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J Biol Chem, Vol. 273, Issue 10, 5932-5938, March 6, 1998
Purification and Characterization of Bacillus
subtilis PyrR, a Bifunctional pyr mRNA-binding
Attenuation Protein/Uracil Phosphoribosyltransferase*
Robert J.
Turner ,
Eric R.
Bonner§,
Gail K.
Grabner, and
Robert L.
Switzer¶
From the Department of Biochemistry, University of Illinois,
Urbana, Illinois 61801
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ABSTRACT |
Bacillus subtilis PyrR has been shown
to mediate transcriptional attenuation at three separate sites within
the pyrimidine nucleotide biosynthetic (pyr) operon.
Molecular genetic evidence suggests that regulation is achieved by PyrR
binding to pyr mRNA. PyrR is also a uracil
phosphoribosyltransferase (UPRTase). Recombinant PyrR was expressed in
Escherichia coli, purified to homogeneity, physically and
chemically characterized, and examined with respect to both of these
activities. Mass spectroscopic characterization of PyrR demonstrated a
monomeric mass of 20,263 Da. Gel filtration chromatography showed the
native mass of PyrR to be dependent on protein concentration and
suggested a rapid equilibrium between dimeric and hexameric forms. The
UPRTase activity of PyrR has a pH optimum of 8.2. The
Km value for uracil is very pH-dependent; the Km for uracil at pH
7.7 is 990 ± 114 µM, which is much higher than for
most UPRTases and may account for the low physiological activity of
PyrR as a UPRTase. Using an electrophoretic mobility shift assay, PyrR
was shown to bind pyr RNA that includes sequences from its
predicted binding site in the second attenuator region. Binding of PyrR
to pyr RNA was specific and UMP-dependent with
apparent Kd values of 10 and 220 nM in
the presence and absence of UMP, respectively. The concentration of UMP
required for half-maximal stimulation of binding of PyrR to RNA was 6 µM. The results support a model for the regulation of
pyr transcription whereby termination is governed by the
UMP-dependent binding of PyrR to pyr RNA and
provide purified and characterized PyrR for detailed biochemical
studies of RNA binding and transcriptional attenuation.
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INTRODUCTION |
The Bacillus subtilis pyrimidine biosynthetic
(pyr) operon encodes all of the enzymes for the de
novo biosynthesis of UMP and two additional cistrons encoding a
uracil permease and the regulatory protein PyrR (1-4). On the basis of
molecular genetic evidence it was proposed that PyrR regulates
pyr expression through a transcriptional attenuation
mechanism that acts at three separate sites within the operon, which
are located in the 5'-untranslated leader, between the first
(pyrR) and second (pyrP) genes, and between the
second and third (pyrB) genes of the operon (3, 5). PyrR is
proposed to regulate the ratio of terminated to readthrough transcripts
at each attenuation site by permitting the formation of a
-independent transcription terminator when exogenous pyrimidines are
available. The binding of PyrR to pyr mRNA interferes
with the formation of an alternative upstream stem-loop structure, the
antiterminator, which is otherwise kinetically and thermodynamically
favored. The presence of a conserved sequence within the 5'-stem of
each antiterminator suggested a site within the pyr mRNA
for interaction with PyrR (3); this site is the locus of several
cis-acting mutants in the first pyr attenuator which are deficient in repression by pyrimidines (6).
In addition, PyrR functions as a novel uracil phosphoribosyltransferase
(UPRTase),1 catalyzing the
formation of UMP and pyrophosphate from uracil and 5-phosphoribosyl
-1-pyrophosphate (PRPP) despite its lack of primary sequence
similarity to other known UPRTases (3, 7). The UPRTase activity of PyrR
was first discovered by Ghim and Neuhard (8), who characterized the
pyrR gene from Bacillus caldolyticus. The role of
the enzymatic function of PyrR is not known; Bacillus
subtilis possesses an additional UPRTase that has been shown to be
quantitatively more important than PyrR (3, 7). It has been
demonstrated that UMP and PRPP function as negative and positive
regulators, respectively, of the pyr operon (3, 5, 9).
Direct biochemical characterization of this attenuation mechanism is
required to test the above proposals. In this paper we describe the
purification of PyrR. Physical and enzymatic properties of PyrR are
described, and the ability of PyrR to bind specifically to
pyr mRNA is demonstrated.
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EXPERIMENTAL PROCEDURES |
Bacterial Strains, Plasmids, Media, and Growth
Escherichia coli strains DH5 (Life Technologies,
Inc.) and TG1 (10) were used for plasmid construction and plasmid
propagation for purification. Luria broth (11) was used for the growth
of cultures for plasmid purification and the purification of native PyrR. Media were supplemented with 100 µg/ml ampicillin when cells harboring plasmids were grown. All liquid cultures were grown aerobically at 37 °C.
