Journal of Bacteriology, April 2001, p. 2709-2714, Vol. 183, No. 8
Department of Biology, The University of
Michigan, Ann Arbor, Michigan 48109-1048
Received 23 October 2000/Accepted 1 February 2001
Two linked mutations affecting glutamate dehydrogenase (GDH)
formation (gdh-1 and rev-2) had been isolated
at a locus near the trp cluster in Klebsiella
aerogenes. The properties of these two mutations were consistent
with those of a locus containing either a regulatory gene or a
structural gene. The gdhA gene from K. aerogenes was cloned and sequenced, and an insertion mutation was
generated and shown to be linked to trp. A region of
gdhA from a strain bearing gdh-1 was sequenced
and shown to have a single-base-pair change, confirming that the locus
defined by gdh-1 is the structural gene for GDH. Mutants
with the same phenotype as rev-2 were isolated, and their
sequences showed that the mutations were located in the promoter region
of the gdhA gene. The linkage of gdhA to
trp in K. aerogenes was explained by
postulating an inversion of the genetic map relative to other enteric
bacteria. Strains that bore high-copy-number clones of gdhA
displayed an auxotrophy that was interpreted as a limitation for
In the enteric bacterium
Klebsiella aerogenes, glutamate dehydrogenase (GDH) carries
out the NADPH-dependent synthesis of glutamate from In 1974, Brenchley and Magasanik (6) described a mutant of
K. aerogenes that had reduced levels of GDH activity, but
they were not able to determine if the mutation responsible,
gdh-1 (then called gdhD1), was in the structural
gene for GDH. In 1976, Bender et al. (5) showed that the
gdh-1 mutation was linked to the trp operon, in
contrast to the Escherichia coli gdhA gene, which is not
linked to trp (14). They further identified a
class of GDH-overproducing mutants (e.g., rev-2) that led to
a fourfold increase in the total GDH activity but was still responsive
to regulation by NAC (although not so strongly as was the wild type). The rev-2 mutation was tightly linked to the locus defined
by gdh-1. The fact that the genetic maps of E. coli and K. aerogenes are similar, coupled with the
fact that regulatory mutations were isolated at this site, led us to
question whether gdh-1 did in fact lie in gdhA,
the structural gene for GDH.
Cloning of gdhA+.
K.
aerogenes strain KB2560 (gltB200 gdh-1 and lysogenic
for Mu cts62 hP1#1) lacks both GOGAT and GDH
activities and cannot grow without exogenous glutamate
(7). An in vivo cloning procedure (13) was
used to generate plasmids that enabled KB2560 to grow in the absence of
glutamate (the strains and plasmids used in this work are listed in
Table 1). Roughly half of these clones contained apparent gltB (GOGAT) clones and the others
contained apparent gdh clones. A 2.4-kb PstI
restriction fragment from one of the GDH clones was subcloned into
pUC19 and tested for complementation. This plasmid, pGDH4, restored GDH
activity to a gdh-1 strain. The DNA sequence of the
PstI fragment was determined and found to contain an open
reading frame (ORF) with near identity (99% at the nucleotide level,
100% at the amino acid level) to the partial gdhA sequence
previously reported for K. aerogenes (22, 35).
In addition, this ORF was 81% identical at the nucleotide level (90%
at the amino acid level) to the gdhA sequence from E. coli (21, 33). Thus, the gdhA+
gene was able to restore GDH activity to a strain carrying the gdh-1 mutation.
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.8.2709-2714.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Growth Inhibition Caused by Overexpression of the Structural Gene
for Glutamate Dehydrogenase (gdhA) from
Klebsiella aerogenes
ABSTRACT
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Abstract
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References
-ketoglutarate and consequently for succinyl-coenzyme A (CoA). Three
lines of evidence supported this interpretation: high-copy-number
clones of the enzymatically inactive gdhA1 allele showed no
auxotrophy, repression of GDH expression by the nitrogen assimilation
control protein (NAC) relieved the auxotrophy, and addition of
compounds that could increase the -ketoglutarate supply or reduce
the succinyl-CoA requirement relieved the auxotrophy.
