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Journal of Bacteriology, February 2000, p. 1150-1153, Vol. 182, No. 4
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Catabolite Repression Control by Crc in 2xYT Medium
Is Mediated by Posttranscriptional Regulation of bkdR
Expression in Pseudomonas putida
Kathryn L.
Hester,1
K. T.
Madhusudhan,1 and
John R.
Sokatch1,2,*
Department of Biochemistry and Molecular
Biology1 and Department of Microbiology
and Immunology,2 University of Oklahoma
Health Sciences Center, Oklahoma City, Oklahoma 73190
Received 21 May 1999/Accepted 11 November 1999
 |
ABSTRACT |
The effect of growth in 2xYT medium on catabolite repression
control in Pseudomonas putida has been investigated using
the bkd operon, encoding branched-chain keto acid
dehydrogenase. Crc (catabolite repression control protein) was shown to
be responsible for repression of bkd operon transcription
in 2xYT. BkdR levels were elevated in a P. putida crc
mutant, but bkdR transcript levels were the same in both
wild type and crc mutant. This suggests that the mechanism
of catabolite repression control in rich media by Crc involves
posttranscriptional regulation of the bkdR message.
 |
TEXT |
The molecular mechanisms of
catabolite repression have been well described in enteric bacteria,
where enzymes of the phosphoenolpyruvate phosphotransferase system
mediate catabolite repression control by regulation of cAMP
concentration via adenylate cyclase activity (19). However,
a similar mechanism does not appear to be present in
Pseudomonas because adenylate cyclase activity and cAMP
pools do not fluctuate with carbon source, nor does addition of cAMP relieve repression of catabolite responsive pathways (12,
18). The only protein thus far shown to be involved in catabolite
repression in Pseudomonas is Crc of P. aeruginosa, but a function has not been identified
(13). However, Crc does not appear to bind DNA (13), suggesting that it is not simply a DNA-binding
negative regulator.
Crc is involved in catabolite repression of P. putida
branched-chain keto acid dehydrogenase (BCKAD), glucose-5-phosphate dehydrogenase, and amidase by glucose and succinate in synthetic media
(11). BCKAD is encoded by the four structural genes of the
bkd operon, which is positively regulated by BkdR
(15). BkdR is a homologue of Lrp (leucine-responsive
protein), which is a global transcriptional regulator in
Escherichia coli (4). However, pseudomonads and
enteric bacteria live in complex media in nature and not in chemically
defined media. Expression of lrp is downregulated in
nutritionally rich media (6), which suggested that this
might also be the case with bkdR. In this report, the effect
of 2xYT medium on the expression of bkdR in wild type and in
a crc mutant of P. putida was studied to
determine if catabolite repression control of the bkd operon
might be accomplished by controlling the level of BkdR in the cell.
Crc downregulates BCKAD activity in 2xYT.
The wild-type
strains of P. putida and P. aeruginosa, their
crc mutants, and the complemented mutants (11)
were grown to an A660 of ~0.6 in 100 ml of
2xYT plus 0.3% valine and 0.1% isoleucine (wt/vol) and then
harvested; cell extracts were then prepared as described earlier
(16). P. putida JS394 had five- to sixfold higher
activity than either PpG2 or JS394 (pJRS196) (Table
1), and a similar result was obtained
when BCKAD activity of PAO8020 was compared to the activities of PAO1
and PAO8020 (pPZ352). These results demonstrate that Crc is involved in
catabolite repression control of BCKAD activity by 2xYT in both
P. putida and P. aeruginosa. However, the BCKAD
activities of the crc were much lower than that obtained in
minimal media (11), indicating that something in addition to
Crc is involved in catabolite repression control in synthetic medium.
It was interesting to investigate whether the
crc mutants
could be complemented with the heterologous
crc. P. aeruginosa PAO8020
was transformed by triparental mating
(
9) with pJRS196, which
contains
crc from
P. putida cloned in pUCPM19 (
11). BCKAD activity
in
P. aeruginosa 8020(pJR196) was similar to that seen
in
P. aeruginosa PAO1 and
P. aeruginosa
PAO8020(pPZ352) (Table
1). This demonstrates
Crc has the same function
in both species and that
P. aeruginosa recognizes the
P. putida crc promoter. Several attempts were made
to
complement the
P. putida crc mutation with pPZ352, but for
some reason, all these attempts were
unsuccessful.
Crc reduces the level of BCKAD in 2xYT.