Expression and Purification of PyrR
B. subtilis PyrR was expressed in E. coli
from plasmid pTSROX3 (pUC18 (12) into which a 0.79-kilobase pair
EcoRI-SphI fragment bearing the pyr
promoter, 5'-leader, and pyrR from pTS185 (3) was inserted),
in which PyrR expression was driven by tandem lac and
pyr promoters. E. coli SØ408 (relA1
rpsL254 metB1 upp-11, from J. Neuhard, University of
Copenhagen), a strain lacking endogenous UPRTase activity,
bearing pTSROX3 was grown in 3 liters of Luria broth, supplemented with
97 µg of ticarcillin and 3 µg of clavulanic acid/ml of culture. The
cells were harvested by centrifugation, washed in cold 0.9% NaCl, and
stored at 80 °C.
All enzyme purification procedures were performed at 4 °C. The pH
values for Tris buffers were determined at 25 °C. The cells were
resuspended with 8 ml of 100 mM Tris acetate, pH 7.0, per g
of cell paste, disrupted by sonication on ice, and cell debris removed
by centrifugation.
Streptomycin sulfate (0.11 volume of a 10% solution freshly prepared
in 100 mM Tris acetate, pH 7.0) was added, and the
precipitate was removed by centrifugation. Further contaminants were
precipitated with 0.538 volume of saturated ammonium sulfate, which was
buffered with 100 mM Tris acetate, pH 7.0, and removed by
centrifugation. PyrR was precipitated from the supernatant solution by
the addition of 0.857 volume of buffered saturated ammonium sulfate and
collected by centrifugation. The precipitate was resuspended in 4 ml of buffer R (100 mM Tris acetate, pH 7.0, 10 mM
Na+Pi, 100 mM NaCl) for every g of
the cell paste used. The solution was dialyzed against buffer R.
The entire sample was loaded onto a 2.2 × 21-cm Q-Sepharose Fast
Flow (Pharmacia) column that had been equilibrated in buffer R. Buffer
R (400 ml) was allowed to flow through the column, and PyrR was eluted
using an 800-ml linear NaCl gradient, from 100 to 300 mM,
in 100 mM Tris acetate, pH 7.0, 10 mM
Na+Pi. Fractions from the trailing half of the
PyrR peak, which eluted at a conductivity equivalent to 217-238
mM NaCl, were pooled. The pooled PyrR sample was then
concentrated approximately 6-fold by pressure dialysis.
Additional impurities were precipitated with an equal volume of
saturated ammonium sulfate and removed by centrifugation. PyrR was
precipitated from the supernatant fluid by the addition of another
equal volume of saturated ammonium sulfate, then collected by
centrifugation. The precipitate was dissolved in 0.5 ml of 10 mM Tris acetate, pH 7.5, per g of cell paste used and
dialyzed against 10 mM Tris acetate, pH 7.5. The dialyzed
solution was divided into aliquots and stored at 80 °C.
UPRTase Assay
UPRTase activity was determined by measuring the conversion of
[2-14C]uracil to [14C]UMP by modifications
of the method of Rasmussen et al. (13).
Method 1--
Method 1 was used during development of the
purification of PyrR. The assay conditions were pH 9.0 at 37 °C, 50 mM Tris acetate, 20 mM 2-mercaptoethanol, 5 mM MgCl2, 1.2 mM PRPP, and 0.1 mM [14C]uracil (about 4.4 × 104 dpm/assay). The assay mix (20 µl, containing all
components but PRPP) was combined with 20 µl of enzyme, which was
diluted in 0.1 M Tris acetate, pH 9.7, and 1 mg/ml BSA.
Reactions were preheated for 1 min at 37 °C, initiated with 10 µl
of 6 mM PRPP, and incubated for 5 min at 37 °C. (For
purified PyrR after the Q-Sepharose step it was necessary to stabilize
the enzyme by including 3 mM PRPP in the assay mix and
initiating the reactions with 10 µl of 0.5 mM
[14C]uracil.) The reactions were stopped by heating at
100 °C for 1 min. Separation of the product [14C]UMP
from [14C]uracil on DEAE-cellulose paper was essentially
as described for Method 2 below.
Method 2--
After purified PyrR was available the assay was
further optimized, and Method 2 was used for kinetic characterization
of the purified protein. Each assay contained 20 µl of 0.125 M buffer, 12.5 mM MgCl2, and 2.5 times the desired final concentration of PRPP. PyrR was diluted into
100 mM buffer containing 1 mg/ml BSA immediately before
assay, and 20 µl was mixed with 20 µl of assay mix and incubated at
37 °C for 5 min. Reactions were initiated by the addition of 10 µl
of [14C]uracil at 5 × the desired final
concentration (1.5-6 × 105 cpm). Reactions occurred
at 37 °C, and 5-µl samples taken at various reaction times
were spotted onto 1-cm2 squares of DEAE-cellulose paper
(Whatman) and dried rapidly. The spotting was found to stop
the reaction very quickly, so heating was not necessary. The
DEAE-cellulose paper was washed four times for 20 min each with water
and once for 15 min with methanol. To determine the total
14C counts in each reaction mixture duplicate 5-µl
samples from each tube were spotted onto squares of DEAE-cellulose
which were not washed. Radioactivity on the DEAE-cellulose paper
squares was determined by liquid scintillation counting. Kinetic data were analyzed using the KinetAsyst (IntelliKinetics, State College, PA)
computer program. At least five concentrations of each substrate were
used at each pH value reported; the data fit well to a Ping Pong Bi Bi
rate equation at all pH values.
