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Infection and Immunity, September 1998, p. 4123-4129, Vol. 66, No. 9
0019-9567/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
SirR, a Novel Iron-Dependent Repressor in
Staphylococcus epidermidis
Philip J.
Hill,1,2,*
Alan
Cockayne,1,2,3
Patrick
Landers,1,2
Julie A.
Morrissey,1,2
Catriona M.
Sims,1,2 and
Paul
Williams1,2,3
Institute of Infections and
Immunity,1
School of Pharmaceutical
Sciences,2 and
School of Clinical
Laboratory Sciences,3 University of Nottingham,
Nottingham NG7 2UH, United Kingdom
Received 6 March 1998/Returned for modification 28 April
1998/Accepted 10 June 1998
 |
ABSTRACT |
In Staphylococcus epidermidis and Staphylococcus
aureus, a number of cell wall- and cytoplasmic
membrane-associated lipoproteins are induced in response to iron
starvation. To gain insights into the molecular basis of iron-dependent
gene regulation in the staphylococci, we sequenced the DNA upstream of
the 3-kb S. epidermidis sitABC operon, which Northern blot
analysis indicates is transcriptionally regulated by the growth medium
iron content. We identified two DNA sequences which are homologous to
elements of the Corynebacterium diphtheriae DtxR regulon,
which controls, in response to iron stress, for example, production of
diphtheria toxin, siderophore, and a heme oxygenase. Upstream of the
sitABC operon and divergently transcribed lies a 645-bp
open reading frame (ORF), which codes for a polypeptide of
approximately 25 kDa with homology to the DtxR family of
metal-dependent repressor proteins. This ORF has been designated SirR
(staphylococcal iron regulator repressor). Within the
sitABC promoter/operator region, we also located a region
of dyad symmetry overlapping the transcriptional start of
sitABC which shows high homology to the DtxR operator
consensus sequence, suggesting that this region, termed the Sir box, is the SirR-binding site. The SirR protein was overexpressed, purified, and used in DNA mobility shift assays; SirR retarded the migration of a
synthetic oligonucleotide based on the Sir box in a metal (Fe2+ or Mn2+)-dependent manner, providing
confirmatory evidence that this motif is the SirR-binding site.
Furthermore, Southern blot analysis of staphylococcal chromosomal DNA
with the synthetic Sir box as a probe confirmed that there are at least
five Sir boxes in the S. epidermidis genome and at least
three in the genome of S. aureus, suggesting that SirR
controls the expression of multiple target genes. Using a monospecific
polyclonal antibody raised against SirR to probe Western blots of
whole-cell lysates of S. aureus, S. carnosus,
S. epidermidis, S. hominis, S. cohnii, S. lugdunensis, and S. haemolyticus, we identified an approximately 25-kDa
cross-reactive protein in each of the staphylococcal species examined.
Taken together, these data suggest that SirR functions as a divalent metal cation-dependent transcriptional repressor which is widespread among the staphylococci.
 |
INTRODUCTION |
Staphylococcus aureus is
well recognized as a human pathogen responsible for a variety of
pyogenic and toxin-related infections (7). In contrast,
coagulase-negative staphylococci such as Staphylococcus
epidermidis have emerged more recently as a major medical problem
with the widespread use of implanted medical devices (7).
Both organisms are now frequent pathogens in hospitals and account for
much morbidity and mortality. S. epidermidis is much less
biologically active than S. aureus being almost devoid of
conventional exotoxins but possessing a marked capacity to adhere to
and form biofilms on the surfaces of implanted medical devices
(7). However, the acquisition of essential nutrients to
facilitate growth in host tissues is a problem common for all bacterial
pathogens, and therefore relevant, to both S. aureus and
S. epidermidis infections. Such growth is critical to the establishment of infection and depends in part on the ability of the
pathogen to scavenge nutrients such as iron (44, 46). Although there is an abundance of iron in the extracellular body fluids, the free ionic iron concentration (10
18 M), due
to the presence of the iron-binding glycoproteins transferrin (in
serum) and lactoferrin (on mucosal surfaces and in polymorphonuclear leukocytes), is far too low to support the growth of bacteria such as
the staphylococci (44, 46). Furthermore, in a number of
bacterial pathogens, this lack of readily available iron constitutes a
major environmental signal which coordinately controls the expression of a number of virulence and metabolic genes unrelated to iron acquisition (21).
