal sequence is missing from both chimeras, obviating concerns that the signal sequence has an integral role in the mechanism of catalysis. Clearly, E. faecalis AP activity is suppressed in the cytoplasm and/or activated by export from the cytoplasm.
Several aspects of AP remain to be characterized. Highly homologous B. subtilis genes are known to be regulated by a complicated circuitry of signaling pathways, possibly because of the bacteria's critical need for phosphate. The control of phoZ expression in E. faecalis has not yet been addressed. The assays described here have shown that AP can function in a highly alkaline environment, but the optimal conditions for activity have not been established. Finally, it would be useful to quantify the rates of expression for AP fusions, since per-cell AP activity can be affected by the rates of expression as well as the chimeric protein's subcellular location. The most commonly used methods for quantifying AP expression would require anti-AP antibodies, which are not available.
A number of alternative reporter enzymes have been described for use in
gram-positive bacteria. The secreted nuclease (Nuc) from
Staphylococcus aureus has been used to identify
Lactococcus lactis genes encoding secreted proteins
(31). Similarly, the
-amylase of B. licheniformis has been used to identify B. subtilis genes that encode secreted proteins (36). Like AP, these
reporter enzymes are active in gram-positive bacteria, there are plate assays that permit identification of active chimeras, and the activity
of these reporter enzymes can be quantified by using spectrophotometric
assays. The AP system presents a number of advantages. The AP plate
assay is based on colony color, while the nuclease and amylase plate
assays both rely on a zone of clearing around colonies grown on
indicator media. Consequently, AP chimeras can be readily evaluated
even when plates are crowded with colonies, phoZ+ sectors arising within colonies can be
visualized, reversion events can be readily identified, and the AP
colony color phenotype can be distinguished for days after the initial
plating. Chimeras formed with other reporter enzymes (although not the
S. aureus nuclease) seem biased toward short insertions
(31). This bias is not seen in the AP fusions, since the
chimeras described here included N-terminal peptides ranging in length
from 16 to 286 residues (Table 3). Finally, the AP reporter enjoys some
procedural advantages over other reporter systems. First, many labs
already have experience in running and evaluating alkaline phosphatase assays. Second, the BamHI site engineered into
'phoZ makes it fairly simple to replace the reporter with
either lacZ or phoA (from E. coli),
should either of these alternative reporter systems be advantageous
(27).
We utilized E. faecalis AP to identify genes encoding exported proteins in GBS. Eight AP chimeras were identified and sequenced. All eight fusions encoded proteins with signal sequence-like segments, and none of the eight chimeras had significant homology with cytoplasmic proteins. Additionally, two had homology with proteins known to be exported in either GAS or GBS. These results demonstrate that 'AP can be used as a means of identifying genes that encode exported proteins in GBS.
Some bacterial strains have high constitutive levels of alkaline phosphatase activity, limiting the utility of AP as a reporter enzyme. This may not be a general problem. The phoZ gene has been used as a reporter enzyme in E. coli, E. faecalis, GAS, GBS, and Streptococcus gordonii (10). In our investigations, only S. aureus RN4220 has exhibited a prohibitively high level of endogenous phosphatase activity (9a). Furthermore, a study of 54 strains isolated from sheep rumina revealed that none of 21 gram-positive strains exhibited detectable levels of phosphatase activity (11). In contrast, 9 of 33 gram-negative species had constitutive phosphatase expression. Thus, the breadth of the range of gram-positive species in which AP can be used is expected to be comparable to that of gram-negative species in which E. coli alkaline phosphatase has been used. If a particular strain exhibits high levels of phosphatase activity, it may be possible to suppress the background by growth on media supplemented with inorganic phosphate. Alternatively, it may be possible to work with derivative strains lacking the gene that encodes their endogenous alkaline phosphatase.
This report identifies the E. faecalis phoZ gene and presents a characterization of its gene product. The export-dependent functionality of the enzyme was used to identify eight genes that encode exported proteins in GBS, using the broad-host-range vector pAN200. This vector can be introduced into GBS, GAS, and E. faecalis and should be useful in identifying exported proteins in a variety of gram-positive bacteria.
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ACKNOWLEDGMENTS |
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This work was supported by NIH grant AI25152 (C.E.R.), The Streptococcus Initiative, and by NIH grant GM35394 (A.C.).
We thank Colin Manoil for providing several of the E. coli strains, the lacY mutants, and advice. Thanks to Donald Chaffin for strains, plasmids, and help with GBS manipulations and to Scott Winram for a critical reading of the manuscript.
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FOOTNOTES |
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* Corresponding author. Mailing address: Department of Pediatrics, Children's Hospital Regional Medical Center CH-31, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105. Phone: (206) 528-2767. Fax: (206) 527-3890. E-mail: cruben{at}chmc.org.
Present address: National Dairy Products Research Center,
Moorepark, Fermoy, County Cork, Ireland.
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