Electrospray Ionization Mass Spectroscopic Analysis of
PyrR
For ESI-MS, PyrR was dissolved in a 50% acetonitrile (v/v) and
0.1% formic acid (v/v) solution by repeated desalting using a
MicroconTM 10 concentrator (Amicon, Beverly, MA) until all
salts were reduced to picomolar concentrations. The sample was
submitted to the University of Illinois School of Chemical Sciences
Mass Spectrometry Laboratory for ESI-MS analysis on a VG Quattro
(quadrupole-hexapole-quadrupole) mass spectrometer system (Fisons
Instruments, VG Analytical; Manchester, U. K.). Data acquisition and
processing were controlled by the VG MassLynx (version 2.0) data system
(Micromass, Manchester, U. K.). MaxEnt (maximum entropy) software
(Micromass) was used for the processing and analysis of zero charge
state electrospray data.
Sulfhydryl Group Titration
Cysteinyl sulfhydryl groups were titrated with 4 mM
5,5'-dithio-bis(2-nitrobenzoate), measuring the increase in absorbance at 412 nm as described by Ellman (14). The buffer used for titration of
native PyrR was 0.1 M KPi, pH 7.3, containing 1 mM EDTA; for denatured PyrR the buffer was 0.1 M Tris-Cl, 1 mM EDTA, 0.5% SDS, pH 8.4. The
concentration of PyrR was determined from its extinction coefficient of
7,100 M 1 cm 1 at 275 nm.
Gel Filtration Analysis of PyrR
A column (1-cm diameter, 95-cm height, 75-ml bed volume) of
Sephadex G-150 (Pharmacia Biotech Inc.) was used to determine the
native molecular weight of PyrR. The buffer used was 50 mM Tris acetate, pH 7.5. The column was loaded with 0.6-1.0-ml samples of
PyrR and eluted at 4 °C. Proteins used to construct a
Mr standard curve for the column were myoglobin,
chicken serum albumin, yeast hexokinase, and bovine -globulin. The
protein concentrations in the eluted fractions were determined by their
absorbance at 280 nm; when the protein was too dilute or the fractions
contained UMP, the protein was determined using the Bradford method
(15) with reagents purchased from Bio-Rad.
Preparation of Transcription Templates
A template for in vitro run-off transcription of
pyr mRNA nucleotides +682 to +761, which correspond to
the anti-antiterminator (or "binding loop") from the
pyrR-pyrP intercistronic region, was created using
PCR. The PCR was performed using the forward primer
5'-CGGAATTCTAATACGACTCACTATAGGGAGATATGAAAACGAATAATAGATCACCTTTTTAA-3' (where an EcoRI site is underlined and is immediately
upstream of a bacteriophage T7 promoter in italics), the reverse primer 5'-CGGGATCCTTTTTGGGCCTTTGTTGTG-3' (where a
BamHI site is underlined), and the pLS361 plasmid (5) as
template. The purified PCR product was digested with EcoRI
and BamHI and ligated into similarly digested pUC18 to
create pBSBL2. This plasmid template was linearized with BamHI before its inclusion in the transcription
reaction.
Similarly, templates for in vitro run-off transcription of
pyr mRNA nucleotides +722 to +796 and +772 to +809,
which correspond to the antiterminator and terminator, respectively,
from the pyrR-pyrP intercistronic region, were created using
PCR. The antiterminator template pBSAT2 was synthesized using
the primers
5'-CGGAATTCTAATACGACTCACTATAGGGAGAGAGGTTGCAAAGAGGTG-3' (where an EcoRI site is underlined and is immediately
upstream of a bacteriophage T7 promoter in italics),
5'-CGGGATCCACGCGTTTACGCAAAGAGGCATACAAAG-3' (where a BamHI site is underlined, and an MluI
site is in italics), and pLS361 as template. The purified PCR product
was digested with EcoRI and BamHI and ligated
into similarly digested pUC18 to create pBSAT2. This plasmid template
was linearized with MluI before its inclusion in the
transcription reaction. The terminator template pBST2 was synthesized
using the primers
5'-CGGAATTCTAATACGACTCACTATAGGGAGAGTCTTTGTATGCCTCTTTGC-3' (where an EcoRI site is underlined and is immediately
upstream of a bacteriophage T7 promoter in italics),
5'-CGTCTAGACCTCTTTGCTTTTTTACGC-3' (where an
XbaI site is underlined), and pLS361 as template. The purified PCR product was digested with EcoRI and
XbaI and ligated into similarly digested pUC18 to create
pBST2. This plasmid template was linearized with XbaI before
its inclusion in the transcription reaction.
