Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR
© Paul et al; licensee BioMed Central Ltd. 2007
Received: 22 September 2006
Accepted: 18 January 2007
Published: 18 January 2007
The glutamate synthase operon (gltBDF) contributes to one of the two main pathways of ammonia assimilation in Escherichia coli. Of the seven most-global regulators, together affecting expression of about half of all E. coli genes, two were previously shown to exert direct, positive control on gltBDF transcription: Lrp and IHF. The involvement of Lrp is unusual in two respects: first, it is insensitive to the usual coregulator leucine, and second, Lrp binds more than 150 bp upstream of the transcription starting point. There was indirect evidence for involvement of a third global regulator, Crp. Given the physiological importance of gltBDF, and the potential opportunity to learn about integration of global regulatory signals, a combination of in vivo and in vitro approaches was used to investigate the involvement of additional regulatory proteins, and to determine their relative binding positions and potential interactions with one another and with RNA polymerase (RNAP).
Crp and a more local regulator, ArgR, directly control gltBDF transcription, both acting negatively. Crp-cAMP binds a sequence centered at -65.5 relative to the transcript start. Mutation of conserved nucleotides in the Crp binding site abolishes the Crp-dependent repression. ArgR also binds to the gltBDF promoter region, upstream of the Lrp binding sites, and decreases transcription. RNAP only yields a defined DNAse I footprint under two tested conditions: in the presence of both Lrp and IHF, or in the presence of Crp-cAMP. The DNAse I footprint of RNAP in the presence of Lrp and IHF is altered by ArgR.
The involvement of nearly half of E. coli's most-global regulatory proteins in the control of gltBDF transcription is striking, but seems consistent with the central metabolic role of this operon. Determining the mechanisms of activation and repression for gltBDF was beyond the scope of this study. However the results are consistent with a model in which IHF bends the DNA to allow stabilizing contacts between Lrp and RNAP, ArgR interferes with such contacts, and Crp introduces an interfering bend in the DNA and/or stabilizes RNAP in a poised but inactive state.
A small number of global regulatory proteins appear to play a central role in integrating the regulatory architecture of Escherichia coli, so as to promote coherent transcriptional responses to environmental changes. Just seven proteins (ArcA, Crp, FIS, Fnr, IHF, Lrp, and NarL) directly control expression of about half of all genes in E. coli . We report here direct evidence that three of these seven proteins, plus a more specific regulator, cooperate to control an operon critical to nitrogen metabolism.
NH4+ + α-Ketoglutarate + NADPH → Glutamate + NADP+ 
At low ammonia concentrations, a two-enzyme cycle is used instead. First, glutamine synthetase (GlnA) produces glutamine from ammonia, glutamate and ATP [equation 2]. Then glutamate synthase (GltBD) produces two molecules of glutamate from glutamine, α-ketoglutarate, and NADPH [equation 3], with one of the glutamate molecules going back into the cycle and the other representing net ammonia incorporation [equation 4, and right side of Fig. 1]. The only difference between equations  and  is the involvement of ATP.
NH4+ + Glutamate + ATP → Glutamine + ADP + Pi 
Glutamine + α-Ketoglutarate + NADPH → 2 Glutamate + NADP+ 
NH4+ + α-Ketoglutarate + NADPH + ATP → Glutamate + NADP+ + ADP + Pi 
In the presence of high ammonia levels, GltBD activity would waste ATP as a result of unnecessary glutamine turnover. The pathway represented by equation 4 is estimated to account for a remarkable 15% of total ATP turnover during growth in glucose minimal medium , so the ATP wastage would be substantial. However, insufficient GltBD activity in the face of dropping ammonia levels would lead to cessation of growth [3, 4] and a competitive disadvantage. Clearly the level of GltBD must be very carefully controlled so as to anticipate the probable near-term needs of the cell.
Our interest in gltBDF, the operon that includes structural genes for GltBD, stems from its membership in the regulon controlled by Lrp (leucine-responsive regulatory protein) . There is no obvious single role for Lrp, but three broad themes stand out. First, Lrp appears to sense the shift between two major E. coli environments, "the gut and the gutter" , activating many amino acid biosynthetic operons (such as gltBDF) and repressing many catabolic ones. Second, and partially overlapping the first, Lrp plays an important role in regulating nitrogen metabolism [2, 5, 7]. Third, Lrp appears to play an important role in preparing the cell for stationary phase [6, 8–13].
Effects of Lrp and IHF on RNAP binding to the gltBDF promoter region
RNA polymerase holoenzyme (RNAP) binds to PgltB in the absence of other proteins, as revealed by electrophoretic mobility shift of a DNA segment from -406 to +131 (relative to the transcription start; not shown). However DNAse I footprinting analysis of this binary complex revealed no obvious regions of protection (Fig. 3B, compare lanes 5 and 6). Since the absence of either Lrp or IHF leads to a >30-fold reduction in gltBDF transcription [5, 14], we investigated whether these two proteins influence RNAP binding to PgltB. Mobility shift experiments were not informative as, under our conditions, the large shift due to RNAP alone was indistinguishable from shifts due to RNAP together with Lrp and/or IHF. However DNAse I protection analysis revealed that the combination of Lrp, IHF and RNAP results in a footprint in the promoter region, with strongly enhanced cleavage at the -19 position of the template strand and protection in the remainder of the region between the -10 and -35 hexamers (Fig. 3B, compare lane 7 to lanes 5 and 6). This protection extended ~30 bp upstream of the -35 hexamer, merging with the footprint of IHF, and some protection was visible even farther upstream between the IHF and Lrp binding sites. A combination of just Lrp and IHF does not result in any additional footprint aside from those of the individual proteins , and in particular the extended protection upstream of the -35 hexamer is not seen in the absence of RNAP (Fig. 3A).
