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10.1146/annurev.micro.57.030502.090820
Annu. Rev. Microbiol. 2003. 57:155–76
doi: 10.1146/annurev.micro.57.030502.090820
c 2003 by Annual Reviews. All rights reserved
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First published online as a Review in Advance on May 1, 2003
NITROGEN ASSIMILATION AND GLOBAL
REGULATION IN ESCHERICHIA COLI
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Larry Reitzer
Department of Molecular and Cell Biology, The University of Texas at Dallas,
Richardson, Texas 75080-0688; email: [email protected]
Key Words Ntr response, σ 54, Lrp, ppGpp, metabolic integration
■ Abstract Nitrogen limitation in Escherichia coli controls the expression of about
100 genes of the nitrogen regulated (Ntr) response, including the ammonia-assimilating
glutamine synthetase. Low intracellular glutamine controls the Ntr response through
several regulators, whose activities are modulated by a variety of metabolites. Ntr
proteins assimilate ammonia, scavenge nitrogen-containing compounds, and appear to
integrate ammonia assimilation with other aspects of metabolism, such as polyamine
metabolism and glutamate synthesis. The leucine-responsive regulatory protein (Lrp)
controls the synthesis of glutamate synthase, which controls the Ntr response, presumably through its effect on intracellular glutamine. Some Ntr proteins inhibit the
expression of some Lrp-activated genes. Guanosine tetraphosphate appears to control Lrp synthesis. In summary, a network of interacting global regulators that senses
different aspects of metabolism integrates nitrogen assimilation with other metabolic
processes.
CONTENTS
INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
PHYSIOLOGICAL CONTEXT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Nitrogen Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Ammonia Assimilation and Intracellular Nitrogen Donors . . . . . . . . . . . . . . . . . . .
Quantitative Nitrogen Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
NITROGEN LIMITATION AND THE NTR RESPONSE . . . . . . . . . . . . . . . . . . . . . .
Proteins Required for General Nitrogen-Limited Growth . . . . . . . . . . . . . . . . . . . . .
Regulation of GS Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The Ntr Regulatory Cascade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Differential Expression of Ntr Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Functions of the Ntr Response and Nac . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
THE σ 54 REGULON: ITS FUNCTION AND RELATION TO THE
NTR RESPONSE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Properties of σ 54 -Dependent Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The Functions of σ 54 -Dependent Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
METABOLIC INTEGRATION: NITROGEN ASSIMILATION AND
CARBON METABOLISM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Lrp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Cyclic AMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
EINtr -NPr-EIINtr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
GUANOSINE TETRAPHOSPHATE, AMINO ACID
SYNTHESIS, AND AMMONIA ASSIMILATION . . . . . . . . . . . . . . . . . . . . . . . . . .
CONCLUDING REMARKS: INTERACTIONS
BETWEEN GLOBAL REGULATORS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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INTRODUCTION
A group of scientists, which included Lavoisier, gave the name azote (without
life) to the major inert component of air—a name that is still recognizable in many
nitrogen-containing compounds. The name nitrogen was derived from niter (potassium nitrate), a not-so-inert component of gunpowder. Nitrogen is present in many
intracellular metabolites and can be assimilated from inorganic or organic sources.
Its assimilation from inorganic sources requires reduction to ammonia, followed
by incorporation into intracellular metabolites. The appropriate distribution of
nitrogen among various pathways usually involves specific or local regulatory
mechanisms, such as endproduct inhibition or endproduct-mediated transcriptional
control. However, a few global regulators control the expression of genes from several pathways and thereby coordinate metabolism. This review focuses on nitrogen
assimilation in Escherichia coli, its regulation, and the role of global regulators
in this regulation. A major theme of this review is the integration of nitrogen
assimilation with other aspects of metabolism.
PHYSIOLOGICAL CONTEXT
Nitrogen Sources
Bacteria assimilate a variety of inorganic nitrogen sources, but Escherichia coli
assimilates only ammonia aerobically. The ability to assimilate particular organic
nitrogen sources also depends on the organism. Organic nitrogen sources are usually monomeric units of macromolecules (e.g., amino acids or nucleobases) or
compounds derived from them (e.g., agmatine or putrescine). E. coli can assimilate
nitrogen from adenine, adenosine, agmatine, L- and D-alanine, allantoin (anaerobically), γ -aminobutyrate, ammonia, arginine, asparagine, aspartate, cytidine, cytosine, glucosamine, glutamine, glutamate, glycine, ornithine, proline, putrescine,
L- and D-serine, threonine, and a few other compounds (76). Ammonia supports
the fastest growth rate and is therefore considered the preferred nitrogen source
for E. coli.
Ammonia Assimilation and Intracellular Nitrogen Donors
The primary products of ammonia assimilation are glutamate and glutamine, the
major intracellular nitrogen donors. Glutamine provides nitrogen for purines,
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pyrimidines, asparagine (when intracellular ammonia is low), tryptophan, histidine, glucosamine, p-aminobenzoate, and arginine (via carbamoyl phosphate).
Glutamate donates nitrogen for most of the E. coli transaminases.
Glutamate dehydrogenase (GDH) or glutamine synthetase (GS) assimilates the
bulk of ammonia in E. coli (75).
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α-ketoglutarate + NH3 + NADPH → glutamate + NADP+ (GDH)
glutamate + ATP + NH3 → glutamine + ADP + PO−2
4 (GS)
+
glutamine + α-ketoglutarate + NADPH → 2 glutamate + NADP (GOGAT)
If GS assimilates ammonia, then glutamate synthase (GOGAT) catalyzes glutamate formation. E. coli contains both the GDH- and the GS-dependent pathways,
and they are not physiologically equivalent. The ATP-consuming GS-GOGAT
pathway in E. coli is used in energy-rich environments, whereas the GDH pathway
is employed in energy-limited (presumably nitrogen-rich) environments (39, 40).
The GS-GOGAT pathway is more appropriate for ammonia assimilation in a
nitrogen-limited environment, since GS has a much lower Km for ammonia than
GDH. Ammonia assimilation by the GS-GOGAT pathway accounts for an astonishing 15% of the cell’s ATP requirement, which is calculated from the fact that
synthesis of 1 g of E. coli requires 40 mmoles of carbon, about 11 mmoles of
nitrogen, and 72 mmoles of ATP (56). [GS is highly conserved (52), which is
consistent with the possibility that it assimilates ammonia in most microbial organisms. Nonetheless, it appears that alanine dehydrogenase assimilates ammonia
in Rhizobium leguminosarum bacteroids, which subsequently secrete alanine to
the pea plant (1).]
Quantitative Nitrogen Requirements
Once ammonia is assimilated, it must be distributed in the correct ratios to a
variety of compounds. The biosynthetic requirement of each nitrogen-containing
metabolite (how much must be synthesized) can be calculated from the chemical
composition of E. coli (the amount of each component that would be obtained
from complete hydrolysis of whole cells) (Table 1). The difference between the
biosynthetic requirement and the cellular composition can be quantitatively large.
For example, 1 g of E. coli contains an estimated 250 µmoles of glutamate in
protein. However, 810 µmoles of glutamate are required for arginine, glutamine,
proline, the polyamines, and peptidoglycan synthesis. Furthermore, glutamate is
the nitrogen donor for at least 1 nitrogen for 11 amino acids and the polyamines,
which requires 7108 µmoles of glutamate. Therefore, the biosynthetic requirement
for glutamate is 8168 µmoles.
Three observations are worth noting from these calculations. First, over one third
of a cell’s nitrogen is present in guanine nucleotides (1142 µmoles of nitrogen,
or 11%), arginine (1124 µmoles, or 11%), adenine nucleotides (948 µmoles, or
9%), and lysine (652 µmoles, or 6%). Second, more carbon skeletons must be synthesized for aspartate and serine than for other amino acids (Table 1, footnote d).