To create a template that contained the same pyr nucleotides
as pBSBL2 but was designed to transcribe the antisense RNA strand corresponding to the anti-antiterminator, two synthetic DNA
oligonucleotides were annealed and used as the template to produce
run-off transcripts directly. The first oligonucleotide, or
"top strand," corresponds to the core T7 promoter sequence
(5'-TAATACGACTCACTATA-3'). The second oligonucleotide, or "bottom
strand," has a sequence that anneals to the T7 promoter at one end
and also nucleotides that are complementary to the desired
pyr transcript (pyr mRNA nucleotides +761 to +682). The sequence of the bottom strand oligonucleotide was
5'-TATGAAAACGAATAATAGATCACCTTTTTAAGGGCAATCCAGAGAGGTTGCAAAGAGGTGCACAACAAAGGCCCAAAAAGTCTCCCTATAGTGAGTCGTATTA-3' (the sequence complementary to the T7 promoter oligonucleotide is
underlined). The top strand (30 pmol) and bottom strand (25 pmol)
oligonucleotides were annealed according to the procedure of Milligan
and Uhlenbeck (16).
Preparation of pyr RNA
pyr RNA for use in the electrophoretic gel mobility
shift assay was prepared by in vitro run-off transcription
using the MEGAshortscriptTM kit from Ambion (Austin, TX) as
described by the manufacturer, except that 1 µl of 75 mM
ATP diluted 1:500 in RNase-free H2O and 5 µl of
[ -32P]ATP (3,000 Ci/mmol, 10 mCi/ml, ICN, Costa Mesa,
CA) were added to each 20-µl reaction mixture. The full-length RNA
product was purified by electrophoresis on a denaturing 20%
polyacrylamide gel (19:1, acrylamide:bisacrylamide) containing 8 M urea. The RNA was visualized by autoradiography, excised,
and eluted with 1 ml of 0.5 M ammonium acetate, 10 mM MgSO4, 0.1% SDS, 1 mM EDTA in
RNase-free H2O at room temperature for at least 3 h.
The elution solution was extracted twice with acid phenol:chloroform
and precipitated with ethanol. The pellet was washed twice with cold
absolute ethanol and air dried. The RNA was resuspended in RNase-free
TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0, in
RNase-free H2O). The molar concentration of each RNA
species was determined from the radioactivity of the full-length RNA,
the specific radioactivity of the ATP in the transcription mixture, and
the number of adenine residues in each transcript. Each RNA was diluted
in RNase-free TE to a stock concentration of 500 pM.
Preparation of Nonspecific RNAs
Nonspecific RNA was prepared as above but using the plasmid
templates as follows. An 18 S rRNA transcript was prepared using the
template provided with the Ambion MEGAshortscriptTM kit; an
actin transcript was prepared using the template provided with the
Ambion MAXIscriptTM kit; and an RNA corresponding to
multiple cloning site DNA was prepared using pSP72 (Promega, Madison,
WI) linearized with HindIII.
Electrophoretic Mobility Shift Assay for RNA Binding
Gel shifts were performed using a Bio-Rad PROTEAN® IIxi
electrophoresis apparatus with the core cooled to 2 °C and the
buffer recirculating between the upper and lower reservoirs. All gel shifts were run on 6% native polyacrylamide (79:1,
acrylamide:bisacrylamide) gels containing 12.5 mM Tris
acetate, pH 7.5, and 2.5% glycerol (v/v), using 12.5 mM
Tris acetate, pH 7.5, containing 1 mM magnesium acetate as
running buffer. Gels were pre-run at 150 V for 90 min and then cooled
by recirculation for 1 h. RNA-binding reaction mixtures were
loaded onto the gel with tracking dyes in a separate lane. The gel was
subjected to electrophoresis at 30 V for 15 min followed by 300 V for
3 h. The gel was blotted onto filter paper, dried, and
radioactivity was visualized by exposing the gels to x-ray film. For
quantitation of the binding data, the dried gel was exposed to a
storage PhosphorImage screen (Molecular Dynamics, Sunnyvale, CA), after
which the data were quantitated with a PhosphorImager using the
ImageQuant software. Binding curves were fit to hyperbolae, and binding
constants were calculated using the KinetAsyst computer program as
described above.
RNA-binding reaction mixtures were assembled on ice. The binding
conditions were modified from the procedure of Batey and Williamson
(17). Each reaction contained 16 µl of binding mix, 2 µl of PyrR
(diluted as described below), and 2 µl RNA (prepared as described
below; final concentration of 50 pM RNA). The binding mix
gave final assay concentrations of 10 mM HEPES-KOH (pH
7.5), 50 mM potassium acetate, UMP (when added), 1 mM magnesium acetate, 0.1 mM EDTA, 0.1 mg/ml
yeast tRNA, 5 µg/ml heparin, 0.01% Igepal CA-630 (Sigma; Igepal
CA-630 is an analog of Nonidet P-40), and 0.08 unit/µl placental
RNase inhibitor (Ambion). PyrR was diluted using 12.5 mM
Tris acetate buffer, pH 7.5, which contained 1 mg/ml RNase-free
acetylated BSA (U. S. Biochemical Corp.). Because PyrR has poor
thermostability at high dilution, the protein must be thawed on ice and
diluted immediately before use. To minimize alternate RNA secondary
structures, the RNA was heated to 75 °C for 15 min, slow cooled for
1 h, and cooled on ice for 5 min before its incorporation into the
binding mixture. The completed binding reactions were incubated on ice
for 1 h before loading on the gel. Immediately before loading them
onto the gel, 2 µl of RNase-free 50% glycerol was added to the
reaction mixtures.