Crp-cAMP regulation of gltBDF transcription
First, we carried out mobility shift assays using purified Crp and a gltBDF DNA fragment containing the region from -406 to +246. Crp bound the glt DNA with an apparent Kd of 35 nM in the presence of 20 μM cAMP (Fig. 5B). Replacing the region between -121 and -48 with heterologous DNA  resulted in loss of detectable binding (Fig. 5C). When cAMP was not added to the gel, but was present in the binding reaction, binding was still observed but the shifted bands were smeared, suggesting that the complexes were unstable under this condition (not shown).
Second, we carried out DNAse I footprint analyses, using purified Crp, cAMP, and PgltB DNA. A defined region of partial protection was seen between -71 and -52 on the non-template strand (Fig. 5E), and -72 to -57 on the template strand (not shown). Thus Crp-cAMP interacts directly with PgltB. The Crp binding is centered at -65.5, in the predicted binding sequence (-76 to -55), and between the -35 hexamer and the IHF binding site (Fig. 2A).
As Crp most often acts as a transcription activator, we explored some possible explanations for its repressive effect on PgltB. One possibility, given the proximity of the Crp and IHF binding sites (Fig. 2A), and the requirement of IHF for activation by Lrp , is that Crp interferes with IHF binding. However mobility shift analysis indicates that Crp and IHF bind independently of one another (Fig. 5D), though the ternary and binary complexes could not be resolved from one another well enough to completely rule out limited negative (or positive) cooperativity in their binding.
ArgR-Arg regulation of gltBDF transcription
Effects of arginine and ArgR on gltB::lacZ expression
LacZ activity (units)1
Addition of arginine3
LP1000 + Arg
LP1270 + Arg
LP2020 + Arg
Deletion of ArgR
LP1050 + Arg
LP2023 (rph+ ΔargR)
The sequence to which ArgR binds was determined by DNase I protection using gltB DNA from -462 to +161. ArgR protected a region upstream of the distal Lrp binding site (Figs. 2A and 8C), extending from -361 to -318 on the non-template strand. This encompasses the two ArgR consensus-matching sites, and is consistent with the Hill coefficient of 2.0. Similar results were obtained for the template strand (not shown; a longer fragment, extending from -575 to +131, gave lower resolution due to the position of the footprint on the fragment).
A second possible basis for repression of gltBDF by ArgR involves interference with the proposed Lrp-RNAP interaction. ArgR does in fact alter the protection pattern generated by the combination of Lrp, IHF, and RNAP (Fig. 9B, asterisks). In the absence of ArgR there is a limited region of RNAP-dependent hypersensitivity that overlaps the ArgR binding site; addition of ArgR and arginine alters this hypersensitivity pattern.
Effects of rph on gltBDF expression
E. coli strains1, plasmids, and primers used in this work
Source or reference
PS2209 gltB (psiQ39)::lacZ (Mu d1-1734)
PS2209 gltB (psiQ32)::lacZ (Mu d1-1734)
PS2209 gltB (psiQ32)::lacZ (Mu d1-1734) lrp-35::Tn10
F- ompT hsdS B (rB-mB-) gal dcm (DE3)
BE1 (W3110 lrp-201:: Tn10) pJWD2
PS2209 gltB::lacZ transcriptional fusion at λatt with -406 to +246 of the gltBDF operon
PS2209 gltB::lacZ transcriptional fusion at λatt with -270 to +246 of the gltBDF operon
LP2010 gltB::lacZ transcriptional fusion at λatt with -406 to +246 of the gltBDF operon
F. C. Neidhardt
F- prototroph rph
F. C. Neidhardt
recA1 endA1 gyrA96 thi-1 hsdR17 supE44 relA1 Δlac-pro [F' proAB lacIqZΔM15 Tn10]
pKK232-8 with promoterless lacZ gene inserted upstream of cat gene in a derivative of pBR322
pBH403 with gltB promoter region cloned from BamHI to SalI
pPM2005 with mutations in the Crp-binding sequence
pTrc 99A (Pharmacia) with the lrp coding sequence cloned into the NcoI site
pET23b (Novagen) with the argR coding sequence cloned into the NdeI/XhoI sites
pET29a (Novagen) with the crp coding sequence inserted into the NdeI/XhoI sites
pET28A (Novagen) with the himA and himD coding sequences inserted in tandem into the NcoI//BamHI sites
CAGTCAATTAATAAAGAATA TAA CGCTAAAGGCGG TTTCTGTACCAATAAGCTTGCC
Role of IHF in mediating activation of gltBD by Lrp
IHF, a DNA-bending protein , is required for activation of gltBDF transcription by Lrp . IHF subtly affects the Lrp-dependent DNAse I footprint (Fig. 3A), suggesting that IHF alters the Lrp-DNA complex (or alters DNAse I access to that complex). In addition, IHF bending could bring the Lrp-DNA complex into activating contact with RNAP at PgltB (Fig. 2B). IHF plays an architectural role at several activated promoters, such as PilvP . We have not directly demonstrated looping, but two results support this view. First, no defined footprint for RNAP was seen at PgltB with either IHF or Lrp alone, only with both together (Fig. 3B and our unpublished results). Second, an earlier study demonstrated that a 5 bp (half helical turn) insertion between the proximal Lrp binding site and the promoter reduced gltB-lacZ expression 3-7-fold, while a 10 bp (full helical turn) insertion at the same location did not reduce fusion expression (Fig. 5B of Wiese et al. ). Bending or looping models do not rule out the possibility of direct RNAP-IHF contacts occurring as well .