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TABLE 1 Cellular composition and biosynthetic requirements for nitrogena
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Compositionb
C for other
compoundsc
alanine
488
arginine
281
asparagine
229
aspartate
229
1565
1794
cysteine
87
153
240
250
810
1060
250
glutamate
glutamine
250
glycine
582
histidine
isoleucine
55
C skeleton
subtotald
N donatione
µmoles
Ng
543
543
488
281
281
1124
229
458
2772
229
229
418
Totalf
1000
979
240
87
7108
8168
250
10226
10476
500
1000
582
90
90
90
270
276
276
276
276
leucine
428
428
428
428
lysine
326
28
354
354
652
methionine
146
7
153
153
146
phenylalanine
176
176
176
176
proline
210
210
210
210
serine
205
1409
1614
1614
205
threonine
241
276
517
517
241
tryptophan
54
54
54
108
tyrosine
131
131
131
131
valine
402
402
402
402
AMP + dAMP
190
948
GMP + dGMP
228
1142
CMP + dCMP
151
454
UMP + dTMP
161
321
Other compoundsh
380
455
All units are µmoles per g dry weight of E. coli grown in glucose-ammonia minimal medium. It is assumed that glutamate
is made by the GS-glutamate synthase route.
a
b
Chemical composition taken from (65), which should be consulted for assumptions. For the amino acids the content from
proteins is presented.
c
This refers to syntheses that require the carbon skeleton of the amino acid, e.g., methionine synthesis requires aspartate.
d
This number is the amount of the carbon skeleton that must be synthesized.
e
After nitrogen donation it is not necessary to resynthesize the carbon skeleton, which is why this number is not contained
within the previous column. For example, 7108 µmoles of α-ketoglutarate for glutamate synthesis come from deamination
of glutamate, and only 1060 µmoles come from citric acid cycle components.
f
This column shows the biosynthetic requirement, i.e., the total µmoles of each amino acid synthesized per g E. coli.
g
This number is the number of nitrogen atoms in each compound times the amount in the composition column (footnote b).
The sum of nitrogen content is about 10,300 µmoles of nitrogen atoms per gram.
h
These include putrescine, spermidine, ethanolamine, glucosamines, and cell wall components. The amounts for each of
these components have been presented (65).
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Both amino acids provide carbon and nitrogen for other amino acids and nucleotides. These properties distinguish aspartate and serine from other amino acids
and might provide a metabolic basis for the specificity of the major chemotactic
receptors. Third, the biosynthetic requirement for glycine (1000 µmoles) is almost equal to that for C1-derivatives in purine, thymine, and methionine synthesis
(1104 µmoles). This stoichiometry necessarily couples nucleotide and amino acid
synthesis and may obviate the need for more complex regulatory mechanisms. It is
conceivable that the amazingly complex regulation directed at the glycine cleavage
enzyme (38) is sufficient for fine-tuning C1 unit synthesis.
NITROGEN LIMITATION AND THE NTR RESPONSE
Proteins Required for General Nitrogen-Limited Growth
Growth in a minimal medium with a single organic nitrogen source is slower than
that with ammonia. Such growth affects the expression of about 100 genes. These
collective changes are considered the nitrogen-regulated (Ntr) response. Loss of a
few metabolic enzymes can prevent the utilization of a variety of nitrogen sources.
This section considers those enzymes.
GLUTAMINE SYNTHETASE Nitrogen-limited growth generally requires both enzymes of the GS-GOGAT pathway of ammonia assimilation. GS catalyzes the
only reaction of glutamine formation, and its complete loss results in glutamine
auxotrophy (75). Basal glnA (GS-encoding) expression from the glnAp1 promoter
(which occurs in a glnG mutant) is sufficient for growth with ammonia and a
few nitrogen sources (aspartate and putrescine), but not with other single nitrogen
sources (A. Kiupakas & L. Reitzer, unpublished observation). Expression of the
glnALG (or glnA-ntrBC) operon from the glnAp2 promoter is required for optimal
GS synthesis and for high levels of two important regulators of the Ntr response,
nitrogen regulator II (NRII, also called NtrB) and nitrogen regulator I (NRI, also
called NtrC), which are required for maximal GS synthesis.
GLUTAMATE SYNTHASE The gltBD operon codes for the two subunits of GOGAT
(75). The proposals that the E. coli gltBD operon also contains gltF (23) and that
GltF regulates the Ntr response (23, 24) have not withstood close scrutiny (35, 36).
gltBD mutants are pleiotrophically defective in nitrogen source utilization and
are said to have an Asm− phenotype (76). E. coli and Klebsiella pneumoniae
mutants can still utilize a few nitrogen sources either because they can readily
generate glutamate (e.g., asparagine, aspartate, glutamate, glutamine) or because
they generate ammonia so rapidly that GDH can synthesize glutamate (e.g.,
D-serine) (93). Two different explanations can account for the Asm− phenotype
(35). The glutamine-excess hypothesis proposes that GS assimilates ammonia into
glutamine, which accumulates in the absence of GOGAT (the major glutaminemetabolizing enzyme) and prevents Ntr gene expression. The products of Ntr genes
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would normally generate glutamate independent of both GOGAT and GDH (e.g.,
arginine catabolism). Alternatively, the glutamate-starvation hypothesis proposes
that glutamate starvation prevents Ntr induction (35). A mechanism by which this
occurs is not stated. A hybrid hypothesis is that glutamine accumulation prevents
Ntr gene expression until glutamate starvation stops metabolism and growth. In
any case, the arguments are complex and subject to several untested assumptions
(35). It is possible that the explanation for the Asm− phenotype involves still other
factors, such as an indirect effect of glutamate starvation.
ASNB, NADE, AND THE AMIDOTRANSFERASES Defects in several nonassimilatory
enzymes can also have pleiotropic effects in nitrogen source utilization. Enteric
bacteria have ammonia- and glutamine-dependent asparagine synthetases, AsnA
and AsnB, respectively. A K. aerogenes asnB mutant fails to grow in ammoniarestricted nitrogen-limited environments because AsnA is insufficient for asparagine synthesis (77). NAD synthetases in E. coli and other bacteria are often, but
not always, ammonia dependent (19, 82). A nadE (formerly nit) mutant with
diminished NAD synthetase fails to grow in ammonia-restricted environments
(15, 82). Glutamine-dependent amidotransferases with defective glutamine binding or amide transferase can inefficiently use ammonia as an alternative substrate
(61). Mutants with such defective amidotransferases fail to grow with organic nitrogen sources (L. Reitzer, unpublished observation). In summary, mutants with
altered enzymes that require a high concentration of ammonia are generally defective in utilization of organic nitrogen sources.
Regulation of GS Activity
GS synthesizes glutamine and assimilates ammonia, and the ratio of these functions
depends on the environment. If GDH assimilates ammonia, then glutamine’s amide
provides 25% of cellular nitrogen and the function of GS is primarily anabolic. If
the GS-GOGAT pathway assimilates ammonia, then glutamine’s amide provides
almost 100% of cellular nitrogen and the assimilatory function is quantitatively
three times more important.
FEEDBACK INHIBITION The anabolic function of GS is controlled by cumulative
feedback inhibition by alanine, glycine, serine, adenosine monophosphate (AMP),
carbamoyl phosphate, cytidine triphosphate (CTP), glucosamine-6-phosphate, histidine, and tryptophan (28). These nine compounds are competitive inhibitors that
bind to the glutamate or nucleotide substrate site (28, 57, 58). The last six require
glutamine for their synthesis and can be considered products of glutamine metabolism. Although serine and glycine synthesis do not require glutamine, these
two amino acids are still excellent indicators of glutamine sufficiency. Nucleotide
synthesis accounts for 74% of the glutamine requirement (ignoring glutamate synthesis), which implies that nucleotide sufficiency indicates glutamine sufficiency.
Nucleotide synthesis also accounts for 42% of the glycine biosynthetic
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requirement, and for most of the consumption of C1 derivatives. Therefore, high
serine and glycine probably indicate nucleotide and glutamine sufficiency. Alanine
is more difficult to rationalize as a GS inhibitor.
ADENYLYLATION Covalent adenylylation is one mechanism that controls the assimilatory function of GS. Each of the 12 subunits of GS can be adenylylated on a
tyrosine residue, which inactivates one subunit and enhances the susceptibility of
the other subunits to cumulative feedback inhibition (87). In other words, adenylylation determines the extent to which GS is anabolic or assimilatory. Loss of the
adenylylation system is a problem during the transition from a nitrogen-limited to
an ammonia-containing (nitrogen-rich) environment, when fully induced unadenylylated GS rapidly depletes intracellular glutamate (53, 54). Such a loss is not a
problem for nitrogen-sufficient cells (other mechanisms regulate GS synthesis) or
for cells in which GS is normally not adenylylated (during nitrogen limitation or
during the transition to steady-state nitrogen-limited growth).
The Ntr Regulatory Cascade
THE CENTRAL ROLE OF GLUTAMINE Nitrogen limitation increases GS specific
activity, GS synthesis, and Ntr gene expression, whereas nitrogen sufficiency decreases all three. Several regulators and environmental factors control this coordinated response, which has been extensively reviewed (3, 11, 60, 69, 70, 75, 87).