TEXT
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Abstract
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References
-ketoglutarate
and ammonia. It is one of only two enzymes in the cell capable of net
assimilation of ammonia into glutamate (for a review, see reference
29). The other enzyme, glutamate synthase (GOGAT), uses
glutamine in place of ammonia and thus functions in conjunction with
glutamine synthetase, the enzyme responsible for assimilating ammonia
into glutamine. GDH is a hexameric protein composed of six identical
subunits (30) and should be coded for by a single
structural gene, gdhA. Glutamate plays two different roles
in cellular metabolism: it is the source of 85% of the nitrogen in
cellular material, and it plays a role in osmoprotection (16,
34). Thus, it seemed reasonable that multiple regulatory loci
might exist. nac (which codes for the nitrogen assimilation
control protein [NAC]) is one such locus. When K. aerogenes is grown in nitrogen-deficient medium, gdhA is strongly repressed by NAC, which is itself under the control of the
global Ntr system (20, 31).
TABLE 1.
Strains and plasmids used in this work
gdhA is linked to trp.
Since the
nature of the gdh-1 mutation was unknown, it was
necessary to construct an authentic gdhA mutation for
genetic mapping. The streptomycin- and
spectinomycin-resistant (Sm Sp) Omega (
) cartridge
(26) was cloned into a unique HpaI site within
the gdhA gene of pGDH4. This inactivated gdhA
gene (gdhA2::) was crossed onto the K. aerogenes chromosome and replaced the resident wild-type gene. The
resulting strain had low levels of GDH, comparable to those of strains
carrying gdh-1 (Table 2).
Another mutant, gdhA12 (in which the promoter and first four
nucleotides of gdhA were replaced with a kanamycin
resistance cassette) also displayed low but nonzero levels of GDH. It
thus appeared that the residual activity observed resulted from an
enzyme other than GDH, and the low levels of GDH observed in a
gdh-1 mutant are not inconsistent with this mutation mapping
to gdhA. The loss of GDH activity in strains carrying
gdhA2:: was cotransducible with the Sm Sp
resistance and was tightly linked to gdh-1. In addition,
gdhA2::, like gdh-1, was linked to
trp but not to nas (data not shown). The linkage of gdhA to trp in K. aerogenes can be
explained by an inversion of a chromosomal region relative to the same
region in Salmonella enterica serovar Typhimurium LT-2. This
inversion is similar to the inversions found in this area of E. coli and S. enterica serovar Enteritidis (4,
19). However, the K. aerogenes inversion appears to
be smaller: gdhA, nar (or nas), and
dad remain outside the boundaries of the inversion, but
trp and pyrF remain inside.
|
The gdh-1 mutation lies within gdhA.
To confirm that gdh-1 was an allele of gdhA, we
tested for complementation between gdh-1 and
gdhA2::. The cloned
gdhA2:: (pGDH5) failed to complement
gdh-1, but prototrophic recombinants arose at significant
frequencies when this plasmid was present in a gltB200 gdh-1
strain. All the plasmids tested in this manner that carried the region
from bp 226 to 303 of the structural gene (as well as flanking DNA)
yielded recombinants at a frequency similar to that of pGDH5. The
plasmid pCB584, which contained only this region and no additional
flanking DNA, also yielded recombinants, but at a lower frequency. This
was presumably due to the small amount of homologous DNA contained in
the fragment. Thus, the only sequence information needed to correct the
deficiency in GDH caused by gdh-1 lies within this region
(which corresponds to amino acids 76 to 101 of the polypeptide).
A regulatory mutation affecting gdhA expression. Another mutation affecting GDH formation (rev-2) that had been isolated previously had higher (but still regulated) levels of GDH under all conditions tested and was also linked to trp (5). The simplest explanation for rev-2 was that it was an up-promoter mutation at gdhA or a structural mutation in gdhA that increased the specific activity of the enzyme. However, rev-2 might have defined a regulatory gene near gdhA. The original rev-2 isolate had been lost, so we used the same selection to isolate seven independent mutants with the same phenotype as the original rev-2 strain. This mutant was isolated as a glutamate-independent revertant of an Ntr-constitutive gltB strain (KC895, ntr-45 gltB200). The parent is a glutamate auxotroph due to the lack of GOGAT activity and the repression of gdhA by the Ntr system (via NAC). Most glutamate prototrophs resulted from mutations that lay in either ntrC or nac and affected the nitrogen regulation of many operons. In contrast, rev-2-like mutants were specific for GDH expression. The gdh-3 mutation was typical of the seven mutations isolated in this study in that it was linked to trp and resulted in increased levels of GDH that were still regulated by nitrogen (Table 2).
