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Journal of Bacteriology, December 1998, p. 6375-6383, Vol. 180, No. 23
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
A Two-Component Signal Transduction System
Essential for Growth of Bacillus subtilis: Implications for
Anti-Infective Therapy
Céline
Fabret and
James A.
Hoch*
Division of Cellular Biology, Department of
Molecular and Experimental Medicine, The Scripps Research
Institute, La Jolla, California
Received 24 August 1998/Accepted 25 September 1998
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ABSTRACT |
A two-component signal transduction system encoded by the
yycF and yycG genes is part of an operon
containing three genes, yycH, yycI, and
yycJ, with no known function and a gene, yycK, coding for an HtrA-like protease. This operon was transcribed during
growth, and its transcription shut down as the cells approached stationary phase. This decreased transcription was not Spo0A dependent. The HtrA protease gene was separately controlled during sporulation from a
G promoter. Studies using insertional
inactivation plasmids revealed that neither yycF nor
yycG could be inactivated, whereas the other genes were
inactivated without loss of viability. A temperature-sensitive YycF
response regulator mutant was isolated and shown to have an H215P
mutation in a putative DNA-binding domain which is closely related to
the OmpR family of response regulators. At the nonpermissive temperature, cultures of the mutant strain stopped growth within 30 min, and this was followed by a decrease in optical density. Microscopically, many of the cells appeared to retain their structure while being empty of their contents. The essential processes regulated by this two-component system remain unknown. A search of the genome databases revealed YycF, YycG, and YycJ homologues encoded by three
linked genes in Streptococcus pyogenes. The high level of identity of these proteins (71% for YycF) suggests that this system may play a similar role in gram-positive pathogens.
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INTRODUCTION |
In order for bacteria to effectively
compete and survive, they have to sense environmental conditions and
respond accordingly. Two-component systems are a predominant mode of
environmental sensing and signal transduction in bacteria. This system
of adaptive responses occurs through sensor kinases that mediate
reversible phosphorylation events controlling downstream effectors
(20, 27). Sensor kinases are generally integral membrane
proteins that respond to specific environmental signals, and response
regulators are often transcription factors whose affinity for DNA is
modulated by phosphorylation. Sensor histidine kinases
autophosphorylate on a conserved histidine residue and serve as
phosphodonors to an invariant aspartic acid residue on a response
regulator protein to which it is paired. The phosphorylated response
regulator is thus able to mediate changes in gene expression, leading
to the appropriate cellular response.
It is generally believed that two-component systems are used to sense
environmental levels of essential substances, such as nitrogen,
phosphate, and carbon sources, as well as a variety of nonessential
molecules that signal adaptive responses. The discovery of
two-component signal transduction involvement in the cell cycle and
division of Caulobacter crescentus showed for the first time
that this mechanism of genetic control had been adopted to regulate
vital functions in the cell (7, 22). Because of the
therapeutic implications of the discovery, it was important to
determine if this adaptation was widespread in bacteria (5).
The complete sequence of the Bacillus subtilis genome (10) provided a resource to inactivate all of the
two-component systems of a single organism by insertional inactivation
and determine the phenotype of such mutations. In a study of this kind,
a two-component signal transduction system was found that could not be
inactivated, and this communication describes the consequences to the
cell of inactivation of this system.
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MATERIALS AND METHODS |
Bacterial strains and plasmids.
The bacterial strains and
plasmids used in this study are listed in Table
1. Plasmids were constructed as follows.
DNA fragments from the yycFIJK region were identified by the
base pair numbering in the sequence submitted to GenBank under
accession no. D78193 (18). For gene disruptions, the PCR was
used to amplify regions encoding an internal part of each gene, with
SphI and BamHI sites added at the ends. After
digestion with appropriate enzymes, PCR fragments were ligated to
SphI-BamHI-digested pJM103 integrative vectors
(21). pJC8 contains a 594-bp internal DNA fragment of the
yycF gene (bp 35285 to 35879). To obtain pJC10, the
chloramphenicol resistance gene from pJC8 was first inactivated by
removing the 400-bp MunI-NcoI 3'-end fragment;
the Klenow-treated plasmid was self-ligated, and then the
chloramphenicol resistance gene, without a terminator, on a 955-bp
HincII-SmaI fragment from pJM105B (21) was inserted into the MluI-blunted site within the coding
region of yycF. pJC9 contains the 3' end of yycF
and the 5' end of yycG on a 475-bp DNA fragment (bp 34867 to
35342). pJC11 to pJC14 contain DNA fragments internal to
yycH (bp 32233 to 33107), yycI (bp 31434 to
31924), yycJ (bp 30423 to 30994), and yycK (bp
29383 to 30167), respectively. For construction of multicopy plasmid
pJC15, containing the yycF promoter region and the entire
yycF gene, a 1,152-bp fragment (bp 1651 to 2803 in the
nucleotide sequence with GenBank accession no. D26185
[18]) was generated by PCR with EcoRI and
BamHI sites on each end and cloned into the
EcoRI-BamHI sites of pHT315. The same PCR
fragment, amplified from the chromosomal DNA of thermosensitive strain
JH17041, was cloned in a similar way into pJM103. The lacZ
transcriptional fusions were made from the
EcoRI-SacI PCR fragment of pJC15 which contains
the yycF promoter region and the 5' terminus of
yycF. The vectors used were pJM783 for integration at the
original locus of the fused promoter and pDH32 for double-crossover
integration at the amyE locus (21). To construct
pJC16, the 750-bp EcoRI-SacI DNA fragment was
blunted by using the Klenow fragment and T4DNA polymerase and then
subcloned into the EcoRI site of Klenow-treated pDH32. For
pJC17, the 750-bp DNA fragment, blunted only at the SacI
site, was ligated to the EcoRI-SmaI-digested
pJM783 vector. A 292-bp HaeIII fragment carrying the DNA
region upstream of the yycK gene (bp 30125 to 30417 in D78193) was first obtained from a PCR-amplified fragment (bp 29383 to
30994), Klenow blunted, and cloned into the SmaI site of
pJM103. The EcoRI-BamHI fragment from this
plasmid was then subcloned into
EcoRI-BamHI-digested pDH32 and pJM783 to produce the pJC18 and pJC20 vectors, respectively.
To create a conditional mutation, a 474-bp
HindIII-
BamHI fragment containing the
ribosome-binding site and the N-terminal
part of
yycF (bp
35526 to 36000) was amplified by PCR and ligated
with the
HindIII-
BamHI-digested integration vector
pMutin4 (
30),
generating plasmid pJC21. Upon transformation
into
B. subtilis JH642 and integration into the chromosome,
pJC21 should disrupt
the
yycF gene and place a second copy
of
yycF, as well as
yycGHIJK,
under the control
of the isopropyl-