Measurements of intracellular glutamine and studies with highly purified uridylyltransferase (UTase)/uridylyl-removing enzyme (UR), the first enzyme of the Ntr
regulatory cascade, suggest that the absolute concentration of glutamine controls
the regulatory cascade (44, 46, 47). High glutamine stimulates UR activity, which
removes uridine monophosphate (UMP) groups from PII-UMP and GlnK-UMP,
whereas low glutamine stimulates UTase activity, which uridylylates PII and GlnK.
Glutamine apparently binds to a single site on UTase/UR, from which it controls
both activities (46).
FUNCTIONAL REDUNDANCY: PII AND GLNK PII and GlnK have 67% amino acid
identity and similar biochemical activities (5–7, 94). The phenotypes of glnB and
glnK mutants, which lack PII and GlnK, respectively, differ only slightly from a
wild-type strain (6). In contrast, a glnB glnK double mutant has serious metabolic
problems, which result from overexpression of Ntr genes (6, 12). Furthermore,
placing glnK under the glnB promoter and vice versa do not result in appreciable
phenotypic differences (5). On the other hand, several observations suggest different functions for PII and GlnK. First, the properties of the two purified regulators
with respect to Ntr control are not identical. Second, they are not synthesized at
the same time. Third, during nitrogen-limited growth GlnK is more abundant than
PII. Fourth, GlnK and PII form heterotrimers whose properties can differ from the
homotrimers (33, 96). Finally, GlnK can have activities that PII does not have (26).
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THE FUNCTION OF NTR REGULATORS IN DIFFERENT ENVIRONMENTS
The
functions of these regulators must be considered in the context of nitrogen-rich
and nitrogen-limited environments and in the transitions between them (summarized in Figure 1). In nitrogen-rich (i.e., ammonia-containing) minimal medium,
GS is adenylylated, glnA is expressed at a basal level, and other Ntr genes are not
expressed. PII is in excess over GlnK because PII synthesis is constitutive, while
glnK is not expressed (6, 17, 95). PII is mostly deuridylylated (33) and stimulates
the adenylylating activity of adenylyltransferase (ATase) and dephosphorylation
of NRI (via NRII), which prevents induction of Ntr genes. α-Ketoglutarate at physiological concentrations binds to unmodified PII and interferes with its interaction
with ATase and NRII. Therefore, α-ketoglutarate is a signal of carbon sufficiency
and relative nitrogen limitation, but only to the extent that PII is not uridylylated
(i.e., in cells with high glutamine).
During the transition to nitrogen-limited growth PII is in excess over GlnK
and is rapidly uridylylated. PII-UMP stimulates deadenylylation of GS and fails to
interact with NRII, which results in phosphorylation of NRI (3, 69). The initial level
of NRI ∼ P is sufficient for activation of glnA, but not for other Ntr operons (4, 80).
In the absence of NRII-stimulated dephosphorylation acetyl phosphate probably
contributes to NRI phosphorylation (31).
During steady-state nitrogen-limited growth the concentrations of two important regulators, GlnK and NRI, are higher. It can be deduced that GlnK becomes
more abundant than PII on the basis of immunological assays and the predominance of GlnK homotrimers and (GlnK)2(PII)1 heterotrimers over (GlnK)1(PII)2
heterotrimers and PII homotrimers (26, 96). Both PII and GlnK are readily uridylylated in vivo and in vitro, and the heterotrimers are presumably rapidly uridylylated (7, 33, 94, 96). Purified GlnK-UMP slowly deadenylylates GS compared
with purified PII-UMP (96). Deadenylylation in a strain with only GlnK-UMP
might be a little slower than deadenylylation in a strain with both GlnK-UMP
and PII-UMP, although this cannot be stated with certainty because cells with
different levels of GS (because of their prior growth) were compared (94). The
rate of deadenylylation suggests that the PII subunits in purified uridylylated
heterotrimers are active (96). Because GlnK can substitute for PII and mediate Ntr induction (6), it can be deduced that GlnK-UMP, like PII-UMP, fails to
interact with NRII, which results in net phosphorylation of NRI. Acetyl phosphate is not required for optimal glnA expression but is required for arginine
−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−→
Figure 1 The Ntr regulatory cascade: regulators and effectors. Regulation is considered for (a) steady-state growth in ammonia-containing minimal medium, (b) the
transition from nitrogen-rich to nitrogen-limited growth, (c) steady-state nitrogenlimited growth, and (d) the transition from nitrogen-limited to nitrogen-rich growth.
Abbreviations: ATase-A, adenylylating ATase; ATase-D, deadenylylating ATase; and
αKG, α-ketoglutarate.
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utilization (and therefore for the ast operon) and presumably for other Ntr genes
(31, 81).
During the transition from a nitrogen-limited to a nitrogen-replete environment
transcription of glnA, an Ntr gene, is rapidly abolished (78), and GS is rapidly
adenylylated (94). GlnK is in excess over PII. Purified GlnK-UMP is deuridylylated 10 times slower than PII-UMP (7). However, because purified GlnK effectively stimulates NRII-mediated dephosphorylation of NRI (7), the accumulation of
deuridylylated GlnK must be sufficient to prevent glnA expression (94). However,
it is not clear whether GlnK stimulates GS adenylylation in vivo. The activity of
purified GlnK in stimulating adenylylation is 40 times less than that of PII (7, 94).
It is more likely that GlnK-independent ATase activity is sufficient for GS adenylylation (7, 33) because glutamine stimulates the adenylylating activity of ATase
and nitrogen-limited cells without either GlnK or PII can rapidly adenylylate GS
(6). In addition to these properties GlnK associates with AmtB, an ammonia transporter/facilitator, and inhibits its activity (26). PII also associates with AmtB but
does not inhibit its activity (26). Therefore, ammonia transport should be impaired
during the transition to an ammonia-containing, nitrogen-rich environment. These
properties have interesting implications. If AmtB and GlnK are made stoichiometrically, then AmtB is in excess over PII. AmtB has the potential to sequester
PII and GlnK or to allosterically affect their activities. If so, AmtB might regulate
nitrogenase synthesis in K. pneumoniae, in which GlnK controls the activity of
NifL (37, 45).
In summary, glutamine ultimately controls the activities and interactions of the
individual regulators of the Ntr regulatory cascade. Considering the importance of
glutamine, it is probably not surprising that synthesis of the two glutamine-sensing
regulators, UTase/UR and ATase, is constitutive. In contrast, nitrogen limitation
controls the synthesis of the other regulators. Glutamine also determines whether
other signals are sensed. In a high-glutamine environment α-ketoglutarate modifies the activities of unuridylylated PII and GlnK, and the products of glutamine
metabolism inhibit GS. In a low-glutamine environment acetyl phosphate contributes to Ntr gene expression. Until recently, it was thought that a single protein,
UTase/UR, sensed the ratio of glutamine to α-ketoglutarate. Such regulation permits the possibility of a high ratio (apparent nitrogen excess) with insufficient
glutamine for numerous glutamine-dependent enzymes (functional nitrogen deficiency). Sensing the absolute concentration of glutamine avoids this problem.
Instead, the ratio of glutamine to α-ketoglutarate is important only when glutamine is high and there is sufficient glutamine to drive the glutamine-dependent
reactions.
Differential Expression of Ntr Genes
SEQUENTIAL EXPRESSION Several mechanisms permit differential expression of
Ntr genes. The transition to nitrogen limitation induces Ntr genes sequentially.
The low NRI ∼ P concentration initially present during the transition to nitrogenlimited growth is sufficient for expression of the glnA operon (80). However, a
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higher NRI concentration is required for nac, glnK, the astCADBE operon, and
probably other Ntr operons (4).
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NITROGEN SOURCE–DEPENDENT CONTROL Growth with different nitrogen sources
induces the glnA operon equally well (84). However, this is not the case for the
activation of astCADBE, gabDTPC, and patA/ygjG and the repression of gltBD
[(35, 50, 83); C. Pybus, B. Schneider & L. Reitzer, unpublished observations]. The
basis for this differential regulation is not known.
PREVENTION OF OVEREXPRESSION Three distinct mechanisms prevent Ntr gene
overexpression. Low NRI activates the glnAp2 promoter of the glnA operon, and
high NRI partially inhibits the activation (86). The binding of NRI to low-affinity
sites apparently mediates this modulation (8). NRI activates nac expression, and
then Nac impairs this activation (32). Finally, a glnK mutant overexpresses several
Ntr genes during nitrogen starvation, which apparently reduces viability (13). This
suggests that one function of GlnK is to prevent such overexpression.