To grow in host tissues, staphylococci must therefore acquire iron.
While there is a considerable amount of information on the
iron-sequestering systems of gram-negative bacteria and their contribution to virulence (46, 48), there is comparatively little information on the staphylococci (44). Although they produce and use siderophores (low-molecular-mass iron chelators), the
genes and gene products involved in their regulation, synthesis, export, or import are unknown (44). Previously, we
identified a number of iron-repressible S. aureus and
S. epidermidis cell wall- and cytoplasmic
membrane-associated proteins which are expressed during growth in vivo
during both human (37, 45) and experimental animal (23,
25) infections. These include a 42-kDa cell wall protein which
functions as a receptor for human transferrin (24, 26) and a
32-kDa cytoplasmic membrane-associated lipoprotein (6, 23,
37). The gene encoding this lipoprotein has recently been cloned
from S. epidermidis and shown to be a component of a
translationally coupled, iron-regulated operon which consists of three
genes (sitABC), the products of which constitute an ABC transporter (6). Although the function and contribution of the sit operon to growth in vivo and to the pathogenesis of
staphylococcal infection are not known, this operon does show
significant homology to a family of streptococcal ABC operons involved
in adherence and genetic competence and which are essential for
virulence (10). Since SitC is not exposed at the
staphylococcal cell surface (6), it is unlikely to function
as an adhesin and is probably involved in the acquisition of metal
ions. Furthermore, the mechanism by which the sit operon is
regulated via the growth medium iron content is not known.
In gram-negative bacteria such as Escherichia coli, the
ferric uptake regulator (Fur) protein is responsible for the
iron-dependent transcriptional regulation of genes involved in the
biosynthesis and transport of siderophores such as aerobactin and
enterobactin and in the regulation of virulence determinants such as
the enterotoxin Stx1 (3, 21, 48). Since the fur
locus was first identified in Salmonella typhimurium
(12) and extensively characterized in E. coli
(21), numerous other Fur homologs have been found in
gram-negative bacteria such as Vibrio cholerae
(21), Pseudomonas aeruginosa (30),
Yersinia pestis (38), and Neisseria
meningitidis (43). In these bacteria, the coordinate
regulation of multiple genes by iron depends on Fur functioning as an
iron-responsive, DNA-binding repressor protein. The 17-kDa Fur protein
functions as a dimer and in the presence of Fe2+ binds to a
consensus sequence termed the Fur box located within the promoter
region of the target genes (3). However, when iron levels
are low, Fur does not bind and the genes are expressed (21).
Although Fur homologs have been identified in both Bacillus
subtilis (5) and S. epidermidis
(19), by far the most intensively investigated
iron-dependent repressor in gram-positive bacteria is DtxR
(41). This protein was first identified as repressor of
diphtheria toxin synthesis in Corynebacterium diphtheriae
(41). Although DtxR is a functional homolog of Fur, it
shares no amino acid homology and belongs to a newly emerging family of
iron-dependent repressors. Apart from C. diphtheriae, DtxR
homologs have now been identified in Streptomyces spp.
(16), Brevibacterium lactofermentum (28), and mycobacteria (11) and also in the
spirochete Treponema pallidum (17), where they
regulate genes encoding iron transport systems, heme oxygenase, and
virulence determinants and genes involved in protecting bacteria from
oxidative stress (11, 16, 17, 28, 34, 41). This finding
suggests that the growing family of DtxR homologs play a central role
in regulating the adaptation, survival, and virulence of gram-positive
pathogens. In this report, we describe the identification and
characterization of a novel DtxR homolog, SirR, from S. epidermidis, which is located immediately upstream of the
sitABC operon and which is common to both S. aureus and the coagulase-negative staphylococci.
 |
MATERIALS AND METHODS |
Bacterial strains, media, and plasmids.