-
D-thiogalactopyranoside
(IPTG)-inducible
promoter P
spac. At the same
time, a transcriptional fusion
between the natural
yycF
promoter and the
lacZ gene is created.
The resulting strain
was designated
JH17040.
The 5.4-kb DNA fragment corresponding to the region from
purA to
yycG (bp 5011 in the sequence with
GenBank accession no.
D26185 to bp 33234 in the sequence with GenBank
accession no.
D78193) was amplified by using the Expand PCR kit
(Boehringer
Mannheim). Conditions recommended by the manufacturer were
used,
except for the PCR program, which was 10 s at 94°C, 20 cycles
of 30 s at 55°C and 4 min at 68°C, and finally 10 min
at 68°C.
To sequence the
yycF gene from the thermosensitive strain,
the primers previously used to construct pJC15 were utilized in
PCRs
carried out with purified chromosomal DNA. After
EcoRI-
BamHI
digestion, the amplified DNA fragment
(1,152 bp) was cloned into
the pJM103 vector and sequenced. For the
yycG gene, the upstream
primer used in the case of pJC9 and
the downstream primer from
the 5.4-kb amplified DNA fragment were
combined (see Fig.
1).
The PCR product (2,139 bp) was digested by
SphI, cloned into pJM103,
and
sequenced.
Media, growth conditions, and genetic techniques.
The
plasmids were transformed first into Escherichia coli DH5
and later into B. subtilis. Transformation of E. coli was performed by electroporation with a Bio-Rad apparatus in
accordance with the manufacturer's recommendations. Selection was done
on Luria-Bertani (LB) broth supplemented, when appropriate, with
50-µg/ml ampicillin or 10-µg/ml chloramphenicol. Transformation of
B. subtilis with chromosomal or plasmid DNA was carried out
as previously described (2). Strains were maintained on
Schaeffer's sporulation medium (SM) (23) and selected with
5 µg of chloramphenicol per ml or (pMutin4) 1 µg of erythromycin
per ml.
-Galactosidase assay.
-Galactosidase activity was
determined as previously described (6) on cells grown in LB
or SM. Specific activity was expressed in Miller units (16).
Sequence analyses.
DNA and protein sequences were analyzed
and manipulated by using programs in the University of Wisconsin
Genetics Computer Group software. The predicted product of each open
reading frame was compared to protein sequence databases by using the
BLAST network service (1). The hydropathy profiles were
obtained with the TMpred program provided by the EMBL worldwide web
servers (8).
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RESULTS |
In a survey of the 35 two-component signal transduction systems in
B. subtilis (5a), the yycF and
yycG genes encoding a two-component system with no known
function could not be inactivated, suggesting that this system was
essential for growth. Sequence analysis of the yycFG region
revealed six open reading frames (18) (Fig.
1). A putative
10 promoter sequence
(TATAAT) was identified in the DNA region upstream of the
yycF open reading frame, but no sequence substantially
similar to the consensus
35 sequence of
A promoters
was found in this region. Downstream from the yycF and
yycG genes, four open reading frames (yycH to
yycK) are closely spaced (<22 bp for the three first open
reading frames and 69 bp between yycJ and yycK)
with no obvious internal transcription terminators. Furthermore, the
overlap between open reading frames yycG and yycH
(Fig. 1) is consistent with a translational coupling strategy. These
data suggested that the six open reading frames may comprise an operon.