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RESULTS AND DISCUSSION |
Overexpression and Purification of PyrR--
B.
subtilis DNA specifying the pyr promoter, 5'-leader,
and pyrR was cloned into pUC18 to generate plasmid pTSROX3,
in which the expression of pyrR was driven from the tandem
lac and pyr promoters. pTSROX3-encoded PyrR was
expressed to about one-third of the total cell protein in E. coli strain SØ408. In other experiments (not shown) the addition
of uracil to the growth medium did not reduce the amount of
pTSROX3-encoded PyrR produced in a different strain of E. coli. Thus, although the PyrR protein regulates its own expression
in B. subtilis (3), such regulation was not observed in an
E. coli background. Because transcriptional attenuation of
pyr genes can be demonstrated with purified PyrR and
E. coli RNA polymerase in vitro (9), we suggest
that the failure to see such attenuation in vivo might
reflect significant differences in the intracellular concentrations of
the regulatory metabolites UMP and PRPP in the two species.
The procedure for purification of PyrR is relatively simple. The most
effective step is ion exchange chromatography on Q-Sepharose. The prior
steps were used primarily to remove non-protein contaminants so that
the fractionation on Q-Sepharose would be more reproducible. The
subsequent ammonium sulfate fractionation is useful to concentrate the
protein and to remove some very minor contaminating proteins, but it
frequently resulted in losses of activity and a reduced specific
activity. This step can be omitted for many uses of the purified PyrR.
At least four trace-contaminating proteins can be detected in the best
preparations of PyrR on overloaded SDS-polyacrylamide gels (not shown);
we estimate these preparations to be at least 98% pure. Specific
UPRTase activities (using assay Method 1) of purified PyrR preparations
have ranged from 6 to 11 µmol/min/mg at pH 9.
Physical Characterization of PyrR--
Two preparations of
purified PyrR were subjected to ESI-MS analysis. Three major
components, comprising about 95% of the total protein, were resolved
(results for one of the preparations are shown in Fig.
1). The mass of the most abundant
component of each sample, approximately 70%, was 20,263 ± 2 Da.
Another component, comprising approximately 10% of each preparation,
had a mass of 131-132 Da smaller than the main component, which
matches the change in mass expected for removal of the
NH2-terminal methionine that is known to be present on the
bulk of PyrR produced in E. coli (3). The third major
component, which comprised about 12% of the total protein, was 28 Da
smaller than the most abundant component. This component and several
other minor components were not identified.

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Fig. 1.
ESI-MS analysis of purified PyrR. Peak
heights are proportional to the relative abundance of the peaks. The
masses determined for each significant peak are printed above the
peak.
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The mass of the major components differed by 75 Da from the mass
predicted by the previously deduced amino acid sequence of PyrR (3).
This discrepancy led us to re-examine the nucleotide sequence of
pyrR. Two GC dinucleotide inversions were discovered which
require codons 34 and 53 to be changed from encoding a serine (UCG) and
proline (CCG) to codons encoding cysteine (UGC) and arginine (CGC),
respectively. These corrections to the PyrR sequence led to a
calculated molecular mass (20,263) that matched exactly the value
determined by ESI-MS. The corrected PyrR sequence contains one
cysteinyl residue/monomer, whereas the previously deduced sequence
predicted none. Titration of the sulfhydryl content of PyrR with
5,5'-dithio-bis(2-nitrobenzoate) (14) demonstrated the presence of 0.8 mol/mol cysteine with the native enzyme and 1.1 mol/mol when PyrR was
denatured with 0.5% SDS. Furthermore, the corrected residues, Cys-34
and Arg-53, are identical to the amino acid residues found in the
corresponding positions in the deduced sequence of the highly
homologous PyrR from B. caldolyticus (8).
The ultraviolet spectrum of PyrR at pH 7.5 yielded an extinction
coefficient of 7.1 mM 1 cm 1 at
275 nm based on determination of its concentration by the Bradford
method (15), which matched very well with an extinction coefficient at
275 nm of 7.5 mM 1 cm 1
calculated for the protein from a content of five tyrosine residues and
no tryptophan residues predicted from the deduced sequence. Furthermore, this result indicates that the purified protein does not
contain significant amounts of nucleotide or nucleic acid contaminants.