S. aureus,
S. epidermidis, Staphylococcus hominis,
Staphylococcus cohnii, Staphylococcus
lugdunensis, and Staphylococcus haemolyticus clinical
isolates were obtained from University Hospital, Nottingham, United
Kingdom. Staphylococcus carnosus TM300 was a gift from F. Götz (Tübingen, Germany). Strains were maintained by
regular subculture on horse blood agar. For broth culture, strains were grown statically for 18 h at 37°C in RPMI 1640 tissue culture medium containing 2 mg of NaHCO3 per ml as described before
(6). RPMI 1640 medium was depleted of iron by batch
incubation with Chelex 100 (Bio-Rad Laboratories) as described
previously (18). Cultures were incubated in 5%
CO2 in air; where indicated, the medium was supplemented
with 20 µM Fe2(SO4)3 to produce
iron-rich growth conditions. Where the effects of different metal ions
on gene expression were examined, metal salts (MgSO4,
MnCl2, CuSO4, CoCl2,
NiCl2, and ZnCl2) were added to iron-depleted
RPMI 1640 at 20 µM. E. coli strains were routinely
cultured at 37°C in Luria-Bertani (LB) broth or LB agar containing
appropriate antibiotics. Plasmid pW32 was derived from a
-Zap II
library and contains a 5.4-kb EcoRI fragment of S. epidermidis genomic DNA which contains the sitABC
operon as previously described (6).
SDS-PAGE and immunoblotting.
Staphylococci were digested
with lysostaphin (80 µg/µl; Sigma) in phosphate-buffered saline (pH
7.4) for 30 min at 37°C prior to solubilization by boiling in sodium
dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) sample
buffer for 5 min, and proteins were separated by SDS-PAGE using a 10%
polyacrylamide gel (1). For immunoblotting, polypeptides
were transferred to BioTrace NT membrane (Gelman) followed by blocking,
incubation with primary antibody (1/500 dilution overnight for
polyclonal antisera or 1/2 dilution overnight for monoclonal antibody)
and conjugate (1/2,000 dilution of anti-rabbit, anti-rat, or anti-mouse
peroxidase conjugate for 4 h), and finally detection of bound
antibody (1).
Overexpression and partial purification of SirR.
Recombinant
plasmids were recovered by alkaline lysis and subjected to restriction
analysis (2). Inserts from positive clones were sequenced
with an ABI automated DNA sequencer. DNA and protein sequence analyses
were performed with LASERGENE software (DNAstar Inc.). To produce
sufficient amounts of SirR to enable in vitro studies, the SirR coding
region was amplified by PCR incorporating NcoI and
HindIII restriction enzyme sites in the primers.
Following digestion, the sirR fragment was inserted into expression vector pTRC99 (Pharmacia) and used to transform E. coli JM107. E. coli carrying the correct construct was
grown to an A600 of 0.5 prior to addition of
isopropyl-
-D-thiogalactopyranoside (IPTG) to 0.5 mM to
induce expression of sirR. Once expression was confirmed by
SDS-PAGE, lysates from E. coli overexpressing sirR were subjected to fractionation by fast protein liquid
chromatography (FPLC) on a MonoQ column (Pharmacia) over a gradient of
0 to 1 M NaCl. Fractions shown to contain SirR by gel retardation
assays, using the 382-bp PCR-derived probe described below, were
further purified by affinity purification on Ni-nitrilotriacetic acid resin (Qiagen) as described by Schmitt and Holmes (36).
Gel retardation assay.