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FIG. 1.
Genetic organization at the B. subtilis
yycFGHIJK operon. purA codes for adenylosuccinate
synthetase and rocR for a positive regulator controlling
arginine utilization. The arrows identify the coding region of the
genes. The restriction sites (SacI and MluI) used
in some constructions are indicated. DNA inserts cloned into plasmids
are represented by solid lines, with the corresponding names. The
original vector for each construction is indicated at the extreme
right. , position of insertion of a terminatorless
Cmr-encoding gene from pJM105B into the cloned DNA. The
5.4-kb fragment shows the extent of the PCRs used to generate the
temperature-sensitive mutant.
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Similarity among yycF, YycG, and
two-component proteins.
The deduced sequences of the putative YycG
and YycF proteins exhibit structural similarity to histidine kinases
and response regulators, respectively, of two-component regulatory
systems. The yycG gene encodes a protein of 611 amino acids
with a calculated molecular mass of 70 kDa. The C-terminal portion of
the protein contains the five blocks of conserved amino acids
characteristic of the histidine protein kinase family (Fig.
2); i.e., a conserved histidine, the site
of phosphorylation, and the N, G1, F, and G2
boxes, which presumably form a nucleotide-binding surface within the
active site (20). The predicted sequence shows the highest similarity to the B. subtilis ResE protein (26)
(30% identity) and slightly less similarity to the PhoR protein
(25) (28 to 29% identity) (Fig. 2). The hydropathy profile
of the N-terminal putative sensory domain suggests the presence of two
stretches of hydrophobic amino acids sufficiently long to span the
membrane (data not shown). Amino acids 35 to 182 could be oriented
toward the environment in the periplasm, perhaps to sense a specific signal.