Does Crp pre-position RNAP in response to energy metabolism?
The flux through the GlnA/GltBD pathway can be quite high in minimal media. ATP is required for the GlnA/GltBD pathway and not for the GdhA pathway (Fig. 1), and governing the relative fluxes through these alternative pathways is probably one of the most critical regulatory problems faced by E. coli. We report direct regulation of PgltB by Crp, in agreement with earlier indirect evidence . A microarray-based global analysis of E. coli genes affected by Crp  did not identify the gltBDF operon, but this probably reflects the rich culture medium (LB) used in that work. Crp is broadly associated with the control of carbon and energy source utilization, usually activating genes for utilization of less-efficient carbon/energy sources (relative to glucose) . Competitions between gdhA and gdhA+ strains [3, 4] reveal a clear advantage for the gdhA+ strain during glucose limitation, suggesting that Crp modulates the relative activities of the two alternative pathways for glutamate synthesis to favor the ATP-independent pathway during growth on suboptimal carbon sources [3, 4]. The reciprocal effects of carbon source and addition of cAMP on GdhA and GltBD activities are consistent with just this role for Crp . In addition, Crp-cAMP represses one of the promoters for the glutamine synthetase gene (glnAp2) , so both enzymes for the GlnA/GltBD pathway are controlled in parallel by Crp.
Our data show that Crp-cAMP binding in vitro (Fig. 5B, E) is correlated with reduced transcription in vivo (Fig. 6), and that RNAP generates a protection pattern at PgltB in the presence of Crp-cAMP (Fig. 7, lane 7) different from the pattern yielded by RNAP in the presence of IHF + Lrp (Fig. 3B, lane 7). The Crp-cAMP repression thus appears to alter RNAP binding rather than blocking it. The Crp footprint is centered at -65.5 relative to the start of gltB transcription, close to the position from which Crp activates class I promoters  where Crp binds between the C-terminal domain of RpoA (αCTD) and region 4 of RpoD (σ70). However optimal spacing from the proximal edge of the Crp binding site to that of the -35 hexamer is 13–16 bp in class I promoters, while in PgltB this spacing is 21 bp (Fig. 2A). Crp may thus repress PgltB by mispositioning or trapping RNAP. Repression has been seen due to mispositioning of RNAP via alternative binding sites , or trapping at the promoter [37, 38]. A recent global analysis suggests that nearly a quarter of σ70 (RpoD)-dependent promoters have bound RNAP that is "poised" but not transcribing . RNAP poised at PgltB would allow a rapid increase of GltBD levels in the face of falling ammonium concentrations, as the GdhA reaction becomes increasingly inefficient (Fig. 1).
Role of ArgR in repressing gltBDF
As shown in Fig. 1, glutamate is a precursor of ornithine, which in turn is converted to arginine. Thus regulation of GltBD in response to arginine is an example of negative feedback regulation. The relatively modest effects are appropriate given the need for glutamate in many other pathways. A similar feedback regulation of glutamate biosynthesis by ArgR was recently observed in Pseudomonas aeruginosa . The mechanism by which ArgR represses PgltB is not clear, but our evidence is consistent with the possibility that ArgR interferes with formation of the final activation complex. As shown in Fig. 8, and illustrated in Fig. 2, ArgR binds far upstream of the promoter, near the Lrp-binding region. However ArgR does not appear to have a major effect on Lrp binding (Fig. 9A). Our working hypothesis is that ArgR allows pre-assembly of the Lrp-IHF-RNAP complex, but blocks a specific contact required for transcriptional activation. This would resemble the suggested role of Crp (see above) in reducing gltBD expression while allowing rapid return to full activation should the appropriate conditions change.
Role of Lrp in regulation of gltBD
Lrp is not simply a signal of amino acid sufficiency. First, gltBDF is one of the operons for which Lrp regulation is relatively insensitive to the coregulator leucine [5, 28]. Second, Lrp levels (like those of the coactivator IHF ) are sensitive to the alarmone ppGpp , which in turn is affected by sufficiency of both amino acids and other nutrients . Lrp levels vary between media, and (like those of the coactivator IHF ) also through the growth cycle .
Much of what is known about regulation of GdhA, GlnA, and GltBD is consistent with the expected reciprocal pattern between the two pathways shown in Fig. 1. One would expect GdhA levels to parallel those of [NH4+], while GlnA and GltBD levels would perhaps follow the inverse of [NH4+] and parallel those of ATP. In fact, gdhA is repressed by Nac, with repression relieved in high [NH4+], while neither gln A nor gltBD appear to respond substantially to Nac [17, 44, 45]. Similarly, transcription of both glnA and gltBD is repressed by Crp-cAMP while effects on gdhA are unclear (this work, [34, 46]). Conversely, both GlnA activity (indirectly, via glnL) and gltBD transcription are boosted by Lrp, which has no obvious effect on gdhA [5, 6, 28].