Functions of the Ntr Response and Nac
Microarray analysis, computer analysis of σ 54-dependent genes, and other studies
suggest that the vast majority of Ntr genes have been identified and that nitrogen
limitation affects about 100 genes. This section considers the functions of these
genes. The functions of individual Ntr genes within specific physiological contexts (e.g., argT-dependent arginine transport within the context of other arginine
transport systems in E. coli) have been reviewed (74).
AMMONIA ASSIMILATION The central role of glutamine in regulation of the Ntr
response suggests that an important physiological function of the Ntr response is to
maintain intracellular glutamine and obviously to control ammonia assimilation.
Several regulatory mechanisms suggest the importance of this function. First, GS
is synthesized before other Ntr proteins. Second, different mechanisms prevent
overexpression of glnA and other Ntr genes. Finally, nitrogen source–dependent
regulation affects expression of Ntr genes, except for glnA.
SCAVENGING Zimmer et al. proposed that numerous Ntr transport systems scavenge nitrogen-containing compounds (100). Nitrogen limitation induces transport
systems for several amino acids (D-alanine, arginine, aspartate, glutamate, glutamine, glycine, histidine, lysine, ornithine, and D-serine), peptides (D-alanylD-alanine, dipeptides, and oligopeptides), polyamines and related compounds
(putrescine, spermidine, and γ -aminobutyrate), cytosine, and nucleosides. Scavenging obviously spares the need to assimilate ammonia.
METABOLIC INTEGRATION Six Ntr operons, astCADBE, codBA, ddpXABCDE,
gabDTPC, patA (ygjG), and ydcSTUVW, contain genes for catabolic enzymes. It
could be argued that these enzymes contribute to scavenging. However, this would
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not explain why so few catabolic enzymes are under Ntr control and why nine
of them degrade compounds that are associated with polyamine metabolism. The
products of astCADBE, gabDTPC, and patA (ygjG) degrade arginine/ornithine,
γ -aminobutyrate, putrescine, respectively [(81, 83); B. Schneider, C. Pybus &
L. Reitzer, unpublished observations). YdcW degrades γ -aminobutyraldehyde, a
product of putrescine catabolism (B. Schneider & L. Reitzer, unpublished observation). In addition to these catabolic enzymes, nitrogen limitation induces two
putrescine or polyamine transport systems, potFGHI and ydcSTUVW (100). At
least 19 Ntr genes transport putrescine, degrade putrescine, or degrade the precursors of putrescine synthesis. Polyamine levels are correlated to the growth
rate (89, 92). These Ntr genes may integrate slower nitrogen-limited growth with
polyamine content.
Metabolic integration could account for why nitrogen limitation represses both
enzymes of glutamate synthesis, the first enzyme of serine synthesis, and AsnC
(the activator of asnA) (12, 35, 64, 71). Nitrogen limitation also induces a peptidase
that degrades D-alanyl-D-alanine, a precursor for peptidoglycan (100), which may
modulate peptidoglycan synthesis. In summary, Ntr genes might integrate slower
growth with several major metabolic pathways. Such a function may account for
the lethality of Ntr gene overexpression (13).
NAC Nac is an Ntr protein that represses the enzymes of glutamate and serine
synthesis and AsnC (12, 35, 64, 71). Nac activates codBA (cytosine metabolism),
ydcSTUVW (putative putrescine transport and catabolism), nupC (nucleoside transport), gabDTPC (γ -aminobutyrate transport and degradation), dppABCDF (dipeptide transport), and fklB-cycA (100). The products of these genes might modulate
the levels of important metabolic intermediates and, by this mechanism, integrate
nitrogen assimilation with other aspects of metabolism. If so, then such integration
is dispensable (or at least redundant) because an E. coli nac mutant does not have
a dramatic phenotype and Salmonella lacks the gene (64).
THE σ 54 REGULON: ITS FUNCTION AND
RELATION TO THE NTR RESPONSE
Properties of σ 54-Dependent Genes
Expression of many Ntr genes requires σ 54, which is the only σ factor in E. coli
that is not homologous to σ 70 (62). σ 54-dependent transcription has several distinctive features (16, 74). It always requires a transcriptional activator. The activators
bind to sites that are analogous to eukaryotic enhancers. The activators hydrolyze
ATP and interact with σ 54-containing RNA polymerase. The activator-RNA polymerase interaction requires either a DNA-bending protein, such as integration host
factor, or a DNA curvature (20, 42). Because of the absolute requirement for an
activator, σ 54-dependent expression can be completely turned off. One advantage
of such control is the wide range of activity, from very low to very high expression
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(PspA and GS, products of σ 54-dependent operons, can be a few percent of E. coli
proteins). Perhaps this dynamic range is important for proteins or pathways that
must at times consume large amounts of energy or metabolic intermediates.
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The Functions of σ 54-Dependent Genes
σ 54 is widespread among bacteria and is required for a variety of functions that
are not associated with nitrogen assimilation (88). About half of the 25 known
or strongly suspected σ 54-dependent operons in E. coli do not specify proteins
of nitrogen metabolism (74). FhlA activates five of these operons, which code for
proteins associated with formate hydrogen lyase. The other σ 54-dependent operons
specify proteins for the phage shock response, zinc tolerance, two products of fatty
acid catabolism, propionate and acetoacetate, and an RNA-modifying enzyme of
unknown function. The products of these genes are associated with a variety of
environmental stresses. FhlA regulon genes are thought to contribute to pH homeostasis during fermentation, which potentially facilitates growth or survival in an
acidic, energy-limited, anaerobic environment (14). The phage shock proteins are
required for survival in an alkaline environment and, more generally, may maintain
the proton motive force during stress (51, 97). Zinc tolerance alleviates the stress
of high zinc. Propionate and acetoacetate are also associated with stress. FadR
participates in the universal stress response by mediating fatty acid degradation,
which would generate propionate and acetoacetate for energy (27, 30). Perhaps
the products of these genes alleviate problems associated with certain stresses
that make nitrogen assimilation difficult (74). Alternatively, expression of these
genes might somehow modulate expression of the σ 54-dependent genes of nitrogen
metabolism. A conceivable modulation mechanism is competition for σ 54, which
is not an abundant protein (48). It is also possible that these genes have no obligatory association with nitrogen assimilation and that strains with certain genes with
the unique properties of σ 54-dependent promoters have a selective advantage.
METABOLIC INTEGRATION: NITROGEN ASSIMILATION
AND CARBON METABOLISM
Ammonia assimilation requires energy and intermediates from central metabolism.
Several mechanisms integrate intermediary metabolism with ammonia assimilation. This section considers three mechanisms that have been identified.
Lrp
The leucine-responsive regulatory protein (Lrp) is a moderately abundant DNAbinding protein (98), but it is not a major nucleoid-binding protein (9, 10). Lrp
has several modes of action: It can either activate or repress gene expression;
leucine can reverse, enhance, or have no effect on this regulation (68). Guanosine tetraphosphate (ppGpp) controls Lrp synthesis (55), which accounts for its
synthesis in amino acid–poor minimal media (25) and during the transition into
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stationary phase (41, 90). Lrp affects the expression of about 10% of the genes
in E. coli (43, 90). Several reviews and a recent microarray analysis consider the
broader functions of Lrp (18, 67, 68, 90).
Lrp has been implicated in several aspects of the Ntr response. Lrp activates
gltBD, which means that Lrp is required for the Ntr response (29). Lrp also controls
the metabolism of alanine, serine, and glycine, which are feedback inhibitors of GS.
Furthermore, Nac, an Ntr protein, represses two Lrp-activated operons, serA and
gltBD (12, 35). Finally, evidence pieced together from different sources suggests
that Lrp and Ntr regulators might independently activate ompF, oppABCDF, ydcSTUVW, and yeaGH (68, 90, 100). In summary, Lrp controls Ntr gene expression,
and regulators of the Ntr response modulate the expression of some Lrp-regulated
genes.
The effects of Lrp without leucine (Figure 2, top panel) and with leucine
(Figure 2, bottom panel) must be considered separately in order to understand
Lrp’s function in ammonia assimilation. Lrp without leucine activates synthesis of
GOGAT and pyridine nucleotide transhydrogenase, which together provide two
of the three substrates for ammonia assimilation. Lrp without leucine represses
two serine deaminases and alanine dehydrogenase. The net effect would appear to
favor ammonia assimilation (and amino acid synthesis) over ammonia generation
(amino acid degradation). The addition of leucine moderately reduces GOGAT
and pyridine nucleotide transhydrogenase, but increases the amino acid degradative enzymes. To the extent that nitrogen is transferred to serine and alanine via
reversible transaminations, leucine will stimulate net amino acid catabolism. Lrp
appears to be one factor that coordinates ammonia assimilation and amino acid
catabolism in an amino acid–poor environment. This hypothesis is supported by the
observation that an lrp mutant has enhanced amino acid degradation (101). It has
been proposed that Lrp mediates the transitions between feast and famine. For the
former, amino acid catabolic functions are appropriate; while for the latter, amino
acid biosynthetic functions (including ammonia assimilation) are more appropriate (18, 66). If Lrp coordinates ammonia assimilation with amino acid catabolism,
then leucine is an indicator of amino acid sufficiency. Alanine may also contribute
to this regulation because alanine also binds Lrp [(59) and references cited therein].