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FIG. 2.
Amino acid sequence alignment of B. subtilis
YycG with B. subtilis ResE (SwissProt accession no. P35164)
and PhoR (SwissProt accession no. P23545). The predicted transmembrane
helix domains are underlined. Conserved motifs present in the histidine
kinase family, designated H, N, G1, F, and G2,
are indicated by lines above the corresponding sequences.
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The
yycF gene encodes a putative protein of 235 amino acids
with a calculated molecular mass of 27 kDa. The deduced amino
acid
sequence shows significant similarity to those of numerous
response
regulator proteins, such as
B. subtilis PhoP (
24)
(54%
identity) and the vancomycin response regulator of
Enterococcus faecium (VanR) (
3) (43% identity).
The YycF response regulator
is characterized by a conserved N-terminal
domain of approximately
125 amino acids, containing the aspartates and
lysine that form
the active
site.
Response regulators have been classified into subfamilies, according to
sequence homologies in their DNA-binding domains (
27,
28).
On the basis of sequence similarity, the YycF protein should
be
assigned to the OmpR-PhoB subgroup, to which
B. subtilis
PhoP
belongs (
11). Proteins from this subclass are thought
to bind
to promoter sequences that are recognized by the major form of
RNA polymerase holoenzyme, corresponding to
B. subtilis
E
A (
27). It thus seems likely that YycF is a
DNA-binding transcriptional
regulator.
Sequence analysis of the predicted YycH, YycI, YycJ, and YycK
products.
The predicted products of yycH,
yycI, and yycJ do not show any significant
matches when compared to the protein sequence in databases. The
calculated molecular masses of these putative proteins are 52.5 kDa for
YycH, 32.5 kDa for YycI, and 30 kDa for YycJ. Based on their
hydrophobicity profiles (data not shown), YycH and YycI could be
exported proteins or could be anchored to the membrane by a segment
close to the N terminus. YycJ is predicted to be a cytoplasmic protein.
The putative YycK protein displays similarity to members of the HtrA
serine protease family (34 to 35% identity with HtrA
from
Synechocystis sp. [
9] and
E. coli [
12]). HtrA is involved
in the proteolysis
of abnormal proteins and is required for resistance
to oxidative and
heat stress in enteric bacteria (
13,
19).
YycK contains the
motif Gly-Asp-Ser-Gly-Gly-Ala-Lys, which is
very similar to the
consensus sequence surrounding the active
serine residues of the
catalytic domains of known serine proteases.
The sequence analysis of
YycK suggests a 42.8-kDa membrane-anchored
protein located outside the
cell.
yycF and yycG are essential genes.
In
an effort to determine the functions of YycF and YycG, we used an
integrative plasmid to interrupt their genes and analyze the mutant
phenotypes. An internal region of each gene was cloned into the pJM103
integrative vector, and the plasmids obtained (pJC8 and pJC9) were used
to transform B. subtilis JH642. Numerous attempts to
integrate these circular plasmids into these genes by a
single-crossover event did not yield transformants, suggesting that
null mutations in yycF or yycG may not be constructed.
The same strategy was used for the other open reading frames,
yycH,
yycI,
yycJ, and
yycK,
to determine if mutation of one
of them was lethal. By using plasmids
pJC11, -12, -13, and -14,
transformants were obtained in each case
(strains JH17026 to JH17029,
respectively), indicating that the
deleterious effect observed
was due to
yycF and
yycG inactivation and not to polar effects
on the downstream
genes.
In addition, attempts to interrupt
yycF with a
chloramphenicol resistance cassette, designed to produce nonpolar
mutations
(
21), were also unsuccessful. Transformation of
B. subtilis with linearized pJC10 plasmid DNA (derived from
pJC8) should have
produced recombinants carrying a terminatorless
chloramphenicol
resistance gene integrated within the
yycF
gene by double crossing
over, allowing transcription of downstream
genes in the putative
operon. Thus, both
yycF and
yycG appear to encode products essential
for
growth.
Transcriptional activity of the yycFG regulatory
region.
To study expression from the yycFG promoter,
the 400 nucleotides preceding the start codon of yycF were
cloned in front of the promoterless lacZ gene in pDH32. The
resulting plasmid (pJC16) was linearized and integrated at the
nonessential amyE locus of B. subtilis JH642,
giving strain JH17022. To eliminate any effects due to the chromosomal
location, the same transcriptional fusion was also introduced directly
into the original yycF locus. To construct this strain,
B. subtilis JH642 was transformed with circular plasmid
pJC17, derived from pJM783, giving strain JH17023.
The strains were grown in SM or LB broth and assayed for