The native molecular weight of PyrR was determined by gel filtration
chromatography at various protein concentrations and in the presence
and absence of the ligands UMP or PRPP (Table I). In general, most of the PyrR migrated
on gel filtration as a single, active peak whose apparent molecular
weight was dependent on the concentration of PyrR loaded. Average
molecular weights from 60,000 to 100,000 were observed; given the
subunit molecular weight of 20,000, these values correspond to trimeric
to pentameric states of aggregation. X-ray crystallographic analysis
has identified two forms of PyrR, one dimeric and the other
hexameric.2 We interpret the
behavior of PyrR on gel filtration chromatography to indicate that the
dimeric and hexameric forms of PyrR are in rapid equilibrium and that
the average molecular weight values observed reflect shifts in that
equilibrium toward the hexameric form as the PyrR concentration is
increased. Mg2+ and UMP tend to favor the more aggregated
form, whereas Mg2+ and PRPP favor the less aggregated form
of PyrR, but these effects are small, and in no case is the protein
fully converted to one state of aggregation. In the absence of
stabilizing ligands PyrR has some tendency to form highly aggregated
inactive species. A much more pronounced ability of substrates to
affect the state of aggregation of the UPRTase from E. coli
was reported by Jensen and Mygind (18), who found that substrates
converted the enzyme from a low molecular weight form, probably a
dimer, to a high molecular weight form, probably a hexamer. B. subtilis PyrR shares with E. coli UPRTase the ability
to be stabilized and activated by prior incubation with
Mg2+ and PRPP (see below), but we did not find evidence for
promotion of aggregation of PyrR by this substrate.
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Table I
Apparent native molecular weight of PyrR as a function of conditions of
gel filtration chromatography on Sephadex G-150
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UPRTase Activity of PyrR--
The UPRTase activity of PyrR was
first identified from the ability of the pyrR gene to
complement the upp mutation in E. coli SØ408 and
assays of UPRTase activity in SØ408 cells bearing a pyrR-encoding plasmid (3). This activity was confirmed by
the very high levels of UPRTase activity in cells in which PyrR was overexpressed and by the increase in specific activity of UPRTase as
PyrR was purified to homogeneity. Assays of the UPRTase activity of
PyrR in crude extracts were initiated by the addition of PRPP because
the presence of many other PRPP-consuming enzymes made preincubation of
the crude extract with PRPP undesirable. When PyrR was purified,
however, the high dilution of the protein needed to bring the assay
into the linear range required preincubation of PyrR with
Mg2+ ions and PRPP to obtain assays that were linear with
time and to avoid inactivation of the enzyme at high dilution. This
approach was suggested to us by the studies of Jensen and Mygind (18), who showed that the UPRTase from E. coli is converted to a
more highly aggregated and more active form by incubation with
Mg2+ and PRPP. In the case of PyrR, stabilization of the
UPRTase activity by Mg2+ and PRPP was especially necessary
when the protein was diluted and incubated at 37 °C instead of
0 °C. Dilution of PyrR into buffer containing 1 mg/ml BSA was also
necessary to prevent losses of UPRTase activity.
The values for the maximal velocity and the Michaelis constants for
PRPP and uracil for the UPRTase reaction catalyzed by PyrR were
determined at 5 mM MgCl2 and 37 °C in the pH
range from 7.7 to 9.7 (Fig. 2). (We were
unable to determine kinetic constants accurately at lower pH values
because of severe substrate inhibition by uracil.) The UPRTase activity
of PyrR consistently displayed a Ping Pong kinetic pattern. Maximal
activity at saturating substrate concentrations was at pH 8.2. The
Michaelis constant for uracil was very dependent on the reaction pH,
rising from around 100 µM at pH 9.2-9.7 to about 1 mM at pH 7.7. The Michaelis constant for PRPP was also
somewhat dependent on pH; the minimal value of 70 µM was
observed at pH 8.7 with larger values observed at both higher and
lower pH. The Km values for PyrR-catalyzed UPRTase are in contrast to the values of about 50 µM for PRPP and 2 µM for uracil observed
with the B. caldolyticus upp-encoded UPRTase at pH 8.6 (19).
We suggest that these kinetic differences between the
pyrR-encoded UPRTase and the upp-encoded UPRTase, which has much greater sequence similarity to other bacterial UPRTases
(7), explain why the upp-encoded enzyme is the
physiologically dominant UPRTase in B. subtilis (7): the
latter enzyme has a much smaller Michaelis constant for uracil and is
thus much more effective in uracil salvage.

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Fig. 2.
pH-activity profile for the UPRTase activity
of PyrR. Values of Vmax (panel
A) and Michaelis constants (panel B) for uracil and
PRPP are shown for the range from pH 7.7 to 9.7. Method 2 was used for
the UPRTase assays. Buffers used were: pH 7.7, HEPES and Tris; pH 8.2, Tris; pH 8.7, Tris and Ser; pH 9.2, Ser and Gly; pH 9.7, Gly.
Counterions were Na+ for HEPES, Gly, and Ser and acetate
for Tris.