Cyclic AMP
Cyclic AMP bound to its receptor protein interferes with expression from the
glnAp2 promoter of the glnA operon and from other Ntr promoters (91). It is
possible that the primary effect of high cyclic AMP is at the glnALG operon and
that lowering its expression prevents synthesis of sufficient NRI to activate other
Ntr genes.
EINtr-NPr-EIINtr
EINtr (PtsP), NPr (PtsO), and EIIANtr (PtsN) are paralogs of sugar phosphotransferase transport proteins in E. coli and other organisms, which might also
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Figure 2 Lrp and nitrogen assimilation. The information is from Newman et al. (68).
The filled arrows and numbers indicate activation, whereas the open arrows and numbers
indicate repression. The top panel compares the effects on the indicated pathways or enzymes between strains with and without Lrp, both without added leucine. The bottom panel
compares the effects of a wild-type strain with and without leucine. SerineEXT is external
serine.
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contribute to coordination of carbon and nitrogen metabolism. Purified EINtr, NPr,
and EIINtr form a phosphorelay, which accepts phosphate from phosphoenolpyruvate (72, 73). EINtr-NPr-EIINtr phosphorylates sugars 1000 times slower than EIHPr-EII systems, which suggests that the former has a regulatory function, not a
transport function (73). EINtr contains a GAF domain, which regulates some σ 54dependent activators, and therefore suggests regulatory potential (2, 79). Furthermore, Bradyrhizobium japonicum EINtr interacts with an aspartokinase isozyme,
which also suggests regulatory potential (49). Genetic evidence suggests that EINtr
and EIINtr, but not NPr, have a regulatory function. An E. coli ptsN mutant (EIINtr
deficient) grew less well with organic nitrogen sources in carbon-limited media,
which suggests positive regulation (72). The mutant grew normally with glucose
as the carbon source and expressed at least one Ntr gene normally (72). In contrast,
a K. pneumoniae ptsN mutant had increased Ntr gene expression, which suggests
negative regulation (63). An E. coli ptsP (EINtr deficient) has not been isolated;
but loss of EINtr in other organisms prevents the expression of important genes
(49, 85). ptsO and ptsN are members of the putative rpoN-yhbH-ptsN-yhbJ-ptsO
operon, whereas ptsP is unlinked (72, 73). yhbH, yhbJ, and ptsO in E. coli, and
their homologs in P. putida, do not appear to contribute to regulation (21, 72). A
model for how the EINtr-NPr-EIINtr system might affect gene expression is not
obvious from these results, and none has been presented.
GUANOSINE TETRAPHOSPHATE, AMINO ACID
SYNTHESIS, AND AMMONIA ASSIMILATION
Slower growth and elevated ppGpp activate lrp expression, which in turn is required
for the Ntr response (29, 55). Therefore, the factors that regulate ppGpp synthesis
are important in the control of nitrogen metabolism. (Where it is stated that ppGpp
controls something, what is meant is that ppGpp appears to mediate this control.
The intent is not to exclude potential indirect effects, such as diminished GTP,
or other potential mechanisms of growth rate control.) Two factors control the
ppGpp concentration: tRNA aminoacylation and energy source availability (22). In
general, ppGpp stimulates amino acid synthesis and inhibits nucleotide synthesis
and nucleobase salvage (22). This pattern suggests a preference for amino acid
synthesis over nucleotide synthesis, which is appropriate with diminished tRNA
aminoacylation.
Nitrogen availability determines which pathways of amino acid synthesis are
affected. In a glucose-ammonia minimal medium, ppGpp0 strains, which cannot synthesize ppGpp, absolutely require arginine, glycine, histidine, leucine,
phenylalanine, serine, threonine, and valine and have weak or strain-dependent
requirements for lysine, methionine, and tyrosine (99). These strains do not require
alanine, asparagine, aspartate, cysteine, glutamate, glutamine, or proline (99). In
a nitrogen-limited environment, ppGpp via Lrp is required for glutamate synthesis, induction of the Ntr response, and ammonia assimilation, and therefore the
synthesis of all the amino acids.
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CONCLUDING REMARKS: INTERACTIONS
BETWEEN GLOBAL REGULATORS
A hierarchy of global regulators affects the pathways of nitrogen metabolism.
Elevated ppGpp stimulates several pathways of amino acid synthesis and inhibits
pathways of nucleotide synthesis. ppGpp activates the synthesis of Lrp, which may
fine-tune the balance between amino acid synthesis and degradation. Lrp positively
controls the synthesis of GOGAT, which affects the level of glutamine, the most
important effector of the Ntr response. Finally, the regulators of the Ntr response
control ammonia assimilation. Numerous environmental factors modify the activities of these global regulators. The interplay of these environmental factors is
both complex and subtle. For example, carbon limitation through growth rate control increases ppGpp, which via Lrp is required for induction of the Ntr response.
However, cyclic AMP interferes with this induction by an unknown mechanism.
Another example is the effect of impaired protein synthesis by uncharged tRNA,
which increases ppGpp and Lrp. Lrp, through its control of glutamate synthase,
induces the Ntr response, which stimulates expression of polyamine catabolic
enzymes. Diminished polyamines complete the regulatory circuit, which should
impair protein synthesis. Both of these examples show mechanisms by which
global regulators and their effectors integrate ammonia assimilation with other
aspects of metabolism.
E. coli Lrp has limited sequence similarity with homologous proteins in other
organisms and is not a global regulator in at least one organism (34). Perhaps
the entire global regulatory network that controls nitrogen metabolism is also not
conserved, but instead has evolved in enteric and related bacteria in response to
environments with large and rapid fluctuations in nutrient availability.
ACKNOWLEDGMENTS
This work was supported in part by grant MCB-0077904 from the National Science
Foundation.
The Annual Review of Microbiology is online at http://micro.annualreviews.org
LITERATURE CITED
1. Allaway D, Lodwig EM, Crompton LA,
Wood M, Parsons R, et al. 2000. Identification of alanine dehydrogenase and its
role in mixed secretion of ammonium and
alanine by pea bacteroids. Mol. Microbiol.
36:508–15
2. Aravind L, Ponting CP. 1997. The GAF
domain: an evolutionary link between di-
verse phototransducing proteins. Trends
Biochem. Sci. 22:458–59
3. Arcondeguy T, Jack R, Merrick M. 2001.
PII signal transduction proteins, pivotal
players in microbial nitrogen control. Microbiol. Mol. Biol. Rev. 65:80–105
4. Atkinson MR, Blauwkamp TA, Bondarenko V, Studitsky V, Ninfa AJ. 2002.
27 Jul 2003
12:20
172
Annu. Rev. Microbiol. 2003.57:155-176. Downloaded from arjournals.annualreviews.org
by WIB6332 - University of Saarland on 01/04/10. For personal use only.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
AR
AR195-MI57-07.tex
AR195-MI57-07.sgm
LaTeX2e(2002/01/18)
P1: IKH
REITZER
Activation of the glnA, glnK, and nac promoters as Escherichia coli undergoes the
transition from nitrogen excess growth
to nitrogen starvation. J. Bacteriol. 184:
5358–63
Atkinson MR, Blauwkamp TA, Ninfa AJ.
2002. Context-dependent functions of the
PII and GlnK signal transduction proteins in Escherichia coli. J. Bacteriol.
184:5364–75
Atkinson MR, Ninfa AJ. 1998. Role of
the GlnK signal transduction protein in the
regulation of nitrogen assimilation in Escherichia coli. Mol. Microbiol. 29:431–47
Atkinson MR, Ninfa AJ. 1999. Characterization of the GlnK protein of Escherichia
coli. Mol. Microbiol. 32:301–13
Atkinson MR, Pattaramanon N, Ninfa
AJ. 2002. Governor of the glnAp2 promoter of Escherichia coli. Mol. Microbiol.
46:1247–57
Azam TA, Ishihama A. 1999. Twelve
species of the nucleoid-associated protein
from Escherichia coli. Sequence recognition specificity and DNA binding affinity.