Modeling analysis  suggests that the major control of relative flux between the alternative pathways shown in Fig. 1 should involve regulation of GlnA activity (via adenylylation and deadenylylation ). Lrp has major effects on GlnA expression and adenylylation status in response to ammonia levels [2, 5, 7]. The effect of Lrp on GlnA expression and activity is indirect, probably involving the direct Lrp effect on GltBD expression that, in turn, modulates the intracellular ratios of α-ketoglutarate, glutamate, and glutamine . This model requires changes in gene expression levels for adaptation to sudden large changes in [NH4+], with gltBD needing to be expressed above a threshold level. The 30-40-fold activation of PgltB by Lrp  is consistent with a major switch above or below this critical threshold expression level. In contrast, the effects of Crp and ArgR (and of leucine, in this case) are smaller, fine-tuning controls that may modulate the flow of glutamine out of the middle of the GlnA-GltBD pathway.
Results from this study demonstrate that the physiologically-important gltBDF operon of E. coli is subject to negative as well as positive control, and involves a third member of the group of seven most-global transcriptional regulatory proteins. In addition to the previously-demonstrated direct positive roles of Lrp and IHF, there are direct negative roles for Crp and ArgR. Lrp and IHF appear to stabilize RNAP binding to the promoter, as no RNAP-dependent footprint appears unless both Lrp and IHF are present. Crp-cAMP can replace Lrp + IHF in potentiating footprint formation by RNAP, though the resulting protection patterns are distinct. ArgR alters, but does not prevent, footprint formation by RNAP + Lrp + IHF. It does not appear that either repressor, Crp or ArgR, acts by interfering with binding of the activators or of RNAP. This study does not explore the specific mechanisms of activation or repression at gltBDF, but the results are consistent with the possibility that Crp and ArgR inhibit transcription in such a way as to leave the RNAP poised for rapid transcription initiation when conditions require it. Given the central importance of the regulation of glutamate biosynthesis, reflected by the involvement of Lrp and two other E. coli global regulatory proteins, it would be instructive to know whether this regulatory mechanism is broadly conserved among related bacterial species adapted to different nutritional environments.
Bacterial strains, plasmids and culture conditions
The strains, plasmids and PCR primers used in this study are listed in Table 2. All strains were derivatives of E. coli K- 12 W3110 or LP2002 (in which the rph mutation of W3110 was corrected; see below). For β-galactosidase assays, strains were grown in glucose minimal MOPS medium [50, 51] containing ampicillin (20 μg/ml for chromosomal and 80 μg/ml for plasmid-borne resistance) or 7.5 mM L-arginine HCl (Sigma) where indicated. Cultures grown to test the effects of Crp-binding site mutations were grown in MOPS defined-rich medium (Teknova, Hollister, CA) containing 100 μg ampicillin per ml and 1 mM isopropyl-β-D-thiogalactoside (IPTG), in the presence or absence of 10 μM dibutyryl-cAMP (BioMol Research Labs, Plymouth Meeting, PA). Plates for most genetic work used agar containing "LB" medium .
Construction of the rph+ strain LP2002 and its derivatives
The widely used E. coli K- 12 strain W3110 contains a frameshift mutation in rph associated with decreased levels of the pyrE product orotate phosphoribosyltransferase . This frameshift was corrected as follows. A 790 bp fragment of rph and downstream sequence was amplified from W3110 chromosomal DNA using the polymerase chain reaction (PCR) and the overlap extension procedure . The primers used were rph1-4 (Table 2). Primers rph2 and rph3 contain the additional base pair required to correct the frame shift in the rph gene (underlined italic in Table 2). The PCR product was cloned into E. coli strain XL-1Blue (Stratagene) using the pGEMT-easy vector (Promega). The insert was then excised with NotI and ligated into NotI-digested suicide vector pKO3 . Electrocompetent W3110 cells were transformed with pKO3 carrying the modified rph gene, and integrants were selected at 43°C. Cells that had lost the plasmid were isolated by plating on LB agar containing 5% sucrose, which selects against the plasmid sacB gene . Colonies from LB-sucrose plates were replica plated onto unsupplemented LB and LB-chloramphenicol (20 μg/ml). Colonies that grew on LB plates but not on LB-chloramphenicol were screened for correction of the frame shift in the rph gene by amplifying the rph region by PCR and sequencing the product. The resulting rph+ strain was designated LP2002.
The lac operon was deleted from strain LP2002 using the overlap extension protocol  with primers lac6-9 (Table 2). The lac6 primer corresponds to nucleotides 814 to 842 within the coding region of lacI; the lac7 primer is complementary to the 5' region of primer lac8; the 3' end of lac8 bridges the deletion region (see below), and lac9 corresponds to nucleotides 1019 to 1044 of the coding region of cynX gene downstream of the lacZYA operon. The final amplified product has a deletion starting immediately upstream of the -10 region of the lacZYA operon and extending to the 3' end of the lacA gene, leaving the last 19 codons of lacA intact. This product was introduced into the chromosome of LP2002 using the suicide vector pKO3 . The ΔlacZYA recombinants were identified as white colonies on LB-Xgal plates, and the deletion was verified by amplifying the chromosomal lac region and sequencing the fragment. The resultant strain was designated LP2010. The gltB-lacZ transcriptional fusion from LP1000 [14, 55] was introduced into LP2010 via P1 transduction  and designated LP2020.