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RNA Binding to PyrR--
The binding of 32P-labeled
RNA to PyrR was measured by an electrophoretic gel mobility shift assay
as described under "Experimental Procedures." In most cases
purified PyrR was used; the radioactive oligonucleotide used for most
of the characterization of binding was an 80-nucleotide segment
corresponding to residues +682 through +761 from the conserved sequence
of the pyrR-pyrP intercistronic region, i.e. the
anti-antiterminator of the second attenuation region (3, 5), which had
been shown in preliminary studies to bind well to PyrR. The specificity
of the interaction between PyrR and pyr mRNA was tested
in two ways. First, to demonstrate that the RNA was bound specifically
by PyrR, gel shift experiments were performed using the 80-nucleotide
pyr RNA and crude extracts from either E. coli
SØ408/pTSROX3, which overexpresses PyrR, or E. coli
SØ408/pUC18, which carries the vector plasmid only. The crude extract
containing overexpressed PyrR clearly contained a protein that binds
RNA; increasing amounts of this extract increased the amount of RNA
bound (Fig. 3). In contrast, the crude
extract from cells that contained the vector only contained no protein that bound detectably to RNA; at the highest concentrations of such
extracts tested some degradation of the RNA was evident. These results
indicate that the PyrR protein binds to RNA and rules out the
possibility that an impurity in the PyrR preparation binds to the RNA
instead.

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Fig. 3.
Binding of pyr mRNA by crude
extracts of E. coli cells in which PyrR was overexpressed
(SØ408/pTSROX3) and a control strain bearing the plasmid vector only
(SØ408/pUC18). Electrophoretic gel mobility shift analysis was
used. Approximately 50 pM pyr mRNA from
pBSBL2/BamHI (nucleotides +682 to +761) and 500 µM UMP were included in all samples. Nucleotide numbers
refer to the start of transcription of the B. subtilis pyr
operon (2) as +1.
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To demonstrate that PyrR binds specifically to pyr mRNA,
the following radioactive RNAs were tested with purified PyrR: the 80-nucleotide segment of pyr RNA described above, an 18 S
rRNA transcript, an actin mRNA transcript, and RNA transcribed from the multiple cloning site of pSP72 (Promega) linearized with
HindIII. PyrR bound only to the pyr mRNA
(data not shown). A more rigorous test of specificity was provided by
examining the binding of PyrR to segments of pyr mRNA
from the same attenuation region corresponding to the antiterminator
stem-loop (mucleotides +722 to +796), the terminator stem-loop
(nucleotides +772 to +809), and the antisense sequence of RNA derived
from the same segment of the attenuator as the 80-nucleotide RNA for
which the sense strand was shown above to bind well to PyrR. None of
these RNA species was bound by PyrR under conditions in which the
80-nucleotide RNA that included the anti-antiterminator sequence bound
very well (Fig. 4). Because all three of
the control RNAs are derived from B. subtilis pyr sequences
and all three are predicted to form stem-loop structures, the failure
of PyrR to bind detectably to these structures is very strong evidence
for its specificity for a defined pyr mRNA sequence.
Moreover, the sequence to which PyrR bound included the sequence that
is conserved in all three pyr attenuation regions (3) and is
positioned such that binding of the protein would disrupt formation of
the antiterminator stem-loop, as predicted by our model (3, 20) for
attenuation control of the pyr operon. More detailed studies
of the specificity of binding of PyrR to pyr mRNAs from
each of the three attenuation regions and determination of specific
sequence and secondary structural requirements for RNA recognition are
in progress in our laboratory.

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Fig. 4.
Specificity of binding of purified PyrR to
various segments of pyr mRNA. Electrophoretic gel
mobility shift analysis was used with 50 pM RNA, 500 µM UMP, and the concentrations of purified PyrR shown.
The anti-antiterminator (binding loop) RNA is from the
pBSBL2/BamHI template, the antiterminator RNA is from the
pBSAT2/MluI template, the terminator RNA is from
the pBST2/XbaI template, and the anti-antiterminator
(binding loop) antisense RNA is from annealed synthetic
oligonucleotides as described under "Experimental Procedures."
Nucleotide numbers refer to the start of transcription of the B. subtilis pyr operon (2) as +1.
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An approximate Kd for the PyrR-pyr
mRNA interaction was determined in gel shift experiments in which
the RNA concentration was held constant and the PyrR concentration was
varied, using triplicate determinations of each point (Fig.
5). At saturating UMP the
Kd determined was 10.2 ± 0.5 nM;
when UMP was omitted from the binding mixtures the
Kd was 216 ± 17 nM. This 20-fold
difference in apparent binding affinity of PyrR for pyr
mRNA in the presence versus the absence of UMP may be sufficiently large to account for the physiological regulation of
pyr attenuation which is known to occur (3), although it is
appreciably smaller than the differences in affinity of well characterized repressor proteins for operator DNA in the presence and
absence of corepressors. It is possible that the conditions used for
measuring binding by gel mobility shift do not reproduce the binding
conditions in vivo adequately. We have tested other gel
mobility shift conditions in which tight, specific binding occurred,
but no dependence of RNA binding on the presence of UMP could be
demonstrated. Thus, the UMP dependence of PyrR binding to RNA is quite
sensitive to the experimental conditions, and the current observations
may not give a reliable estimate of the degree of this dependence
in vivo.