Gel retardation assays were performed
essentially as described in the protocol for the Boehringer Mannheim
digoxigenin gel shift kit. Briefly DNA probes containing the putative
Sir box were end labeled with digoxigenin-11-ddUTP (Boehringer
Mannheim) by using terminal transferase (Promega) according to the
manufacturers' instructions. Two different DNA probes were used: a
382-bp PCR product (oligonucleotide primer sequences,
5'-TTCACTTACTGATGGTGG-3' and 5'-CTTTGAGAAGAGATGATT-3')
containing the 5' coding regions of sitA and
sirR and the complete intergenic region; and a synthetic oligonucleotide probe containing the Sir box (oligonucleotide sequences, 5'-TAAAATAAATTAGGTTAACCTAAACTTTTTATTA-3' and
5'-TAATAAAAAGTTTAGGTTAACCTAATTTATTTTA-3'). The end-labeled
fragments were incubated for 15 min at room temperature with partially
purified SirR or FPLC fractions in 20 µl (total volume) in buffer
containing 20 mM Tris HCl (pH 7), 5 mM MgCl2, 40 mM KCl, 2 mM dithiothreitol, 10% (vol/vol) glycerol, 1 µg of poly(dI-dC), and
5 µg of bovine serum albumin. Freshly prepared FeSO4 or
MnSO4 was added at 125 µM. In some experiments, the
divalent metal ion chelator EDTA at a concentration of 0.1 mM was also added to the reaction mixture. Samples were immediately electrophoresed at 100 V on a 5% nondenaturing polyacrylamide gel in 0.5×
Tris-borate-EDTA buffer (2) and then electroblotted onto a
positively charged nylon membrane. The digoxigenin-labeled probe
was detected by using anti-digoxigenin-alkaline phosphatase conjugate
and the luminogenic substrate CDPstar (Boehringer Mannheim). The signal was captured with a Berthold Luminograph LB980 or by exposure to X-ray
film.
Production of antibodies.
A monospecific polyclonal
antiserum to SirR was raised in adult female New Zealand White rabbits.
Total-cell protein from E. coli overexpressing
sirR was subjected to SDS-PAGE; after electrophoresis, the
Coomassie blue-stained band corresponding to SirR was excised from the
gel and electroeluted, and the denatured protein was used for
immunization. A mouse monoclonal antibody to the S. epidermidis 32-kDa lipoprotein, SitC, was produced as described
before (6).
Southern and Northern blot analyses.
Staphylococcal
chromosomal DNA was digested with restriction endonucleases,
electrophoresed, and transferred to a Hybond N+ membrane.
The blot was probed with digoxigenin-labeled Sir box oligonucleotides
as described above and visualized with CDPstar. A 3-kb
EcoRV-EcoRI fragment from pW32 containing
sitABC and most of sirR was labeled with
digoxigenin and used as the probe for Northern blot analysis. Total RNA
was extracted from S. epidermidis 901 grown for 18 h
under iron-rich or iron-restricted conditions in RPMI 1640, using a
Qiagen RNeasy total RNA kit. Northern blotting was performed as
described by Ausubel et al. (2).
Identification of transcriptional start site.
The
transcriptional start of the sitABC operon was mapped by
primer extension incorporating [35S]dATP, using avian
myeloblastosis virus reverse transcriptase (Promega) and RNA template
prepared from S. epidermidis 901 grown under iron-restricted
conditions, essentially as described by Ausubel et al. (2).
Manual DNA sequencing for transcriptional mapping was carried out by
using Sequenase version 2.0 according to the manufacturer's
instructions.
Nucleotide sequence accession number.
The sequence of
sirR is available in the GenBank database under accession
no. X99128.
 |
RESULTS |
Identification of DNA coding for SirR and its putative operator
site.