Construction of ΔargR strains
A portion of argR was deleted from strains LP1000 and LP2020 as follows. The argR gene from strain PS2209 (W3110 Δlac-169 from F. C. Neidhardt) was amplified from chromosomal DNA by PCR, using the primers arg1 and arg2 (Table 2). The amplified product was ligated into the pGEMTeasy vector (Promega). The argR fragment was excised from the vector with NotI, and the region of argR coding for amino acids 15–90 were deleted in-frame by removing a DraI/EcoRV fragment from the argR gene and religating the blunt ends. This fragment was ligated into suicide vector pKO3  and introduced into strains LP1000 and LP2020. Prospective mutants were screened by amplifying the argR region from their genomic DNA; the amplified fragment was shorter in the deletion mutants. The ΔargR strains were designated LP1050 (LP1000 derivative) and LP2023 (LP2020 derivative).
CipherGen ProteinChip™ assays
Surface-enhanced laser desorption and ionization (SELDI) ProteinChip technology (Ciphergen Biosystems, currently distributed by BioRad, Hercules, CA) was used to identify proteins binding to the upstream region of the gltBDF operon. In this approach, biotin-labeled gltB DNA (from -406 to +246) was attached to streptavidin-coated chips and incubated with centrifugally-cleared whole-cell extracts. The masses of proteins that bound to the DNA fragments were determined using SELDI mass spectroscopy. This binding experiment was carried out under nonstringent conditions so as to detect relatively weak binding interactions. E. coli cells (strain W3110) were grown in glucose minimal MOPS medium and opened using glass beads in a BeadBeater (BioSpec Products, Bartlesville, OK). PS-1 (carbonyl diimidazole) ProteinChips were coated with streptavidin (Pierce, Immunopure™) at 0.2 microgram/spot, washed, and the unbound sites were blocked with 1 M ethanolamine (pH 8.0). The DNA, generated by PCR using biotinylated primers, was first bound to the streptavidin on the chip, and then incubated with cell extract in 20 mM Tris-acetate (pH 8.0), 0.1 mM EDTA, 0.1 mM dithiothreitol, 250 mM NaCl, 4 mM Mg acetate, 12.5% glycerol (v:v), and 200 μg/ml of salmon sperm DNA (Amersham Pharmacia Biotech, N.J.). The chips were washed with 20 mM Tris-acetate containing 0.1% Triton X-100. The matrix EAM-1 (Ciphergen) was added to the chip prior to SELDI mass analysis.
Expression and purification of Lrp, ArgR, Crp and IHF
In all cases, protein purity was assessed from single (or, in the case of IHF, double) Coomassie-stained bands when μg amounts were loaded onto SDS polyacrylamide gels. Lrp was purified from strain JWD3 and isolated as previously described . The genes argR, crp, himA and himD (the latter two coding for IHF subunits) were amplified from strain W3110 chromosomal DNA. The argR gene was amplified using primers arg3 and arg4 (Table 2), cloned into the expression vector pET23b (Novagen) at the Nde I/Xho I sites creating pLP1060, and introduced into the expression host BL21(DE3) (Novagen) which carries an inducible gene for T7 RNAP. The protein was purified from the resulting strain LP1060, as described by Sunnerhagen et al. .
The crp gene was amplified using primers crp5 and crp6 (Table 2), ligated into the Nde I/Xho I sites of expression vector pET29a (Novagen) to create pLP1070, and introduced into strain BL21(DE3) resulting in strain LP1070. The overexpressed protein was purified using a nickel affinity column (Pharmacia) since the wild type Crp (without a his-tag) binds nickel columns with moderate affinity .
The genes himA and himD were amplified from W3110 chromosomal DNA using primers himA1 and himA2 and primers himD1 and himD2 (Table 2). The amplified products were ligated in tandem into the expression vector pET28a (Novagen) at the Nco I/Bam HI sites to create pLP1080, and introduced into strain BL21(DE3). The strain was designated LP1080. IHF with an N-terminal histidine tag on HimA was purified using a 3 ml Hi-Trap Heparin Sepharose column from Pharmacia .
Construction of PgltB-lacZ fusion and variant with altered Crp-binding site
The promoter region upstream of gltB was amplified from E. coli chromosomal DNA using primers gltP1-2 (Table 2), and the resulting PCR product was digested with BamHI and SalI. This product was ligated into pBH403, a derivative of pKK232-8 with a promoterless lacZ gene between two bidirectional transcription terminators, to generate pPM2005 (Table 2). This process was repeated with a mutagenic primer pair (gltcrp1-2, Table 2) to generate pPM2006, which has alterations within the Crp-binding site in the glt promoter. Plasmids were sequence confirmed and used to transform the ΔlacZ W3110 derivative PS2209.
Cultures were grown to exponential phase in the indicated media. Samples were taken at 30-min intervals throughout the growth period. Levels of β-galactosidase were determined by o-nitrophenyl-β-D-galactoside (ONPG) hydrolysis as described by Platko et al. . β-galactosidase levels were plotted against culture absorbance, and points were fitted via linear regression. The resulting slope yields the β-galactosidase acitivity.