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Fig. 5.
Dependence of PyrR binding to RNA on PyrR
concentration and UMP. Electrophoretic gel mobility shift
experiments were performed with purified PyrR as shown and 50 pM pyr RNA from the pBSBL2/BamHI
template (nucleotides +682 to +761). UMP was at 500 µM
when present. Each data point is the average of three independent trials, and the error bars indicate the S.D. of these
determinations.
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The concentration of UMP which gives half-maximal stimulation of PyrR
binding to pyr mRNA was estimated by gel shift
experiments in which the PyrR and RNA concentrations were held constant
and the concentration of UMP was varied from 0 to 500 µM.
On the basis of the curves shown in Fig. 5, 80 nM PyrR was
chosen to give a substantial difference between the fraction of bound
RNA in the presence versus the absence of UMP. Fig.
6 demonstrates that 5.8 ± 0.8 µM UMP gave half-maximal stimulation of PyrR binding.
This value is comparable to the concentration of 2.5 µM
UMP which was shown previously to give half-maximal stimulation of
transcriptional termination with a pyr template by PyrR
in vitro (9).

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Fig. 6.
Concentration dependence of UMP stimulation
of RNA binding by PyrR. Experimental conditions were as in Fig. 5,
except that the concentration of purified PyrR was held constant at 80 nM. Each data point is the average of three independent
trials.
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Relationships between PyrR and other RNA-binding Attenuation
Proteins--
Although our studies have concentrated on PyrR from
B. subtilis, it has become clear that PyrR homologs are
found in many species of bacteria in which they probably also regulate
pyr gene expression; examples include B. caldolyticus (8), Enterococcus faecalis
(21),3 Lactobacillus
plantarum (22), and Lactococcus lactis (23). Recently,
a Thermus species has been shown to encode a PyrR that probably binds to pyr mRNA but acts as a translational
repressor (24). Genes with strong sequence similarity to
pyrR have been found in two other species, but it is less
clear whether they function as RNA-binding regulatory proteins in these
cases (25, 26).
PyrR is a member of a small group of proteins that regulate gene
expression by binding to mRNA and affecting transcriptional termination at a downstream site (27), but we suggest that many more
such proteins remain to be discovered. The B. subtilis trp RNA-binding attenuation protein, TRAP, is the only well characterized example of a regulatory protein that is functionally quite similar to
PyrR (28-31). Like PyrR, TRAP brings about transcriptional termination by binding to a specific site on mRNA and preventing formation of
an antiterminator hairpin, which permits formation of a downstream transcription terminator (28, 29). However, TRAP has no known enzymatic
activity. Its quaternary structure (30) and the nature of RNA sequences
recognized by TRAP are very different from PyrR (30, 31).2
A somewhat different class of mRNA-binding regulatory proteins comprises proteins, such as E. coli BglG (32) and B. subtilis SacT and SacY (33-36), which act by binding to a
transcription terminator that precedes the genes to be regulated and
suppressing termination. PyrR and TRAP binding to RNA is regulated by
the end products of the operons they control, i.e. by UMP
and tryptophan, respectively, whereas the ability of BglG, SacT, and
SacY to bind to RNA is regulated by reversible phosphorylation. Not
only do these systems present novel mechanisms for the control of gene expression in bacteria, but we believe they provide favorable objects
for the detailed study of protein-RNA recognition in general.
 |
ACKNOWLEDGEMENTS |
We acknowledge Robin Dodson for assistance
with developing RNA gel mobility shift assays and other helpful
assistance in working with RNA.
 |
FOOTNOTES |
*
This work was supported in part by United States Public
Health Service Grant GM47112 (to R. L. S.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
Supported by the National Institutes of Health Cell and Molecular
Biology Training Grant GMO7283. Present address: Scripps Research
Institute, Skaggs Institute for Chemical Biology, CVN-20, 10550 N. Torrey Pines Rd., La Jolla, CA 92037.
§
Supported by a fellowship from the National Science Foundation.
¶
To whom correspondence should be addressed: Dept. of
Biochemistry, University of Illinois, 600 S. Mathews Ave., Urbana, IL 61801. Tel.: 217-333-3940; Fax: 217-244-5858; E-mail:
rswitzer{at}uiuc.edu.
1
The abbreviations used are: UPRTase, uracil
phosphoribosyltransferase; PRPP, 5-phosphoribosyl -1-pyrophosphate;
BSA, bovine serum albumin; ESI-MS, electrospray ionization mass
spectroscopy; PCR, polymerase chain reaction.
2
Tomchick, D. R., Turner, R. J., Smith, J. L.,
and Switzer, R. L. (1998) Structure, in press.
3
S.-Y. Ghim, C. Kim, and R. L. Switzer,
unpublished experiments.
 |
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