Plasmid pW32 was derived from a
-Zap II genomic library
and contains a 5.4-kb EcoRI fragment of S. epidermidis DNA which includes sitABC operon
(6). DNA sequence analysis of pW32 plasmid indicated that
upstream of the sitABC operon, and divergently transcribed,
lies a 645-bp open reading frame that codes for a polypeptide of
approximately 25 kDa with homology to the DtxR family of
metal-dependent repressor proteins (Fig.
1 and Table 1). This open reading frame has been
designated sirR (staphylococcal iron regulator repressor).
Alignment of the deduced SirR protein sequence with the DtxR family
reveals that it is most closely related (38% identical) to TroR from
the spirochete T. pallidum, followed by IdeR (33%) found in
the mycobacteria (Table 1). Furthermore, SirR, like TroR, is located
adjacent to a putative ABC transporter system (17) with
homology to the streptococcal family of multifunctional ABC operons
involved in adherence and genetic competence (10). Although
this staphylococcal gene product exhibits only 29% identity with DtxR,
the metal coordination sites are conserved (Fig. 1).

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FIG. 1.
Comparison of the deduced amino acid sequences of SirR
and DtxR. Identical amino acid residues are boxed. Solid arrows
indicate residues identified from the DtxR crystal structure as metal
coordination sites (M1), the open arrows indicate metal-binding site 2 (M2), and the hatched arrow indicates the cysteine residue (C102)
positioned within M2 which is replaced by a glutamate residue in SirR
and TroR.
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DNA sequence analysis of the region 5' to the sitABC operon
and transcriptional start analysis of this operon have identified a
promoter sequence with similarity to E. coli
70 promoters and a region of dyad symmetry overlapping
the transcriptional start of sitABC termed the Sir box (Fig.
2A). This box shows high homology to the
DtxR operator consensus sequence (20), suggesting that this
region is SirR-binding site, and so it has been designated the Sir box.
To map the transcriptional start site of the sitABC operon,
RNA was prepared from S. epidermidis 901 grown in
iron-restricted RPMI 1640 medium. Primer extension analysis indicated
that the transcriptional start site was 38 nucleotides upstream of the TTG translational start and overlaps the Sir box (Fig. 2).

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FIG. 2.
(A) Nucleotide sequence of the S. epidermidis
sitABC operon promoter region. The 10 and 35 promoter
sequences are underlined; the putative ribosome-binding site (RBS) and
translation start codon of sitA are shown in bold. The
vertical arrow indicates the transcriptional start of the
sitABC operon, and the Sir box is indicated by convergent
horizontal arrows. (B) Comparison of the S. epidermidis Sir
box nucleotide sequence with sequences of known DtxR- and DesR-binding
sites in C. diphtheriae and S. lividans. The
19-bp consensus sequence for DtxR derived by Lee et al. (20)
is also shown.
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When grown in an iron-rich growth medium, the 32-kDa SitC lipoprotein
is not expressed. To determine whether the sit operon is
regulated by iron at the transcriptional level, RNA was prepared from
S. epidermidis 901 grown in RPMI 1640 under iron-rich and iron-restricted conditions. Northern blot analysis using a DNA probe
which hybridizes to both sirR and the sitABC
operon revealed that expression of the 3-kb sitABC operon in
response to iron is controlled at the transcriptional level (Fig.
3). In addition, Fig. 3 shows that the
0.7-kb sirR transcript is monocistronic and not influenced
by the iron content of the growth medium.

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FIG. 3.
Northern blot analysis of S. epidermidis sirR
and sitABC transcripts. Total RNA was isolated from S. epidermidis 901 grown in iron-sufficient (+) or iron-deficient
( ) RPMI 1640 medium. The 2.7-kb sitABC transcript and the
0.7-kb sirR transcript are indicated by arrows.
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SitC responds to divalent metal ions other than iron.