-galactosidase activity. The results obtained were generally
identical
for both constructions, indicating a promoter that functions
primarily
during vegetative growth. As shown in Fig.
3A, the
yycF promoter
in cells
grown in SM was active during exponential growth, reaching
a peak of 17 U 1 h before the onset of sporulation, whereupon
it dramatically
decreased toward zero as the cells entered stationary
phase.

-Galactosidase production in cells grown in LB broth (where
the
culture sporulates poorly) was similar throughout exponential
growth,
but relative to growth in SM, the rate of decrease was
delayed and
levels remained higher in the later stages. The activity
was maximum at
the onset of stationary phase and slowly decreased
during the following
2 h (data not shown). These results are consistent
with expression
from the promoter upstream of
yycF being turned
off by some
regulatory protein related to the end of growth or
the onset of
sporulation.

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FIG. 3.
Expression of the yycFG and yycK
promoters. (A) Growth in SM (open symbols) of JH17022 ( ) or JH17023
( ) and -galactosidase specific activity of the
yycF-lacZ promoter fusions (solid symbols). (B) Growth in SM
(open symbols) of JH17023 ( ), JH17024 (spo0A strain with
the yycF-lacZ fusion integrated into the amyE
locus) ( ), JH17025 (spo0A mutant with the fusion in the
chromosomal yycF locus) ( ), and -galactosidase
specific activity of the promoter fusion (solid symbols). (C) Effect of
variations in the level of the YycF and YycG proteins on the growth in
SM (open symbols) and expression of the operon (solid symbols) of
JH17040 without IPTG ( ), with 50 µM IPTG ( ), with 0.5 mM IPTG
(X), and with 1 mM IPTG (+). Growth of JH17023 ( ) is plotted as a
control. (D) Growth in SM (open symbols) and -galactosidase specific
activity (solid symbols) of JH642 with the yycK-lacZ fusion
integrated into the amyE locus (pJC18) ( ) or into the
yycK locus (pJC20) ( ).
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To investigate the possibility that Spo0A, the major transcription
factor required for sporulation, might repress the expression
of the
yycF and
yycG genes upon entry into stationary
phase, the
transcriptional fusions were introduced into a
spo0A mutant strain
(JH646). For construction of strains
JH17024 (fusion integrated
into the
amyE locus) and JH17025
(fusion integrated into the
yycF locus), JH646
(
spo0A12) was transformed with chromosomal DNAs
from JH17022
and JH17023, respectively. The

-galactosidase activities,
assayed on
cells grown in SM, were similar to those in the wild-type
strains (Fig.
3B). Therefore, Spo0A does not appear to play a
role in the regulation
of the expression of the
yycF and
yycG genes.
In order to determine if the
yycF and
yycG gene
products autoregulate their own synthesis,

-galactosidase activity
was assayed
in a strain in which the level of YycF and YycG was
controlled
by the P
spac promoter of the pMutin 4 vector, pJC21,
and the
yycF promoter was coupled to
lacZ to determine its level
of expression. In this strain,
JH17040 containing integrated pJC21,
the level of proteins YycF and
YycG was regulated by the amount
of IPTG added. As seen in Fig.
3C,
modulation of
yycFG expression
by varying the concentration
of IPTG had no obvious effect on
the transcription of
yycF
and
lacZ.