Our attempts to clone the gdh-3 allele by multicopy complementation of gdhA1 were unsuccessful. Therefore, we tested directly whether the gdh-3 mutation was a promoter mutation affecting gdhA. The 5' region of the gdhA gene from the gdh-3 strain was amplified by PCR and cloned in front of a promoterless lacZ (pCB1205). This construct showed an increased level of
-galactosidase
expression compared with the wild-type gdhA promoter
lacZ fusion (Table 2). The DNA sequence of this region was
determined and contained a single nucleotide change of G to A at
position 
14 relative to the start of transcription (Fig.
1a) of wild-type gdhA (as
determined below). An identical analysis of the other six independently
isolated mutants revealed the same nucleotide change.
|
10 region for the gdhA promoter. The
change created a close match to a 10 recognition region that is
spaced 16 nucleotides away from a possible 35 binding region of the
wild-type promoter (Fig. 1a). The proposed 10 region in the wild-type
promoter is spaced 19 nucleotides from this 35 region and 15 nucleotides from another possible 35 region. Thus, the proposed novel
10 site would result in a promoter that has more favorable spacing between the consensus hexamers than does the wild-type promoter (28).
We were surprised to discover that all seven of our independent
isolates bore the same mutational change. Perhaps this is a hot spot
for spontaneous mutation, or it may reflect the fact that the selection
depends on relief of NAC-mediated repression of gdhA.
Clearly, GDH formation in the gdh-3 strain under nitrogen limitation was much higher than in the wild type. Moreover, the relative strength of the NAC-mediated repression was much weaker in
this strain (ca. 2.5-fold) than in the wild type (at least eightfold).
A simple explanation for the reduced repression by NAC is that a
stronger binding site for RNA polymerase made the polymerase a better
competitor for the site. But repression of gdhA by NAC is
complex, and other explanations remain possible.
Overproduction of GDH activity leads to auxotrophy.
Our
inability to isolate gdh-3 clones via the in vivo cloning
protocol (which uses a high-copy-number origin of replication) led us
to suspect that overproduction of GDH activity might prevent growth in
minimal medium. However, our original gdhA+
clone was present in high copy numbers. Closer analysis of strains freshly transformed with either pS4BC (high-copy-number
gdhA+ Mu plasmid) or pGDH4 (high-copy-number
gdhA+ pUC plasmid) revealed that these strains
could not grow on glucose ammonia minimal medium (GN) (Table
3) and that secondary mutations which
suppressed this growth defect occurred at a high frequency (5 × 10
4 for a wild-type strain carrying pGDH4). The growth
defect was relieved by the addition of glutamate to the medium. This
auxotrophy was not seen when the (inactive) gdhA1 allele
replaced gdhA+ on the high-copy-number plasmid
pCB644. In 1976, Struhl and Magasanik described a mutant of K. aerogenes that they explained had a reduced ability to form
succinyl-coenzyme A (CoA) from -ketoglutarate (32). The
similarity between the phenotypes of that mutant and our GDH
overproducers was striking and led us to the hypothesis that the
overproducers converted most of the available -ketoglutarate to
glutamate. This in turn would lead to a limitation for succinyl-CoA. Three sets of observations supported this hypothesis. First,
enzymatically active GDH was required for the phenotype. Second,
conditions that reduced GDH production reduced the severity of the
phenotype. Third, conditions that reduced the demand for succinyl-CoA
and/or -ketoglutarate also reduced the severity of the phenotype.
|
|
-D-thiogalactopyranoside (IPTG)-inducible tac promoter controls nac
expression, the addition of IPTG was enough to allow the strain to grow
on GN (Table 3). In addition, when KC3228 was grown with glutamine or
serine as the limiting nitrogen source, GDH levels were reduced roughly fourfold (Table 4) and the strain was able to grow. The addition of
lysine to the medium also reduced GDH levels approximately twofold. The
mechanism of this repression was unclear but was apparently linked to
transcription, since gdhA promoter fusions to
lacZ also reflected this lysine-dependent repression (data not shown).