The
production of diphtheria toxin is known to be repressed in a
DtxR-dependent manner by iron and various divalent metal cations,
including Co2+, Mn2+, and Ni2+
(15, 39). To investigate whether the sitABC
operon is similarly controlled by metal cations, we used a monoclonal
antibody raised against SitC (6) to probe immunoblots of the
whole-cell proteins of S. epidermidis 901 grown in
iron-depleted RPMI 1640 supplemented with different divalent metal
cations. Figure 4 shows that SitC production in S. epidermidis is fully repressed by the
presence of iron and Mn2+ but unaffected by the presence of
Co2+, Cu2+, Ni2+, Zn2+,
or Mg2+ in the growth medium.

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FIG. 4.
Immunoblot analysis of SitC production in S. epidermidis grown in iron-restricted RPMI 1640 or supplemented
with cobalt, copper, iron, magnesium, manganese, nickel, or zinc (added
at 20 µM). Whole-cell proteins prepared by lysostaphin digestion of
staphylococcal suspensions adjusted to the same optical density were
subjected to SDS-PAGE, immunoblotted, and probed with a monoclonal
antibody to SitC. Lane 1, no addition; lane 2, Co2+; lane
3, Cu2+; lane 4, Fe2+; lane 5, Mg2+; lane 6, Mn2+; lane 7, Ni2+;
lane 8, Zn2+.
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DNA gel retardation assays.
To demonstrate that SirR is
capable of binding to the Sir box in a metal ion-dependent manner, we
partially purified the protein by FPLC and Ni-nitrilotriacetic acid
affinity chromatography. In DNA gel retardation assays using a
synthetic oligonucleotide based on the Sir box sequence, SirR retarded
movement of the oligonucleotide in the presence of Fe2+
(Fig. 5) or Mn2+, and this
retardation could be abolished by the inclusion of the divalent metal
ion chelator EDTA in the buffer. Furthermore, binding of SirR to the
labeled Sir box oligonucleotide could be abolished by competition with
the unlabeled Sir box but not by nonspecific DNA (data not shown).

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FIG. 5.
DNA gel mobility shift assay of synthetic Sir box
(labeled with digoxigenin) with partially purified SirR in the presence
(+) or absence ( ) of Fe2+. The Sir box oligonucleotide is
clearly retarded only in the presence of both SirR and
Fe2+.
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SirR is a global regulator.
To determine whether SirR is
present in other staphylococci, we subjected whole-cell lysates of
S. aureus, S. carnosus, S. epidermidis, S. hominis, S. cohnii, S. lugdunensis, and S. haemolyticus to Western blotting
using monospecific anti-SirR antibodies. The presence of an
immunoreactive polypeptide of ca. 25 kDa, corresponding to SirR, from
each of the strains tested (Fig. 6)
indicates that SirR is common to the staphylococci. Southern blotting
of S. epidermidis and S. aureus chromosomal DNA
using the synthetic Sir box used for the gel retardation studies as a
probe confirms that there are at least five Sir boxes in the S. epidermidis genome and at least three Sir boxes in the genome of
S. aureus. This finding provides evidence that the SirR
regulon may contain a number of operons expressed only by staphylococci
growing under iron restriction (Fig. 7).

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FIG. 6.
Immunoblot analysis of SirR production in
coagulase-negative staphylococci grown in iron-restricted RPMI 1640 medium. Whole-cell proteins prepared by lysostaphin digestion were
subjected to SDS-PAGE, immunoblotted, and probed with a monospecific
polyclonal antibody to SirR. Lane 1, S. epidermidis; lane 2, S. cohnii; lane 3, S. hominis; lane 4, S. carnosus; lane 5, S. lugdunensis; lane 6, S. warneri; lane 7, S. aureus.
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FIG. 7.
Southern blot analysis showing the presence of multiple
Sir boxes in genomic DNA prepared from S. epidermidis 901 and S. aureus BB restricted with MunI (lanes 2 and 5), HindIII (lanes 3 and 6), and SalI
(lane 4). Lane 1, -HindIII marker; lanes 2 to 4, S. epidermidis; lanes 5 and 6, S. aureus.