BCKAD is a multienzyme
complex with three components. The E1 component of P. putida
BCKAD is an 
heterotetramer (10), the structure of
which has just recently been determined (1). The E2
component is a transacylase (2), and the E3 component is a
specific lipoamide dehydrogenase (3). In mammalian cells, BCKAD activity is regulated by a posttranslational modification: E1
contains two phosphorylation sites, and the phosphorylation state
regulates activity of the complex (17). Although P. putida E1
is not phosphorylated (10), it is possible
that catabolite repression of P. putida BCKAD activity could
be the result of some other kind of posttranslational modification of
BCKAD or could be the result of reduction in transcription of the
bkd operon. To distinguish between these two possibilities
first, Western blots with anti-E1
serum (10) were
employed. P. putida PpG2, JS394, and JS394(pJRS196), and
P. aeruginosa strains PAO1, PAO8020, and PAO8020(pJRS196)
were grown to an A660 of ~0.6 in 100 ml of 2xYT plus 0.3% valine and 0.1% isoleucine (wt/vol) and then
harvested. Cell extracts were then prepared as described earlier
(16). Five micrograms of protein was loaded onto a sodium
dodecyl sulfate (SDS)-8.5% polyacrylamide gel electrophoresis (PAGE)
gel, blotted to Hybond-enhanced chemiluminescence (ECL) membrane, and
treated with anti-E1
serum. As seen in Fig.
1, E1
protein levels were greatly
increased in the crc mutants P. putida JS394 and
P. aeruginosa PAO8020 compared to the other four strains.
The increase in E1
reflected the increased BCKAD activities found in
these extracts (Table 1). Therefore, repression of BCKAD activity by
Crc is due to a reduction in the amount of BCKAD. P. putida
PpG2 grown in glucose minimal medium had no BCKAD activity, nor could
E1
be detected by Western blots.

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FIG. 1.
Western blot with anti-E1 serum (10) of
crc mutants grown in 2xYT plus valine-isoleucine. The
extracts in lanes 1 to 6 were from cultures grown in 2xYT plus 0.3%
valine and 0.1% isoleucine (wt/vol); the extract in lane 7 was from a
culture grown in glucose minimal medium. Each lane contained 5 µg of
protein. Lane 1, P. putida PpG2; lane 2, P. putida JS394; lane 3, P. putida JS394(pJRS196); lane 4, P. aeruginosa PAO1; lane 5, P. aeruginosa
PAO8020; lane 6, P. aeruginosa PA8020(pJRS196); lane 7, P. putida PpG2 grown in glucose. All cultures were grown to
an A660 of between 0.6 and 0.8, and cell
extracts were prepared as described before (16).
Electrophoresis was done in an SDS-8.5% PAGE gel. Western blots were
screened by using the ECL-Western blotting analysis system (Amersham
Pharmacia Biotech) with Hybond-ECL nitrocellulose membranes according
to the manufacturer's instructions. To determine whether the ECL
detection method was quantitative, increasing amounts of PpG2 grown in
valine-isoleucine-lactate medium were loaded on a gel and used for
Western blotting with anti-E1 serum. The blot was scanned with a
Molecular Dynamics densitometer, and pixel values versus micrograms of
protein were graphed and shown to be a linear plot (data not shown).
|
|
Crc regulates the level of BkdR produced in 2xYT.
To
characterize the role of BkdR in catabolite repression of BCKAD
activity, Western blots with anti-BkdR serum were used to measure BkdR
levels in wild type and the crc mutant of P. putida in grown in 2xYT plus valine-isoleucine and
valine-isoleucine synthetic media. Then, 200 µg of cell extracts from
P. putida PpG2, JS394, and JS394(pJRS196) grown in 2xYT plus
0.3% valine-0.1% isoleucine, along with P. putida PpG2
grown in 0.3% valine-0.1% isoleucine synthetic medium
(16) alone or with 40 mM succinate, were loaded on an
SDS-12% PAGE gel, blotted to Hybond-P membrane, and treated with
anti-BkdR serum. As seen in Fig. 2,
P. putida JS394 grown in 2xYT plus valine-isoleucine had
higher levels of BkdR than either PpG2 or JS394(pJRS196) grown under
the same conditions. This result demonstrates that Crc plays a major
role controlling the level of BkdR in 2xYT and suggests that relief of
catabolite repression control in crc mutants is due to a
higher level of BkdR. BkdR levels of P. putida PpG2 were
much higher in minimal media than in 2xYT (lanes 4 to 5 of Fig. 2),
corresponding to the higher BCKAD activity in minimal medium
(11). Also, the amount of BkdR was not repressed when
succinate was added to the inducing medium, suggesting a different kind
of control in minimal media. No BkdR was detected in P. putida JS386 which contains a bkdR-lacZ translational
fusion (14).