Mobility shift and DNase I protection assays
RNA polymerase holoenzyme was purchased from Epicentre Biotechnologies (Madison, WI). Assays were carried out as described in Paul et al.  except where indicated. In electrophoretic mobility shift experiments involving ArgR, the reaction mixture and the polyacrylamide gel both contained 5 mM L-arginine, and the running buffer (1 × TBE [90 mM Tris borate, pH 8.3, 0.2 mM EDTA]) contained 1 mM L-arginine. Crp-DNA binding was carried out in a buffer modified from Seoh and Tai  containing 10 mM Tris-HCl (pH 8.0), 50 mM KCl, 1.0 mM EDTA, 0.1 mM DTT, 50 μg/ml BSA, 10 μg/ml poly (dI-dC):poly(dI-dC) from Pharmacia and 12.5% glycerol. cAMP (20 mM, Sigma) was added to the reaction buffer, the gel and the running buffer (0.5 × TBE). The buffer for DNase I protection assays (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 1 mM CaCl2, 2 mM dithiothreitol, 50 mg of bovine serum albumin/ml and 2 μg of poly(dI-dC):poly(dI-dC)/ml) contained 5 mM L-arginine or 20 mM cAMP for reactions involving ArgR and Crp respectively.
The authors thank George M. Church of Harvard University, Cambridge, MA, for the plasmid pKO3, Ruth Van Bogelen of Pfizer Inc., Ann Arbor, MI, for help with the SELDI analysis, and the anonymous reviewers for helpful comments. This project was supported in part by a grant from the U.S. National Science Foundation to RGM and RMB (MCB-9807237), and by a grant to RMB from the U.S. National Institutes of Health (AI054716).
- Martinez-Antonio A, Collado-Vides J: Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol. 2003, 6 (5): 482-489. 10.1016/j.mib.2003.09.002.View ArticlePubMedGoogle Scholar
- Reitzer L: Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol. 2003, 57: 155-176. 10.1146/annurev.micro.57.030502.090820.View ArticlePubMedGoogle Scholar
- Helling RB: Pathway choice in glutamate synthesis in Escherichia coli. J Bacteriol. 1998, 180 (17): 4571-4575.PubMed CentralPubMedGoogle Scholar
- Helling RB: Why does Escherichia coli have two primary pathways for synthesis of glutamate?. J Bacteriol. 1994, 176 (15): 4664-4668.PubMed CentralPubMedGoogle Scholar
- Ernsting BR: Characterization of the regulon controlled by the leucine responsive regulatory protein. J Bacteriol. 1992, 174 (4): 1109-1118.PubMed CentralPubMedGoogle Scholar
- Tani TH: Adapation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc Nat Acad Sci USA. 2002, 99: 13471-13476. 10.1073/pnas.212510999.PubMed CentralView ArticlePubMedGoogle Scholar
- Calvo JM, Matthews RG: The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol Rev. 1994, 58 (3): 466-490.PubMed CentralPubMedGoogle Scholar
- Zinser ER, Kolter R: Prolonged stationary-phase incubation selects for lrp mutations in Escherichia coli K-12. J Bacteriol. 2000, 182 (15): 4361-4365. 10.1128/JB.182.15.4361-4365.2000.PubMed CentralView ArticlePubMedGoogle Scholar
- Colland F, Barth M, Hengge-Aronis R, Kolb A: Sigma factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and Lrp transcription factors. EMBO J. 2000, 19 (12): 3028-3037. 10.1093/emboj/19.12.3028.PubMed CentralView ArticlePubMedGoogle Scholar
- Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A: Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol. 1999, 181 (20): 6361-6370.PubMed CentralPubMedGoogle Scholar
- Bouvier J, Gordia S, Kampmann G, Lange R, Hengge-Aronis R, Gutierrez C: Interplay between global regulators of Escherichia coli: effect of RpoS, Lrp and H-NS on transcription of the gene osmC. Mol Microbiol. 1998, 28 (5): 971-980. 10.1046/j.1365-2958.1998.00855.x.View ArticlePubMedGoogle Scholar
- Landini P, Hajec LI, Nguyen LH, Burgess RR, Volkert MR: The leucine-responsive regulatory protein (Lrp) acts as a specific repressor for sigmaS-dependent transcription of the Escherichia coli aidB gene. Mol Microbiol. 1996, 20 (5): 947-955. 10.1111/j.1365-2958.1996.tb02536.x.View ArticlePubMedGoogle Scholar
- Levinthal M, Pownder T: Hns, RpoS and Lrp mutations affect stationary-phase survival at high osmolarity. Res Microbiol. 1996, 147 (5): 333-342. 10.1016/0923-2508(96)84708-5.View ArticlePubMedGoogle Scholar
- Paul L: Activation from a distance: Roles of Lrp and integration host factor in transcriptional activation of gltBDF. J Bacteriol. 2001, 183 (13): 3910-3918. 10.1128/JB.183.13.3910-3918.2001.PubMed CentralView ArticlePubMedGoogle Scholar
- Prusiner S: Adenosine 3':5'-cyclic monophosphate control of the enzymes of glutamine metabolism in Escherichia coli. Proc Nat Acad Sci USA. 1972, 69 (10): 2922-2926. 10.1073/pnas.69.10.2922.PubMed CentralView ArticlePubMedGoogle Scholar
- Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW: A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J Biol Chem. 2006, 281 (8): 4802-4815. 10.1074/jbc.M512312200.View ArticlePubMedGoogle Scholar
- Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S: Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc Natl Acad Sci U S A. 2000, 97 (26): 14674-14679. 10.1073/pnas.97.26.14674.PubMed CentralView ArticlePubMedGoogle Scholar
- Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P: GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli. Microbiology. 2004, 150 (Pt 1): 61-72. 10.1099/mic.0.26659-0.View ArticlePubMedGoogle Scholar
- Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 2005, 33 (Database issue): D334-7. 10.1093/nar/gki108.PubMed CentralView ArticlePubMedGoogle Scholar
- D'Ari R, Jaffe A, Bouloc P, Robin A: Cyclic AMP and cell division in Escherichia coli. J Bacteriol. 1988, 170 (1): 65-70.PubMed CentralPubMedGoogle Scholar
- Magasanik B: Global regulation of gene expression. Proc Natl Acad Sci U S A. 2000, 97 (26): 14044-14045. 10.1073/pnas.97.26.14044.PubMed CentralView ArticlePubMedGoogle Scholar
- Hogema BM, Arents JC, Inada T, Aiba H, van Dam K, Postma PW: Catabolite repression by glucose 6-phosphate, gluconate and lactose in Escherichia coli. Mol Microbiol. 1997, 24 (4): 857-867. 10.1046/j.1365-2958.1997.3991761.x.View ArticlePubMedGoogle Scholar
- Lin SH, Lee JC: Determinants of DNA bending in the DNA-cyclic AMP receptor protein complexes in Escherichia coli. Biochemistry. 2003, 42 (17): 4809-4818. 10.1021/bi027259+.View ArticlePubMedGoogle Scholar
- Charlier D: The arginine regulon of Escherichia coli K12: A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression. J Mol Biol. 1992, 226: 367-386. 10.1016/0022-2836(92)90953-H.View ArticlePubMedGoogle Scholar
- Tian G D. Lim, J. Carey, and W. K. Maas: Binding of the arginine repressor of Escherichia coli K12 to its operator sites. J Mol Biol. 1992, 226: 387-397. 10.1016/0022-2836(92)90954-I.View ArticlePubMedGoogle Scholar
- Wiese DE, Ernsting BR, Blumenthal RM, Matthews RG: A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli. J Mol Biol. 1997, 270 (2): 152-168. 10.1006/jmbi.1997.1057.View ArticlePubMedGoogle Scholar
- Weiss JN: The Hill equation revisited: uses and misuses. FASEB J. 1997, 11 (11): 835-841.PubMedGoogle Scholar
- Ernsting BR J. W. Denninger, R. M. Blumenthal and R. G. Matthews: Regulation of gltBDF operon of Escherichia coli: How a leucine-insensitive operon is regulated by leucine-responsive regulatory protein. J Bacteriol. 1993, 175: 7160-7169.PubMed CentralPubMedGoogle Scholar
- Jensen KF: The Esherichica coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol. 1993, 175: 3401-3407.PubMed CentralPubMedGoogle Scholar
- Swinger KK, Rice PA: IHF and HU: flexible architects of bent DNA. Curr Opin Struct Biol. 2004, 14 (1): 28-35. 10.1016/j.sbi.2003.12.003.View ArticlePubMedGoogle Scholar
- Parekh BS, Sheridan SD, Hatfield GW: Effects of integration host factor and DNA supercoiling on transcription from the ilvPG promoter of Escherichia coli. J Biol Chem. 1996, 271 (34): 20258-20264. 10.1074/jbc.271.34.20258.View ArticlePubMedGoogle Scholar
- Giladi H, Koby S, Prag G, Engelhorn M, Geiselmann J, Oppenheim AB: Participation of IHF and a distant UP element in the stimulation of the phage lambda PL promoter. Mol Microbiol. 1998, 30 (2): 443-451. 10.1046/j.1365-2958.1998.01079.x.View ArticlePubMedGoogle Scholar
- Gosset G, Zhang Z, Nayyar S, Cuevas WA, Saier MH: Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli. J Bacteriol. 2004, 186 (11): 3516-3524. 10.1128/JB.186.11.3516-3524.2004.PubMed CentralView ArticlePubMedGoogle Scholar
- Tian ZX, Li QS, Buck M, Kolb A, Wang YP: 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. 2001, 41 (4): 911-924. 10.1046/j.1365-2958.2001.02561.x.View ArticlePubMedGoogle Scholar
- Savery NJ, Lloyd GS, Busby SJ, Thomas MS, Ebright RH, Gourse RL: Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at class I cyclic AMP receptor protein-dependent promoters. J Bacteriol. 2002, 184 (8): 2273-2280. 10.1128/JB.184.8.2273-2280.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Tagami H, Aiba H: An inactive open complex mediated by an UP element at Escherichia coli promoters. Proc Natl Acad Sci USA. 1999, 96 (13): 7202-7207. 10.1073/pnas.96.13.7202.PubMed CentralView ArticlePubMedGoogle Scholar
- Schroder O, Wagner R: The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription by trapping RNA polymerase in the initiation complex. J Mol Biol. 2000, 298 (5): 737-748. 10.1006/jmbi.2000.3708.View ArticlePubMedGoogle Scholar
- Liu M, Garges S, Adhya S: lacP1 promoter with an extended -10 motif. Pleiotropic effects of cyclic AMP protein at different steps of transcription initiation. J Biol Chem. 2004, 279 (52): 54552-54557. 10.1074/jbc.M408609200.View ArticlePubMedGoogle Scholar
- Reppas NB, Wade JT, Church GM, Struhl K: The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Molec Cell. 2006, 24: 747-757. 10.1016/j.molcel.2006.10.030.View ArticlePubMedGoogle Scholar