Strongly hybridizing bands are indicated by arrowheads.
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 |
DISCUSSION |
In both S. aureus and S. epidermidis, a
number of cell wall- and cytoplasmic membrane-associated proteins, the
production of which depends on the growth medium iron content, have
been identified (6, 24, 37, 45). Of these, we have recently cloned and sequenced an iron-regulated 32-kDa lipoprotein, SitC, which
is encoded by a component of the sitABC operon
(6). Analysis of DNA sequence 5' to sitABC failed
to identify a region with any homology to a Fur box, indicating that
sitABC expression is unlikely to be modulated by the
Fur-like protein recently identified in S. epidermidis
(19). However, in the present report, we have provided
evidence suggesting that the iron-dependent regulation of the
sit operon may be mediated via SirR, a protein related to
the DtxR family of metal-dependent transcriptional repressors, the
target for which is a 19-bp palindrome termed the Sir box. Since
S. epidermidis contains a Fur homolog, this raises the
intriguing possibility that staphylococci possess two distinct families
of metal-dependent repressor proteins.
The S. epidermidis Fur-like protein described by Heidrich et
al. (19) is located upstream of a putative superoxide
dismutase, and both genes contain a sequence motif with low similarity
to Fur boxes but no Sir box. This staphylococcal fur gene
therefore may, like the E. coli homolog, bind to its own
promoter and autoregulate its expression (8). The lack of an
additional Sir box within the sirR operator indicates that
sirR is, however, unlikely to be autoregulated. Although the
staphylococcal Fur protein is unable to complement an E. coli
fur mutant, the E. coli Fur protein does recognize
weakly the Fur box in front of the S. epidermidis fur gene
(19). Whether this staphylococcal Fur-like protein is
functional and regulates the superoxide dismutase gene and other target
genes has yet to be established. In this context, it is perhaps worth noting that Fur boxes overlapping numerous B. subtilis
genes, as well as three different Fur homologs, have been identified (5).
Transcriptional mapping of the S. epidermidis sit operon
indicates that the Sir box is located within the promoter/operator of
the sit operon. DNA mobility shift analysis using a
synthetic Sir box oligonucleotide confirmed that SirR bound in a
metal-dependent manner, indicating that this motif is indeed the SirR
target. The Sir box is closely related to the C. diphtheriae
DtxR-binding site, conforming to the DtxR box consensus sequence and
sharing some 12 of 19 identical nucleotides with the DtxR-binding site located within the promoter/operator of the diphtheria toxin gene (20). In C. diphtheriae, at least six other genes
are regulated by DtxR and contain DtxR-binding sites (20,
34). These include hmuO, the product of which is a
heme oxygenase required for the utilization of heme and hemoglobin
(34), and irp1, which codes for an iron-regulated
38-kDa protein (34). While the function of IRP1 is not
known, it may be functionally homologous to SitC since both proteins
are lipoproteins anchored to the outer surface of the cytoplasmic
membrane, they contain similar signal peptidase II cleavage sites, and
both are probably involved in metal ion transport (6, 34).
Whether irp1, like sitC, is part of an operon
coding for an ABC transporter is not known, but it does show homology
with the siderophore receptor FhuD from B. subtilis. It is
possible that in the staphylococci, SirR regulates multiple genes, a
hypothesis supported by (i) immunoblot data revealing an antigenically
conserved 25-kDa protein in the staphylococci and (ii) Southern blot
analysis which revealed a number of Sir boxes in the genomes of both
S. epidermidis and S. aureus, indicating that
SirR may, in common with DtxR and Fur, be a pleiotropic regulator of
gene expression in these gram-positive pathogens.
The DNA target for DtxR was identified by DNase I footprinting analysis
as a 27-bp interrupted palindrome which overlaps the basal promoter of
the operons that it controls (13, 36, 39), while in vitro
affinity selection has identified the minimal DtxR operator to be a
9-bp palindrome separated by a single base pair (40). In
addition, binding of DtxR to its operator site has been shown to occur
in the presence of divalent metal ions (e.g., Mn2+ and
Co2+) other than Fe2+ (35, 39).