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FIG. 2.
Levels of BkdR in wild type and in the crc
mutant of P. putida. These cultures were grown and harvested
as in Fig. 1, and 200 µg of each cell extract was loaded onto an
SDS-12% PAGE gel, blotted to Hybond-P membrane, and treated with
anti-BkdR (14). More protein was used than in the experiment
of Fig. 1 because of the low copy number of BkdR per cell.
Hybond-polyvinylidene difluoride (PVDF) membranes (Amersham) were used
in this experiment because PVDF has a better binding capacity for
low-molecular-weight proteins. Proteins were separated by
electrophoresis in an SDS-12% PAGE gel. Lane 1, P. putida
grown in 2xYT plus 0.3% valine-0.1% isoleucine; lane 2, P. putida JS394 grown in 2xYT plus 0.3% valine-0.1% isoleucine;
lane 3, P. putida JS394(pJRS196) grown in 2xYT plus 0.3%
valine-0.1% isoleucine; lane 4, P. putida PpG2 grown in
0.3% valine-0.1% isoleucine synthetic medium; lane 5, P. putida PpG2 grown in 0.3% valine-0.1% isoleucine plus 40 mM
succinate; lane 6, P. putida JS386 grown in 2xYT plus 0.3%
valine-0.1% isoleucine; lane 7, 20 ng of purified BkdR.
|
|
Repression of BCKAD activity by 2xYT involves posttranscriptional
regulation of bkdR expression.
Since both BCKAD and
BkdR levels are elevated in the JS394 grown in 2xYT supplemented with
valine and isoleucine (Fig. 1 and 2), mRNA levels of bkdR
and bkdA1, which encodes E1
, were of interest in
determining the mechanism of action of Crc in repression by 2xYT.
P. putida PpG2, JS394, and JS394(pJRS196) were grown in 2xYT
plus valine-isoleucine medium. P. putida JS382
(15), a mutant with a deletion in bkdR, which
does not produce bkd operon mRNA, was grown under the same
conditions for use as a negative control. At mid-log phase, total RNA
was purified from each culture. Five micrograms total RNA was
transferred to a GeneScreen Plus membrane by means of a vacuum suction
HYBRI-SLOT Filtration Manifold (Life Technologies). The membrane was
prehybridized for 1 h at 42°C and then hybridized overnight with
0.5 µCi of bkdA1 or bkdR mRNA probes at the
same temperature. After a washing at 65°C, the membrane was exposed
to a Phosphor Screen (Molecular Dynamics) overnight. The membrane was
stripped by boiling for 30 min in 0.1× SSC (1× SSC is 0.15 M NaCl
plus 0.015 M sodium citrate) plus 1% SDS and then prehybridized and
hybridized as described above with 0.3 µCi of 5'-end-labeled 16S RNA
probe. The adjusted pixel value for each mRNA was obtained by
normalizing each slot pixel value to its 16S RNA value and then
averaging the duplicates and subtracting the average of the normalized
P. putida JS382 pixel values. After hybridization and a
washing, the membrane was exposed to a Phosphor Screen for 1 to 2 h.
Probes for
bkdA1 and
bkdR were generated from PCR
fragments and were labeled with Ambion's Prime-A-Probe kit; a larger
PCR
fragment was primed internally with a third primer, so that the
single-stranded DNA (ssDNA) probe could be gel purified away from
the
PCR product. A 286-bp
bkdA1 PCR fragment was amplified with
primers S73 (nucleotides [nt] 1615 to 1641) and S114 (nt 1901
to
1883). This fragment was primed internally with S87 (nt 1698
to 1681),
yielding an 83-base ssDNA probe complementary to the
bkd
operon mRNA. A 511-bp
bkdR PCR fragment was amplified with
primers S88 (nt 916 to 935) and S58 (nt 1427 to 1411). This fragment
was primed internally with two different primers: S40 (nt 1287
to 1300)
produced a 140-base ssDNA probe, while S39 (nt 1022 to
1036) produced a
405-base probe, both complementary to
bkdR mRNA.
For the 16S
RNA probe, the primer S179 (nt 33 to 10), which is
complementary to the
mRNA, was 5'-end-labeled with T4 kinase.