Our hypothesis was that the large amounts of GDH in the cell depleted
the -ketoglutarate levels in the cell, but a direct test of this
hypothesis was complicated by the fact that K. aerogenes does not transport -ketoglutarate. However, the
replacement of glucose with citrate or succinate as the sole carbon
and energy source circumvented this complication. These compounds feed
into the tricarboxylic acid cycle and increase the flux into
-ketoglutarate and succinyl-CoA (1, 11). Under these
conditions, overexpression of GDH did not affect the growth rate.
Furthermore, addition of lysine and methionine, which need succinyl-CoA
for synthesis (12, 23), reduced the demand for
succinyl-CoA and the severity of the phenotype. However, the addition
of both lysine and methionine was not sufficient to restore the full
growth rate to a GDH overproducer. This is consistent with the
observation that the addition of these two amino acids did not fully
restore wild-type growth to -ketoglutarate dehydrogenase mutants of
E. coli (15).
By comparing GDH activities and growth rates in strains KC3228 and
KC4356, it was possible to show that lysine and methionine reduced the
severity of the phenotype independent of repression effects. This was
most clearly shown by comparing three cultures (Table 4) that each had
about 12,000 U of GDH activity per mg: KC3228 (high-copy-number
gdhA+) grown in GN supplemented with glutamate,
lysine, and methionine and KC4356 (medium-copy-number
gdhA+) grown in either GN or GN supplemented
with glutamate. While all three conditions provided roughly the same
amount of GDH, the doubling time of KC4356 decreased from 235 min to 83 min with the addition of glutamate, and KC3228 with all three
supplements grew faster still, doubling every 56 min. The effect of
methionine alone is easily seen by examining the results for strain
KC3228. In GN supplemented with glutamate, the strain had 30,700 U of GDH activity per mg and a doubling time of 102 min. The addition of
methionine to the medium maintained high levels of GDH (34,900 U/mg),
but the strain doubled faster (a doubling time of 76 min). The effect
of lysine was harder to isolate because of the twofold repression
caused by the addition of lysine to the medium. Nevertheless, strain
KC4356 grown without lysine had high levels of GDH (11,300 U/mg) and
had a doubling time of 83 min, while strain KC3228 grown in the
presence of lysine had even higher levels of GDH (19,100 U/mg) yet grew
faster, doubling every 67 min. Thus the addition of lysine, methionine,
or both appeared to reduce the requirement for succinyl-CoA and allow
faster growth.
Other growth conditions relieved the auxotrophy, but these
conditions reduced both the total GDH activity and the demand for succinyl-CoA and -ketoglutarate. For example, growth with
serine as the sole nitrogen source severely limits the rate at which ammonia is supplied to the cell. This in turn limits the amount of
-ketoglutarate that GDH can convert to glutamate, thus slowing the
drain on the -ketoglutarate supply. However, when ammonia is
limiting for K. aerogenes, GDH formation is severely
repressed. Nevertheless, it is clear that when strain KC3228 was grown
with serine as the sole nitrogen source, it grew as well as wild-type K. aerogenes, despite the fact that it had 160 times as much
GDH as the wild type. Thus, restricting ammonia, a substrate of the GDH
reaction, had an effect independent of repression.
Finally, it is not surprising that the gdhA1 mutation
of K. aerogenes is enzymatically inactive. The
gdhA1 allele of E. coli affects a
lysine critical for catalytic activity (K92); this mutant GDH can still
form hexamers but does not have enzymatic activity (18).
The gdhA1 allele of K. aerogenes changes the
glycine at position 94 to a glutamate; such a severe change close to an
active-site residue would be expected to have an effect on enzymatic activity.
Nucleotide sequence accession number. The DNA sequence of a 2.4-kb PstI restriction fragment from a gdh strain cloned in this study has been deposited in the GenBank nucleotide sequence database under accession no. AF332586.
| |
ACKNOWLEDGMENTS |
|---|
We thank Robert Helling for critical review of the manuscript.
This work was supported by Public Health Service grant GM 47156 from the National Institutes of Health to R.A.B.
| |
FOOTNOTES |
|---|
* Corresponding author. Mailing address: Department of Biology, The University of Michigan, Ann Arbor, MI 48109-1048. Phone: (734) 936-2530. Fax: (734) 647-0884. E-mail: rbender{at}umich.edu.
Present address: Department of Cancer Cell Biology, Harvard School
of Public Health, Boston, Mass.
| |
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Journal of Bacteriology, April 2001, p. 2709-2714, Vol. 183, No. 8
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.8.2709-2714.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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