J. Biol. Chem. 274:33105–13
Azam TA, Iwata A, Nishimura A, Ueda
S, Ishihama A. 1999. Growth phasedependent variation in protein composition of the Escherichia coli nucleoid. J.
Bacteriol. 181:6361–70
Bender RA. 1991. The role of the NAC
protein in the nitrogen regulation of Klebsiella aerogenes. Mol. Microbiol. 5:2575–
80
Blauwkamp TA, Ninfa AJ. 2002. Nacmediated repression of the serA promoter
of Escherichia coli. Mol. Microbiol. 45:
351–63
Blauwkamp TA, Ninfa AJ. 2002. Physiological role of the GlnK signal transduction protein of Escherichia coli:
survival of nitrogen starvation. Mol.
Microbiol. 46:203–14
Bock A, Sawers G. 1996. Fermentation.
See Ref. 64a, pp. 262–82
Broach J, Neumann C, Kustu S. 1976.
Mutant strains (nit) of Salmonella ty-
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
phimurium with a pleiotropic defect in nitrogen metabolism. J. Bacteriol. 128:86–
98
Buck M, Gallegos MT, Studholme DJ,
Guo Y, Gralla JD. 2000. The bacterial
enhancer-dependent σ 54 (σ N) transcription factor. J. Bacteriol. 182:4129–36
Bueno R, Pahel G, Magasanik B. 1985.
Role of glnB and glnD gene products in
regulation of the glnALG operon of Escherichia coli. J. Bacteriol. 164:816–22
Calvo JM, Matthews RG. 1994. The
leucine-responsive regulatory protein, a
global regulator of metabolism in Escherichia coli. Microbiol. Rev. 58:466–90
Cantoni R, Branzoni M, Labo M, Rizzi M,
Riccardi G. 1998. The MTCY428.08 gene
of Mycobacterium tuberculosis codes for
NAD+ synthetase. J. Bacteriol. 180:
3218–21
Carmona M, Claverie-Martin F, Magasanik B. 1997. DNA bending and the initiation of transcription at σ 54-dependent
bacterial promoters. Proc. Natl. Acad. Sci.
USA 94:9568–72
Cases I, Perez-Martin J, de Lorenzo V.
1999. The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source
inhibition of the σ 54-dependent Pu promoter of the TOL plasmid. J. Biol. Chem.
274:15562–68
Cashel M, Gentry DR, Hernandez VJ,
Vinella D. 1996. The stringent response.
See Ref. 64a, pp. 1458–96
Castano I, Bastarrachea F, Covarrubias
AA. 1988. gltBDF operon of Escherichia
coli. J. Bacteriol. 170:821–27
Castano I, Flores N, Valle F, Covarrubias
AA, Bolivar F. 1992. gltF, a member of the
gltBDF operon of Escherichia coli, is involved in nitrogen-regulated gene expression. Mol. Microbiol. 6:2733–41
Chen CF, Lan J, Korovine M, Shao ZQ,
Tao L, et al. 1997. Metabolic regulation
of lrp gene expression in Escherichia coli
K-12. Microbiology 143:2079–84
Coutts G, Thomas G, Blakey D, Merrick
M. 2002. Membrane sequestration of the
27 Jul 2003
12:20
AR
AR195-MI57-07.tex
AR195-MI57-07.sgm
LaTeX2e(2002/01/18)
REGULATION OF NITROGEN METABOLISM
27.
Annu. Rev. Microbiol. 2003.57:155-176. Downloaded from arjournals.annualreviews.org
by WIB6332 - University of Saarland on 01/04/10. For personal use only.
28.
29.
30.
31.
32.
33.
34.
35.
signal transduction protein GlnK by the
ammonium transporter AmtB. EMBO J.
21:536–45
DiRusso CC, Nystrom T. 1998. The fats
of Escherichia coli during infancy and old
age: regulation by global regulators, alarmones and lipid intermediates. Mol. Microbiol. 27:1–8
Eisenberg D, Gill HS, Pfluegl GM,
Rotstein SH. 2000. Structure-function
relationships of glutamine synthetases.
Biochim. Biophys. Acta 1477:122–45
Ernsting BR, Atkinson MR, Ninfa AJ,
Matthews RG. 1992. Characterization of
the regulon controlled by the leucineresponsive regulatory protein in Escherichia coli. J. Bacteriol. 174:1109–18
Farewell A, Diez AA, DiRusso CC, Nystrom T. 1996. Role of the Escherichia
coli FadR regulator in stasis survival and
growth phase-dependent expression of the
uspA, fad, and fab genes. J. Bacteriol.
178:6443–50
Feng J, Atkinson MR, McCleary W, Stock
JB, Wanner BL, Ninfa AJ. 1992. Role
of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J.
Bacteriol. 174:6061–70
Feng J, Goss TJ, Bender RA, Ninfa AJ.
1995. Repression of the Klebsiella aerogenes nac promoter. J. Bacteriol. 177:
5535–38
Forchhammer K, Hedler A, Strobel H,
Weiss V. 1999. Heterotrimerization of PIIlike signalling proteins: implications for
PII-mediated signal transduction systems.
Mol. Microbiol. 33:338–49
Friedberg D, Midkiff M, Calvo JM. 2001.
Global versus local regulatory roles for
Lrp-related proteins: Haemophilus influenzae as a case study. J. Bacteriol.
183:4004–11
Goss TJ, Perez-Matos A, Bender RA.
2001. Roles of glutamate synthase, gltBD,
and gltF in nitrogen metabolism of Escherichia coli and Klebsiella aerogenes.
J. Bacteriol. 183:6607–19
P1: IKH
173
36. Grassl G, Bufe B, Muller B, Rosel M,
Kleiner D. 1999. Characterization of the
gltF gene product of Escherichia coli.
FEMS Microbiol. Lett. 179:79–84
37. He L, Soupene E, Ninfa A, Kustu S. 1998.
Physiological role for the GlnK protein
of enteric bacteria: relief of NifL inhibition under nitrogen-limiting conditions. J.
Bacteriol. 180:6661–67
38. Heil G, Stauffer LT, Stauffer GV. 2002.
Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/
GcvR interaction and allow GcvAmediated activation of the Escherichia
coli gcvTHP operon. Microbiology 148:
2203–14
39. Helling RB. 1994. Why does Escherichia
coli have two primary pathways for synthesis of glutamate? J. Bacteriol. 176:
4664–68
40. Helling RB. 1998. Pathway choice in glutamate synthesis in Escherichia coli. J.
Bacteriol. 180:4571–75
41. Hengge-Aronis R. 1999. Interplay of
global regulators and cell physiology in
the general stress response of Escherichia
coli. Curr. Opin. Microbiol. 2:148–52
42. Hoover TR, Santero E, Porter S, Kustu S.
1990. The integration host factor stimulates interaction of RNA polymerase with
NIFA, the transcriptional activator for nitrogen fixation operons. Cell 63:11–22
43. Hung SP, Baldi P, Hatfield GW. 2002.
Global gene expression profiling in Escherichia coli K12. The effects of leucineresponsive regulatory protein. J. Biol.
Chem. 277:40309–23
44. Ikeda TP, Shauger AE, Kustu S. 1996.
Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation. J. Mol. Biol.
259:589–607
45. Jack R, De Zamaroczy M, Merrick M.
1999. The signal transduction protein
GlnK is required for NifL-dependent nitrogen control of nif gene expression
in Klebsiella pneumoniae. J. Bacteriol.
181:1156–62
27 Jul 2003
12:20
Annu. Rev. Microbiol. 2003.57:155-176. Downloaded from arjournals.annualreviews.org
by WIB6332 - University of Saarland on 01/04/10. For personal use only.
174
AR
AR195-MI57-07.tex
AR195-MI57-07.sgm
LaTeX2e(2002/01/18)
P1: IKH
REITZER
46. Jiang P, Peliska JA, Ninfa AJ. 1998. Enzymological characterization of the signaltransducing uridylyltransferase/uridylylremoving enzyme (EC 2.7.7.59) of
Escherichia coli and its interaction with
the PII protein. Biochemistry 37:12782–
94
47. Jiang P, Peliska JA, Ninfa AJ. 1998.
The regulation of Escherichia coli glutamine synthetase revisited: role of 2ketoglutarate in the regulation of glutamine synthetase adenylylation state.