The accession numbers for each
sequence are as follows:
bkd operon,
M57613; and 16S RNA,
D85995.
Two identical blots were prepared by loading each RNA sample in
duplicate onto a slot blot. These blots were first probed
with
radiolabeled ssDNA probes to either
bkdR or
bkdA1
mRNA. After
this, the blots were stripped and reprobed with a
radiolabeled
16S RNA oligonucleotide to normalize blots for the amount
of RNA
loaded.
The levels of
bkdA1 mRNA were typically four- to sixfold
higher in
P. putida JS394 than in PpG2 or JS394(pJRS196)
(Table
2).
This result, taken together
with the BCKAD assays and the Western
blots of E1

levels, indicates
that regulation of
bkd operon expression
by 2xYT occurs by
reducing transcription. However,
bkdR mRNA levels
in JS394
were always similar to or slightly lower than the levels
seen in PpG2
and JS394(pJRS196) (Table
2). This suggests that
the mechanism of
regulation of
bkdR expression by 2xYT occurs
at a
posttranscriptional level.
The data in our related study demonstrated that Crc was involved in
catabolite repression control of BCKAD, glucose-6-phosphate
dehydrogenase, and amidase in synthetic media (
11). In the
present
study, it has been shown that the amount of BkdR was elevated
in the
crc mutant, JS394 (Fig.
2) but that the amount of
bkdR mRNA was unchanged (Table
2), which suggests that Crc
acts posttranscriptionally
in controlling BkdR levels. In contrast,
bkdA1 mRNA, BCKAD activities
(Table
2) and E1

protein
levels (Fig.
1) were all elevated in
the
P. putida crc
mutant, indicating that expression of the
bkd operon was
regulated at the transcriptional level. It was also
shown in
(
11) that
lacZ expression was increased two- to
threefold
in the mutant with transposon-inactivated
crc
(
P. putida JS391)
carrying a
bkdR-lacZ
translational fusion. However,
lacZ is inserted
after the
44th amino acid codon of BkdR (
14), and this transcript
would look very different to Crc than the normal
bkdR message.
Crc shares sequence similarity with a group of DNA repair enzymes,
although no endo- or exonuclease activity has been identified
(
13). It is possible that Crc's nuclease activity is very
specific,
such as acting only on secondary RNA structure, resulting in
functional
degradation of mRNA. Crc could effect posttranscriptional
regulation
of
bkdR expression by affecting the efficiency of
translation
or the stability of functional mRNA. Two types of secondary
structures
are responsible for controlling mRNA stability: 5' hairpins
and
3' hairpins. The 5' untranslated region of the
E. coli
ompA transcript
functions in vivo as a growth-rate-regulated mRNA
stabilizer (
7).
The hairpin in this untranslated region is
not only specific for
the
ompA gene but also confers
stability when fused to other genes
(
5). The half-life of
the mRNA was drastically reduced when
the stem-loop structure was moved
more than ten nucleotides away
from the 5' end (
5). These
results indicate that the stabilization
provided by the hairpin is due
to inhibition of endonuclease cleavage.
Another secondary structure
that can confer stability to a transcript
is a 3' hairpin. Stem-loop
structures at the 3' end of a transcript
were originally thought to
function only as

-independent transcriptional
terminators, but more
recently these structures have been shown
to protect mRNA from
degradation by the exonucleases RNase II
and PNPase (
8).
One possible explanation for the function of Crc in rich media is that
there is a ligand in 2xYT which causes a conformational
change in Crc,
thereby activating it. Activated Crc would now
have endonuclease
activity which causes functional degradation
of
bkdR
message. There is some support for this hypothesis, since
Yuste et al.
(
20) showed that use of fresh Luria-Bertani medium
resulted
in catabolite repression of the
alk operon of
Pseudomonas oleovorans, whereas spent medium did
not.
 |
ACKNOWLEDGMENTS |
This research was supported by Public Health Service grant DK21737
and Presbyterian Health Foundation grant C5142801 (both to J.R.S.) and
Environmental Protection Agency STAR fellowship grant U-915028-01-0 (to
K.L.H.).
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Biochemistry and Molecular Biology, University of Oklahoma Health
Sciences Center, P.O. Box 26901, Oklahoma City, OK 73190. Phone: (405) 271-2227. Fax: (405) 271-3091. E-mail:
john-sokatch{at}ouhsc.edu.
 |
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Journal of Bacteriology, February 2000, p. 1150-1153, Vol. 182, No. 4
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
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