-Galactosidase activities
were similar,
regardless of the IPTG concentration used. Moreover,
the strain
required IPTG for growth. These data suggest that this
two-component
system does not regulate its own
expression.
The noncoding DNA region (69 bp) upstream of the
yycK gene
was checked for the presence of a potential promoter. The pJC18
vector
was integrated into the
amyE locus of JH642, and

-galactosidase
activity was assayed on cells grown in SM or LB
broth. No activity
was detected when cells were grown in LB broth (data
not shown),
but in SM,

-galactosidase expression started between 3 and 4
h (Fig.
3D). A putative
G-dependent promoter
was identified in this DNA fragment with the

10 sequence CATATTA
[consensus, CAT(AT)(AC)TA] (
17) and the

35
sequence GAGTT [consensus, G(AC)AT(AG)] (
17). The
possibility
that
yycK was transcribed from the
yycFG promoter was analyzed
by using the pJC20 vector to
transform JH642 and to obtain a transcriptional
fusion with
lacZ in the original
yycK locus.

-Galactosidase production
measured in cells grown in SM showed
expression during exponential
phase, followed by a decay as the cells
neared stationary phase
and renewed expression during sporulation (Fig.
3D). Thus, the
yycK gene belongs to the
yycFGHIJ
operon and is under the control
of two promoters: one for
expression during exponential growth
and one for expression
starting at stage III of sporulation, probably
in the
forespore.
Isolation of a thermosensitive mutation in the yycFG
operon.
Upstream of the yycFG operon, four genes are
located for tRNA-Phe, tRNA-Asp, tRNA-Glu, and tRNA-Lys, preceded by the
purA gene encoding the adenylosuccinate synthetase involved
in adenine biosynthesis (Fig. 1). The region encompassing all of these
genes plus the yycF and yycG genes (5.4 kb) was
amplified by PCR, and the resulting DNA fragment was used to transform
strain Mu8u5u16 to Ade+. About 3,200 transformants were
transferred to replicate plates and incubated at 30 or 47°C. One
strain did not grow at 47°C on either minimal medium or SM plates.
In order to locate the mutation giving the phenotype, chromosomal DNA
was prepared from the thermosensitive mutant strain
(JH17041) and used
as template DNA in PCRs to amplify the entire
yycF gene (the
fragment in pJC15 [Fig.
1]) and the entire
yycG gene (see
Materials and Methods). The amplified DNA fragments
were then cloned
and sequenced. Only one alteration was found,
and that was localized in
the
yycF gene. Mutation of A to C at
position 35303 (sequence with GenBank accession no.
D78193)
changed histidine 215 to a
proline.
To determine if this mutation was responsible for the thermosensitive
phenotype, the PCR-amplified fragment containing the
yycF
mutant gene was cloned into the integrative pJM103 vector
and used to
transform JH642. The fragment was identical to that
cloned into pJC15
(Fig.
1). Among the transformants, 35% displayed
a thermosensitive
phenotype. The same experiment, when done with
the identical
PCR-amplified fragment from the parental strain,
did not result in
thermosensitivity.
A second experiment was done to confirm that the
yycF
mutation was responsible for the thermosensitive phenotype. The
fragment
in plasmid pJC19 (Fig.
1) was obtained in two pieces by two
PCRs
from the DNA of thermosensitive strain JH17041, and they were
ligated to the chloramphenicol resistance gene and cloned into
pJM105A.
This placed the Cm
r cassette upstream of the promoter and
allowed the insertion of
the entire fragment into the chromosome as a
double-crossover
event. Sequence analyses confirmed the presence of
only a single
mutation in
yycF, as previously described.
Transformation of this
plasmid in JH642 gave 30% thermosensitive
transformants.
Growth and phenotypic characteristics of the thermosensitive
strain.
The thermosensitive and parental strains were grown in LB
broth at 30°C until an optical density at 525 nm (OD525)
of 0.4 was reached; when half of each culture was transferred to
47°C. At 30°C, both strains grew similarly (Fig.
4). Upon a shift to 47°C, the
thermosensitive strain stopped growing after approximately 30 min and
the OD525 decreased. When cultures were observed with a
microscope, the thermosensitive strain at the permissive temperature produced chains of cells characteristic of early exponential-phase cultures that persisted longer than parental strains under the same
conditions (Fig. 5A). Within an hour from
when the cultures were shifted to the nonpermissive temperature, the
chains of the thermosensitive mutant cells were interspersed with empty
sections, as if some of the cells had lost their cytoplasmic contents
and only the cell wall remained (Fig. 5B). The parental strain showed none of this behavior and had separated into single or double cells
after 1 h at 47°C (data not shown).