Biochemistry 37:12802–10
48. Jishage M, Iwata A, Ueda S, Ishihama
A. 1996. Regulation of RNA polymerase
sigma subunit synthesis in Escherichia
coli: intracellular levels of four species of
sigma subunit under various growth conditions. J. Bacteriol. 178:5447–51
49. King ND, O’Brian MR. 2001. Evidence
for direct interaction between enzyme
INtr and aspartokinase to regulate bacterial oligopeptide transport. J. Biol. Chem.
276:21311–16
50. Kiupakis AK, Reitzer L. 2002. ArgRindependent induction and ArgR-dependent superinduction of the astCADBE
operon in Escherichia coli. J. Bacteriol.
184:2940–50
51. Kleerebezem M, Crielaard W, Tommassen J. 1996. Involvement of stress protein PspA (phage shock protein A) of
Escherichia coli in maintenance of the
protonmotive force under stress conditions. EMBO J. 15:162–71
52. Kumada Y, Benson DR, Hillemann D,
Hosted TJ, Rochefort DA, et al. 1993.
Evolution of the glutamine synthetase
gene, one of the oldest existing and functioning genes. Proc. Natl. Acad. Sci. USA
90:3009–13
53. Kustu S, Hirschman J, Burton D, Jelesko
J, Meeks JC. 1984. Covalent modification
of bacterial glutamine synthetase: physiological significance. Mol. Gen. Genet.
197:309–17
54. Kustu S, Hirschman J, Meeks JC. 1985.
Adenylylation of bacterial glutamine syn-
55.
56.
57.
58.
59.
60.
61.
62.
63.
64.
64a.
65.
thetase: physiological significance. Curr.
Top. Cell. Regul. 27:201–13
Landgraf JR, Wu J, Calvo JM. 1996. Effects of nutrition and growth rate on Lrp
levels in Escherichia coli. J. Bacteriol.
178:6930–36
Lengeler JW, Drews G, Schlegel HG.
1999. Biology of the Prokaryotes: Blackwell Science
Liaw SH, Jun G, Eisenberg D. 1994. Interactions of nucleotides with fully unadenylylated glutamine synthetase from
Salmonella typhimurium. Biochemistry
33:11184–88
Liaw SH, Pan C, Eisenberg D. 1993. Feedback inhibition of fully unadenylylated
glutamine synthetase from Salmonella typhimurium by glycine, alanine, and serine. Proc. Natl. Acad. Sci. USA 90:4996–
5000
Lin R, Ernsting B, Hirshfield IN,
Matthews RG, Neidhardt FC, et al. 1992.
The lrp gene product regulates expression
of lysU in Escherichia coli K-12. J. Bacteriol. 174:2779–84
Magasanik B. 1996. Regulation of nitrogen utilization. See Ref. 64a, pp. 1344–56
Mergeay M, Gigot D, Beckmann J, Glansdorff N, Pierard A. 1974. Physiology and
genetics of carbamoylphosphate synthesis
in Escherichia coli K12. Mol. Gen. Genet.
133:299–316
Merrick MJ. 1993. In a class of its own—
the RNA polymerase sigma factor σ 54
(σ N). Mol. Microbiol. 10:903–9
Merrick MJ, Coppard JR. 1989. Mutations
in genes downstream of the rpoN gene
(encoding σ 54) of Klebsiella pneumoniae
affect expression from σ 54-dependent promoters. Mol. Microbiol. 3:1765–75
Muse WB, Bender RA. 1998. The
nac (nitrogen assimilation control) gene
from Escherichia coli. J. Bacteriol. 180:
1166–73
Neidhardt FC, ed. 1996. Escherichia coli
and Salmonella: Cellular and Molecular
Biology. Washington, DC: ASM
Neidhardt FC, Umbarger HE. 1996.
27 Jul 2003
12:20
AR
AR195-MI57-07.tex
AR195-MI57-07.sgm
LaTeX2e(2002/01/18)
REGULATION OF NITROGEN METABOLISM
66.
Annu. Rev. Microbiol. 2003.57:155-176. Downloaded from arjournals.annualreviews.org
by WIB6332 - University of Saarland on 01/04/10. For personal use only.
67.
68.
69.
70.
71.
72.
73.
74.
75.
Chemical composition of Escherichia
coli. See Ref. 64a, pp. 13–16
Newman EB, D’Ari R, Lin RT. 1992. The
leucine-Lrp regulon in E. coli: a global
response in search of a raison d’etre. Cell
68:617–19
Newman EB, Lin R. 1995. Leucineresponsive regulatory protein: a global
regulator of gene expression in E. coli.
Annu. Rev. Microbiol. 49:747–75
Newman EB, Lin RT, D’Ari R. 1996. The
leucine/Lrp regulon. See Ref. 64a, pp.
1513–25
Ninfa AJ, Atkinson MR. 2000. PII signal
transduction proteins. Trends Microbiol.
8:172–79
Ninfa AJ, Jiang P, Atkinson MR, Peliska
JA. 2000. Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli. Curr. Top. Cell.
Regul. 36:31–75
Poggio S, Domeinzain C, Osorio A, Camarena L. 2002. The nitrogen assimilation control (Nac) protein represses asnC
and asnA transcription in Escherichia coli.
FEMS Microbiol. Lett. 206:151–56
Powell BS, Court DL, Inada T, Nakamura Y, Michotey V, et al. 1995. Novel
proteins of the phosphotransferase system encoded within the rpoN operon of
Escherichia coli. Enzyme IIANtr affects
growth on organic nitrogen and the conditional lethality of an erats mutant. J. Biol.
Chem. 270:4822–39
Rabus R, Reizer J, Paulsen I, Saier
MH Jr. 1999. Enzyme INtr from Escherichia coli. A novel enzyme of the
phosphoenolpyruvate-dependent phosphotransferase system exhibiting strict
specificity for its phosphoryl acceptor,
NPr. J. Biol. Chem. 274:26185–91
Reitzer L, Schneider BL. 2001. Metabolic
context and possible physiological themes
of σ 54-dependent genes in Escherichia
coli. Microbiol. Mol. Biol. Rev. 65:422–
44
Reitzer LJ. 1996. Ammonia assimilation
and the biosynthesis of glutamine, gluta-
76.
77.
78.
79.
80.
81.
82.
83.
84.
85.
P1: IKH
175
mate, aspartate, asparagine, L-alanine, and
D-alanine. See Ref. 64a, pp. 391–407
Reitzer LJ. 1996. Sources of nitrogen and
their utilization. See Ref. 64a, pp. 380–90
Reitzer LJ, Magasanik B. 1982. Asparagine synthetases of Klebsiella aerogenes: properties and regulation of synthesis. J. Bacteriol. 151:1299–313
Reitzer LJ, Magasanik B. 1985. Expression of glnA in Escherichia coli is regulated at tandem promoters. Proc. Natl.
Acad. Sci. USA 82:1979–83
Reizer J, Reizer A, Merrick MJ, Plunkett
G 3rd, Rose DJ, Saier MH Jr. 1996. Novel
phosphotransferase-encoding genes revealed by analysis of the Escherichia coli
genome: a chimeric gene encoding an enzyme I homologue that possesses a putative sensory transduction domain. Gene
181:103–8
Rothstein DM, Pahel G, Tyler B, Magasanik B. 1980. Regulation of expression from the glnA promoter of Escherichia coli in the absence of glutamine
synthetase. Proc. Natl. Acad. Sci. USA
77:7372–76
Schneider BL, Kiupakis AK, Reitzer LJ.
1998. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180:4278–86
Schneider BL, Reitzer LJ. 1998. Salmonella typhimurium nit is nadE: defective nitrogen utilization and ammoniadependent NAD synthetase. J. Bacteriol.
180:4739–41
Schneider BL, Ruback S, Kiupakis
AK, Kasbarian H, Pybus C, Reitzer
L. 2002. The Escherichia coli gabDTPC operon: specific γ -aminobutyrate
catabolism and nonspecific induction. J.
Bacteriol. 184:6976–86
Schneider BL, Shiau SP, Reitzer LJ. 1991.
Role of multiple environmental stimuli in
control of transcription from a nitrogenregulated promoter in Escherichia coli
with weak or no activator-binding sites.
J. Bacteriol. 173:6355–63
Segura D, Espin G. 1998. Mutational
27 Jul 2003
12:20
176
Annu. Rev. Microbiol. 2003.57:155-176. Downloaded from arjournals.annualreviews.org
by WIB6332 - University of Saarland on 01/04/10. For personal use only.
86.
87.
88.
89.
90.
91.
92.
93.
AR
AR195-MI57-07.tex
AR195-MI57-07.sgm
LaTeX2e(2002/01/18)
P1: IKH
REITZER
inactivation of a gene homologous to
Escherichia coli ptsP affects poly-βhydroxybutyrate accumulation and nitrogen fixation in Azotobacter vinelandii. J.