- Hashim S D. H. Kwon, A. Abdelal and C. D. Lu: The arginine regulatory protein mediates repression by arginine of the operons encoding glutamate synthase and anabolic glutamate dehydrogenase in Pseudomonas aeruginosa. J Bacteriol. 2004, 186: 3848-3854. 10.1128/JB.186.12.3848-3854.2004.PubMed CentralView ArticlePubMedGoogle Scholar
- Aviv M, Giladi H, Schreiber G, Oppenheim AB, Glaser G: Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation. Mol Microbiol. 1994, 14 (5): 1021-1031. 10.1111/j.1365-2958.1994.tb01336.x.View ArticlePubMedGoogle Scholar
- Landgraf JR, Wu J, Calvo JM: Effects of nutrition and growth rate on Lrp levels in Escherichia coli. J Bacteriol. 1996, 178 (23): 6930-6936.PubMed CentralPubMedGoogle Scholar
- Magnusson LU, Farewell A, Nystrom T: ppGpp: a global regulator in Escherichia coli. Trends Microbiol. 2005, 13 (5): 236-242. 10.1016/j.tim.2005.03.008.View ArticlePubMedGoogle Scholar
- Camarena L, Poggio S, Garcia N, Osorio A: Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein. FEMS Microbiol Lett. 1998, 167 (1): 51-56. 10.1111/j.1574-6968.1998.tb13206.x.View ArticlePubMedGoogle Scholar
- Muse WB, Bender RA: The nac (nitrogen assimilation control) gene from Escherichia coli. J Bacteriol. 1998, 180 (5): 1166-1173.PubMed CentralPubMedGoogle Scholar
- Zheng D, Constantinidou C, Hobman JL, Minchin SD: Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res. 2004, 32 (19): 5874-5893. 10.1093/nar/gkh908.PubMed CentralView ArticlePubMedGoogle Scholar
- Bruggeman FJ, Boogerd FC, Westerhoff HV: The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica. FEBS J. 2005, 272 (8): 1965-1985. 10.1111/j.1742-4658.2005.04626.x.View ArticlePubMedGoogle Scholar
- Jaggi R, van Heeswijk WC, Westerhoff HV, Ollis DL, Vasudevan SG: The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction. EMBO J. 1997, 16 (18): 5562-5571. 10.1093/emboj/16.18.5562.PubMed CentralView ArticlePubMedGoogle Scholar
- Jiang P, Peliska JA, Ninfa AJ: The regulation of Escherichia coli glutamine synthetase revisited: role of 2-ketoglutarate in the regulation of glutamine synthetase adenylylation state. Biochemistry. 1998, 37 (37): 12802-12810. 10.1021/bi980666u.View ArticlePubMedGoogle Scholar
- Neidhardt FC P. L. Bloch, and D. F. Smith: Culture medium for enterobacteria. J Bacteriol. 1974, 119: 736-747.PubMed CentralPubMedGoogle Scholar
- Sambrook J E. F. Fritsch, and T. Maniatis: Molecular cloning: a laboratory manual. 1989, Cold Spring Harbor, NY. , Cold Spring Harbor Laboratory, 2Google Scholar
- Bertani G: Lysogeny at mid-twentieth century: P1, P2, and other experimental systems. J Bacteriol. 2004, 186 (3): 595-600. 10.1128/JB.186.3.595-600.2004.PubMed CentralView ArticlePubMedGoogle Scholar
- Ge L and P. Rudolph: Simultaneous introduction of multiple mutations using overlap extension PCR. Biotechniques. 1997, 22 (1): 28-30.PubMedGoogle Scholar
- Link AJ Phillips, D. and Church, G.M.: Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization. J Bacteriol. 1997, 179 (20): 6228-6237.PubMed CentralPubMedGoogle Scholar
- Miller JH: Experiments in molecular genetics. 1972, Cold spring harbor, N. Y. , Cold Spring Harbor Laboratory PressGoogle Scholar
- Sunnerhagen M M. Nilges, G. Otting, and J. Carey: Solution structure of the DNA-binding domain and model for the complex of mutlifunctional hexameric arginine repressor with DNA. Nat Struct Biol. 1997, 4 (10): 819-825. 10.1038/nsb1097-819.View ArticlePubMedGoogle Scholar
- Wickstrum JR and S. M. Egan: Ni+-Affinity purification of untagged cAMP receptor protein. Biotechniques. 2002, 33 (4): 728-730.PubMedGoogle Scholar
- Filutowicz M H. Grimek, and K. Appelt: Purification of Escherichia coli integration host factor (IHF) in one chromatographic step. Gene. 1994, 147: 149-150. 10.1016/0378-1119(94)90056-6.View ArticlePubMedGoogle Scholar
- Platko JV D. A. Willins, and J. M. Calvo: The ilvIH operon of Escherichia coli is positively regulated. J Bacteriol. 1990, 172: 4563-4570.PubMed CentralPubMedGoogle Scholar
- Seoh HK and P. C. Tai: Catabolic repression of secB expression is positively controlled by cyclic AMP (cAMP) receptor protein-cAMP complexes at the transcriptional level. J Bacteriol. 1999, 181: 1892-1899.PubMed CentralPubMedGoogle Scholar
- Brosius J: Plasmid vectors for the selection of promoters. Gene. 1984, 27 (2): 151-160. 10.1016/0378-1119(84)90136-7.View ArticlePubMedGoogle Scholar
- Knowle D, Lintner RE, Touma YM, Blumenthal RM: Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems. J Bacteriol. 2005, 187 (2): 488-497. 10.1128/JB.187.2.488-497.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Makarova KS, Mironov AA, Gelfand MS: Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2001, 2 (4): RESEARCH0013-10.1186/gb-2001-2-4-research0013.PubMed CentralView ArticlePubMedGoogle Scholar