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FIG. 4.
Growth characteristics of the temperature-sensitive
strain. Growth curves of the Mu8u5u16 ( ) and JH17041
(temperature-sensitive) ( ) strains in LB broth at 30°C (open
symbols) or at 47°C (solid symbols). Time zero is when the culture
was shifted to 47°C from 30°C.
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FIG. 5.
Cellular effect of the thermosensitive mutation. Strain
JH17041 was grown in LB broth at 30°C to an OD525 of
0.35, when half the culture was shifted at 47°C. Phase-contrast
images of cells taken 1.5 h after the shift are shown. A, 30°C
(OD525 = 1.7); B, 47°C (OD525 = 0.6).
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DISCUSSION |
On the basis of the sequence similarity of its C-terminal domain,
the YycF response regulator has been assigned to the OmpR subfamily.
The crystal structure of the E. coli OmpR C-terminal domain
revealed that members of the subfamily belong to the winged helix-turn-helix family of DNA-binding proteins (Fig.
6) (15). Of the 17 residues
known to make up the hydrophobic core of OmpR, all are either identical
or conserved hydrophobic in YycF. Analogy with other winged
helix-turn-helix proteins and correlation with mutagenesis data have
allowed the identification of important structural features: a
recognition helix, a wing involved in DNA binding, and an extensive
loop preceding the recognition helix involved in interaction with the
subunit of RNA polymerase (15). The residues thought to
be important for DNA binding in OmpR, such as Arg182, Val203, and
Thr224, are identical in YycF, and Ser200 is replaced with a similar
amino acid, threonine. The thermosensitive mutation of YycF was
localized to the loop connecting the
3 helix to the
6 and
7
C-terminal strands. Substitution of a proline for a histidine at this
site may perturb the DNA-binding properties of this region by
destabilizing the interaction of
6 and
7 with the rest of the
molecule at elevated temperature.