Bacteriol. 180:4790–98
Shiau SP, Schneider BL, Gu W, Reitzer LJ.
1992. Role of nitrogen regulator I (NtrC),
the transcriptional activator of glnA in enteric bacteria, in reducing expression of
glnA during nitrogen-limited growth. J.
Bacteriol. 174:179–85
Stadtman ER. 1990. Discovery of glutamine synthetase cascade. Methods Enzymol. 182:793–809
Studholme DJ, Buck M. 2000. The biology of enhancer-dependent transcriptional regulation in bacteria: insights
from genome sequences. FEMS Microbiol. Lett. 186:1–9
Tabor CW, Tabor H. 1985. Polyamines in
microorganisms. Microbiol. Rev. 49:81–
99
Tani TH, Khodursky A, Blumenthal RM,
Brown PO, Matthews RG. 2002. Adaptation to famine: a family of stationaryphase genes revealed by microarray
analysis. Proc. Natl. Acad. Sci. USA
99:13471–76
Tian ZX, Li QS, Buck M, Kolb A, Wang
YP. 2001. The CRP-cAMP complex and
downregulation of the glnAp2 promoter
provides a novel regulatory linkage between carbon metabolism and nitrogen
assimilation in Escherichia coli. Mol. Microbiol. 41:911–24
Tweeddale H, Notley-McRobb L, Ferenci T. 1998. Effect of slow growth
on metabolism of Escherichia coli,
as revealed by global metabolite pool
(“metabolome”) analysis. J. Bacteriol.
180:5109–16
Tyler B. 1978. Regulation of the assimilation of nitrogen compounds. Annu. Rev.
Biochem. 47:1127–62
94. van Heeswijk WC, Hoving S, Molenaar
D, Stegeman B, Kahn D, Westerhoff HV.
1996. An alternative PII protein in the
regulation of glutamine synthetase in Escherichia coli. Mol. Microbiol. 21:133–
46
95. van Heeswijk WC, Rabenberg M, Westerhoff HV, Kahn D. 1993. The genes
of the glutamine synthetase adenylylation
cascade are not regulated by nitrogen in
Escherichia coli. Mol. Microbiol. 9:443–
57
96. van Heeswijk WC, Wen D, Clancy P, Jaggi
R, Ollis DL, et al. 2000. The Escherichia
coli signal transducers PII (GlnB) and
GlnK form heterotrimers in vivo: fine
tuning the nitrogen signal cascade. Proc.
Natl. Acad. Sci. USA 97:3942–47
97. Weiner L, Model P. 1994. Role of an
Escherichia coli stress-response operon
in stationary-phase survival. Proc. Natl.
Acad. Sci. USA 91:2191–95
98. Willins DA, Ryan CW, Platko JV, Calvo
JM. 1991. Characterization of Lrp, and Escherichia coli regulatory protein that mediates a global response to leucine. J. Biol.
Chem. 266:10768–74
99. Xiao H, Kalman M, Ikehara K, Zemel
S, Glaser G, Cashel M. 1991. Residual
guanosine 30 ,50 -bispyrophosphate synthetic activity of relA null mutants can be
eliminated by spoT null mutations. J. Biol.
Chem. 266:5980–90
100. Zimmer DP, Soupene E, Lee HL,
Wendisch VF, Khodursky AB, et al. 2000.
Nitrogen regulatory protein C-controlled
genes of Escherichia coli: scavenging
as a defense against nitrogen limitation.
Proc. Natl. Acad. Sci. USA 97:14674–
79
101. Zinser ER, Kolter R. 2000. Prolonged
stationary-phase incubation selects for lrp
mutations in Escherichia coli K-12. J.
Bacteriol. 182:4361–65
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CONTENTS
FRONTISPIECE, Julian Davies
GATHERING NO MOSS, Julian Davies
MOLECULAR PATHOGENICITY OF THE ORAL OPPORTUNISTIC PATHOGEN
ACTINOBACILLUS ACTINOMYCETEMCOMITANS, Brian Henderson,
Sean P. Nair, John M. Ward, and Michael Wilson
BRUCELLA STATIONARY-PHASE GENE EXPRESSION AND VIRULENCE,
R. Martin Roop II, Jason M. Gee, Gregory T. Robertson,
John M. Richardson, Wai-Leung Ng, and Malcolm E. Winkler
HOW BACTERIA ASSEMBLE FLAGELLA, Robert M. Macnab
A SALVAGE PATHWAY FOR PROTEIN SYNTHESIS: TMRNA AND
TRANS-TRANSLATION, Jeffrey H. Withey and David I. Friedman
ASSEMBLY DYNAMICS OF THE BACTERIAL CELL DIVISION PROTEIN
FTSZ: POISED AT THE EDGE OF STABILITY, Laura Romberg
and Petra Anne Levin
NITROGEN ASSIMILATION AND GLOBAL REGULATION IN ESCHERICHIA COLI,
Larry Reitzer
ON THE TRAIL OF A CEREAL KILLER: EXPLORING THE BIOLOGY OF
MAGNAPORTHE GRISEA, Nicholas J. Talbot
BACTERIAL MEMBRANE LIPIDS: WHERE DO WE STAND? John E. Cronan
SPATIAL AND TEMPORAL CONTROL OF DIFFERENTIATION AND CELL CYCLE
PROGRESSION IN CAULOBACTER CRESCENTUS, Nora Ausmees and
Christine Jacobs-Wagner
BACTERIAL MOTILITY ON A SURFACE: MANY WAYS TO A COMMON GOAL,
Rasika M. Harshey
TRANSPOSABLE ELEMENTS IN FILAMENTOUS FUNGI, Marie-Josée Daboussi
and Pierre Capy
BACTERIOPHAGE-INDUCED MODIFICATIONS OF HOST RNA POLYMERASE,
Sergei Nechaev and Konstantin Severinov
VACCINIA VIRUS MOTILITY, Geoffrey L. Smith, Brendan J. Murphy, and
Mansun Law
vi
xii
1
29
57
77
101
125
155
177
203
225
249
275
301
323
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CONTENTS
vii
MEASLES VIRUS 1998–2002: PROGRESS AND CONTROVERSY, Glenn F. Rall
343
THE UNCULTURED MICROBIAL MAJORITY, Michael S. Rappé and
Stephen J. Giovannoni
369
PATHWAYS OF OXIDATIVE DAMAGE, James A. Imlay
GENE ORGANIZATION: SELECTION, SELFISHNESS, AND SERENDIPITY,
Jeffrey G. Lawrence
MULTIPLE SIGMA SUBUNITS AND THE PARTITIONING OF BACTERIAL
TRANSCRIPTION SPACE, Tanja M. Gruber and Carol A. Gross
NATURAL SELECTION AND THE EMERGENCE OF A MUTATION PHENOTYPE:
AN UPDATE OF THE EVOLUTIONARY SYNTHESIS CONSIDERING
MECHANISMS THAT AFFECT GENOME VARIATION, Lynn Helena Caporale
ARCHAEAL DNA REPLICATION: EUKARYAL PROTEINS IN A BACTERIAL
CONTEXT, Beatrice Grabowski and Zvi Kelman
MOLECULAR GENETICS OF MYCOBACTERIUM TUBERCULOSIS PATHOGENESIS,
Josephine E. Clark-Curtiss and Shelley E. Haydel
THE BACTERIAL RECA PROTEIN AS A MOTOR PROTEIN, Michael M. Cox
DNA MISMATCH REPAIR: MOLECULAR MECHANISMS AND BIOLOGICAL
FUNCTION, Mark J. Schofield and Peggy Hsieh
KAPOSI’S SARCOMA–ASSOCIATED HERPESVIRUS IMMUNOEVASION AND
TUMORIGENESIS: TWO SIDES OF THE SAME COIN? Patrick S. Moore
and Yuan Chang
THE SECRET LIVES OF THE PATHOGENIC MYCOBACTERIA,
Christine L. Cosma, David R. Sherman, and Lalita Ramakrishnan
BACTERIAL BIOFILMS: AN EMERGING LINK TO DISEASE PATHOGENESIS,
Matthew R. Parsek and Pradeep K. Singh
INDEXES
Subject Index
Cumulative Index of Contributing Authors, Volumes 53–57
Cumulative Index of Chapter Titles, Volumes 53–57
ERRATA
An online log of corrections to Annual Review of Microbiology chapters
(if any, 1997 to the present) may be found at http://micro.annualreviews.org/
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