Since the cloning and sequencing of dtxR (4), mutational analysis has identified specific residues which are important for the function of DtxR in terms of its interaction with DNA
(e.g., R47) or divalent metal binding (e.g., H98, C102, and H106), and
subsequent crystallographic studies have placed these functional assays
in the context of a high-resolution crystal structure (9, 29,
31-33, 40, 47). From this work, four domains necessary for the
regulatory functions of DtxR have been identified. These are an
N-terminal, helix-turn-helix DNA-binding domain, two metal ion-binding
sites, and a dimerization/stabilization domain (9, 29,
31-33). From secondary structure predictions and a comparison of
the amino acid sequences of SirR and DtxR, SirR appears to contain
three N-terminal helices at positions 1 to 16 (helix 1), 27 to 33 (helix 2), and 38 to 49 (helix 3) similar to those found in DtxR
(31), with residues highly conserved in the DNA recognition
helix (helix 3 at G38 to R50 in DtxR) of other DtxR homologs (i.e.,
P39, V41, S42, V45, R47, and E49) also being conserved in SirR.
Metal-binding site 1 of DtxR has metal coordination sites at H79, E83,
and H98, residues which are conserved in SirR. The DtxR metal-binding
site 2 has metal coordination sites at E105 and H106, both of which are
retained in SirR. In DtxR, C102 has been shown to be important for
activity since it resides in metal-binding site 2 (42),
although it does not directly appear to provide a metal-binding ligand
(31). In SirR, residue C102 is replaced by a glutamate
residue, a conservative substitution also found in TroR, the DtxR
homolog from T. pallidum. In contrast to TroR, SirR, like
the other DtxR homologs so far described, also contains a region
homologous to the DtxR dimerization domain located in helix 5 of DtxR
(31).
Using DNA gel retardation studies, we have provided in vitro evidence
to support the function of SirR as a metal-dependent repressor in that
SirR binds to a synthetic Sir box only in the presence of divalent
metal ions such as Fe2+ and Mn2+. These data
are further supported by in vivo data, as Western blot analysis shows
that Mn2+ as well as Fe2+ can modulate SitC
production. Given that the sit operon is related to a family
of streptococcal ABC transporters found to be essential for virulence
and competence and which also transport Mn2+ or
Zn2+ ions (10), it is possible that SirR
functions in vivo as a Mn2+ rather than an
Fe2+-dependent repressor. In E. coli,
Mn2+, Fe2+, and Co2+ are all
capable of repressing in vivo expression of transcriptional fusions to
the promoters of Fur-regulated genes (21). However, in
E. coli, the Fur target genes are involved in the
biosynthesis and transport of Fe3+ chelators such as
aerobactin which have only a low affinity for divalent metal cations
such as Fe2+ (27). Determination of the nature
of the ligand transported via the SitABC transporter in S. epidermidis requires the construction of defined mutants. Such
mutants will enable us to determine whether SirR is involved in the
regulation of genes involved in the uptake of iron or other metal
cations, an important consideration given the existence of Fur-like
proteins in the staphylococci.
 |
ACKNOWLEDGMENT |
This work was supported by program grant G9219778 from the
Medical Research Council to P.W.
 |
FOOTNOTES |
*
Corresponding author. Present address: School of
Biological Sciences, Sutton Bonington Campus, University of Nottingham,
Sutton Bonington, Leicestershire LE12 5RD, United Kingdom. Phone: 115 9516169. Fax: 115 9516162. E-mail:
Phil.Hill{at}nottingham.ac.uk.
Editor:
V. A. Fischetti
 |
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Infection and Immunity, September 1998, p. 4123-4129, Vol. 66, No. 9
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Copyright © 1998, American Society for Microbiology. All rights reserved.
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