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FIG. 6.
Sequence alignment of the DNA-binding domains of
B. subtilis YycF and E. coli OmpR (SwissProt
accession no. P03025). A schematic diagram of the secondary structure
of OmpR is shown (15). The dots mark residues corresponding
to the OmpR hydrophobic core. The position of thermosensitive mutation
is shaded.
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The YycG kinase is related to the ResE and PhoR kinases of B. subtilis. All of these kinases appear to have two
membrane-spanning regions which form a putative periplasmic loop of
about 140 amino acids. The active-site histidine of the cytoplasmic
catalytic domain is preceded by about 160 amino acids forming a domain
with no known function in all cases. The highest homology among these proteins is found in the catalytic domain, with less in the cytoplasmic domain. Very little amino acid sequence conservation was found among
all three kinases in the putative periplasmic domain, but YycF and ResE
have 34% identical and similar residues in this region. If all of
these proteins evolved from an ancestral protein, there appears to be
more pressure to conserve the histidine- and ATP-binding regions.
The YycF response regulator is likely to regulate several genes which
remain unidentified. Clearly, loss of this activity in the
thermosensitive mutant results in rapid cessation of growth. The
cellular effect of this loss as revealed by microscopy was the
generation of empty cells which maintained their structural rigidity.
This was especially apparent in septated chains of cells characteristic
of low-density cultures when transferred to the nonpermissive
temperature. The molecular basis of this phenomenon is unknown. YycF
may control some genes whose products are essential for normal cell
growth and are likely to be integrated with other cell cycle-dependent
events, since transcription of the operon containing the
yycF and yycG genes occurs only during growth and is shut off as the cells approach stationary phase. This shutoff is not
mediated by the sporulation regulator Spo0A but may be due to loss of
an inducing signal from, or dependent on, cell growth. Clearly, there
are many unknown features of this system, including what signals
regulate the YycG kinase.
Essential two-component signal transduction systems have been found in
C. crescentus. In C. crescentus, a system of
histidine kinases and response regulators controls cell division and
motility (7, 22). The growth signals that this system
interprets to affect cell division remain obscure. Similarly, YycF and
YycG are likely to respond to growth signals in B. subtilis.
In fact, very little is known about how cells coordinate processes such as cell wall and membrane growth with DNA replication to precisely control cell division. Certainly, bacteria do this well and very quickly. It seems possible that YycF regulates one aspect of these processes and that YycG responds to vital growth signals involved in
the coordination.
A yycFG-like operon was found in the Streptococcus
pyogenes genome (Fig. 7). This
gram-positive bacterium is a member of the group A streptococci and is
known to be responsible for a wide variety of human diseases
(29). Homologies were found with the response regulator YycF
(71% identity) and the histidine kinase YycG (44% identity), as well
as with the predicted YycJ protein (55% identity) (Fig. 7). No open
reading frames corresponding to yycH, yycI, or
yycK were identified.

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|
FIG. 7.
Organization of the yycFG-like genes in
S. pyogenes M1 GAS (sequenced at Oklahoma University
[http://www.genome.ou.edu/strep.html]) and amino acid sequence
alignment of the predicted products (YycFGJSt) with the
homologs in B. subtilis (YycFGJBs). Conserved
motifs in the histidine kinase proteins are indicated by lines above
the corresponding sequences.
|
|
This very high identity between the B. subtilis and S. pyogenes YycF proteins suggests that they carry out the same
function in the two organisms. If the consequences of loss of YycF
activity are the same in both organisms, inhibition of YycF in S. pyogenes should effectively curtail growth and result in rapid
cell death. This system may be a target for a series of two-component
signal transduction inhibitors with bactericidal properties that have recently been described. These inhibitors were especially effective on
gram-positive pathogens, such as methicillin-resistant
Staphylococcus aureus. Since the genome sequence of S. aureus is proprietary, it cannot be determined by us whether a
YycF equivalent exists in this organism, but the S. pyogenes
results suggest that such a system is common to gram-positive
microorganisms (4). Resistance to these inhibitors was
multifactorial, indicating that more than one target was being affected
by the inhibitors (4). This may indicate that more than one
kinase is essential for growth or that general kinase inhibition is a
lethal event. The ResE-ResD signal transduction system to which YycG
and YycF are closely related is essential for growth in the absence of
glucose. How many other systems of their type, when mutated singly or
in combination, would have this phenotype has yet to be determined. The
presence of similar two-component systems in gram-positive pathogens
suggests that kinase or response regulator inhibitors would be
effective bactericidal anti-infective agents (4, 5, 14).
 |
ACKNOWLEDGMENTS |
This research was supported in part by grant GM19416 from the
National Institute of General Medical Sciences, National Institutes of
Health, USPHS. We thank B. A. Roe, S. P. Linn, L. Song, X. Yuan, S. Clifton, M. McShan, and J. Ferretti for the S. pyogenes data made available through the Streptococcal Genome
Sequencing Project funded by AI38406 from the USPHS.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Division of
Cellular Biology, Department of Molecular and Experimental Medicine,
The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037. Phone: (619) 784-7905. Fax: (619) 784-7966. E-mail: hoch{at}scripps.edu.
Publication 11729-MEM from the Department of Molecular and
Experimental Medicine at The Scripps Research Institute.
 |
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