Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli

New classes of mutants in complementary chromatic adaptation provide evidence for a novel four-step phosphorelay system

Complementary chromatic adaptation appears to be controlled by a complex regulatory system with similarity to four-step phosphorelays. Such pathways utilize two histidine and two aspartate residues for signal transduction. Previous studies of the signaling system controlling complementary chromatic adaptation have uncovered two elements of this pathway, a putative sensor, RcaE, and a response regulator, RcaC. In this work, we describe a second response regulator controlling complementary chromatic adaptation, RcaF, and identify putative DNA binding and histidine phosphoacceptor domains within RcaC. RcaF is a small response regulator with similarity to SpoOF of Bacillus subtilis; the latter functions in the four-step phosphorelay system controlling sporulation. We have also determined that within this phosphorelay pathway, RcaE precedes RcaF, and RcaC is probably downstream of RcaE and RcaF. This signal transduction pathway is novel because it appears to use at least five, instead of four, phosphoacceptor domains in the phosphorelay circuit.

NodV and NodW, a second flavonoid recognition system regulating nod gene expression in Bradyrhizobium japonicum

In Bradyrhizobium japonicum, members of two global regulatory families, a LysR-type regulator, NodD1, and a two-component regulatory system, NodVW, positively regulate nod gene expression in response to plant-produced isoflavone signals. By analogy to other two-component systems, NodV and NodW are thought to activate transcription via a series of phosphorylation steps. These include the phosphorylation of NodV in response to the plant signal and the subsequent activation of NodW via the transfer of the phosphoryl group to an aspartate residue in the receiver domain of NodW. In this study, we demonstrated that NodW can be phosphorylated in vitro by both acetyl phosphate and its cognate kinase, NodV. In addition, in vivo experiments indicate that phosphorylation is induced by genistein, a known isoflavone nod gene inducer in B. japonicum. By using site-directed mutagenesis, a NodWD70N mutant in which the aspartate residue at the proposed phosphorylation site was converted to an asparagine residue was generated. This mutant was not phosphorylated in either in vitro or in vivo assays. Comparisons of the biological activity of both the wild-type and mutant proteins indicate that phosphorylation of NodW is essential for the ability of NodW to activate nod gene expression.

NodV and NodW, a second flavonoid recognition system regulating nod gene expression in Bradyrhizobium japonicum

In Bradyrhizobium japonicum, members of two global regulatory families, a LysR-type regulator, NodD1, and a two-component regulatory system, NodVW, positively regulate nod gene expression in response to plant-produced isoflavone signals. By analogy to other two-component systems, NodV and NodW are thought to activate transcription via a series of phosphorylation steps. These include the phosphorylation of NodV in response to the plant signal and the subsequent activation of NodW via the transfer of the phosphoryl group to an aspartate residue in the receiver domain of NodW. In this study, we demonstrated that NodW can be phosphorylated in vitro by both acetyl phosphate and its cognate kinase, NodV. In addition, in vivo experiments indicate that phosphorylation is induced by genistein, a known isoflavone nod gene inducer in B. japonicum. By using site-directed mutagenesis, a NodWD70N mutant in which the aspartate residue at the proposed phosphorylation site was converted to an asparagine residue was generated. This mutant was not phosphorylated in either in vitro or in vivo assays. Comparisons of the biological activity of both the wild-type and mutant proteins indicate that phosphorylation of NodW is essential for the ability of NodW to activate nod gene expression.

Phosphoprotein PII from cyanobacteria--analysis of functional conservation with the PII signal-transduction protein from Escherichia coli

The signal transduction protein PII from Escherichia coli is modified by uridylylation, whereas its counterpart from the cyanobacterium Synechococcus PCC 7942 is phosphorylated at a seryl residue. To elucidate functional conservations between these proteins, we compared the Synechococcus PII protein with the known properties of the E. coli PII protein. Similar to the E. coli protein, Synechococcus PII binds the metabolites 2-oxoglutarate and ATP in a mutually dependent manner. The synergism of ligand binding was analyzed in detail. The ATP-binding site of Synechococcus PII could be labelled with 5'-p-fluorosulfonylbenzoyladenosine. By heterologous expression of the cyanobacterial glnB gene in E. coli we showed that Synechococcus PII can be modified by the E. coli PII uridylyltransferase. The presence of Synechococcus PII prevents signal transduction of E. coli PII to NtrB, presumably by non-functional competition. We therefore propose that the primary function of Synechococcus PII is to sense 2-oxoglutarate, the carbon skeleton required for nitrogen assimilation.

Protein phosphorylation affects binding of the Escherichia coli transcription activator UhpA to the uhpT promoter

Expression of the Escherichia coli sugar phosphate transporter UhpT is induced by extracellular glucose 6-phosphate through a transmembrane signaling process dependent on the sensor kinase UhpB and the UhpT homolog, UhpC. These proteins are thought to regulate the phosphorylation of the transcription activator, UhpA. To examine the effect of protein phosphorylation on the binding of UhpA to target sequences in the uhpT promoter region, the UhpA protein was overexpressed and purified. Purified UhpA was phosphorylated by acetyl phosphate in a reaction that was dependent on Mg2+ and on the presence of aspartate 54, the site of phosphorylation in homologous response regulators. Gel electrophoretic mobility shift and DNase I and hydroxyl radical protection assays showed that UhpA bound specifically to the region of the uhpT promoter extending from -80 to -50 bp, relative to the transcription start site. At higher concentrations of UhpA, binding was extended to the -32 region. Binding to the -64 element exhibited positive cooperativity and was stimulated severalfold by phosphorylation of UhpA, whereas extension to the downstream region was more strongly affected by phosphorylation. The consensus sequences for the high affinity UhpA-binding sites in the -64 element and for the downstream, low affinity sites are proposed. The pattern of in vitro binding by UhpA agreed with the in vivo observations that phosphorylation-independent assembly of the transcription initiation complex can occur at elevated concentrations of UhpA.

The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli

Under anaerobic conditions, especially at low pH, Escherichia coli converts pyruvate to D-lactate by means of an NADH-linked lactate dehydrogenase (LDH). This LDH is present in substantial basal levels under all conditions but increases approximately 10-fold at low pH. The ldhA gene, encoding the fermentative lactate dehydrogenase of E. coli, was cloned using lambda 10E6 of the Kohara collection as the source of DNA. The IdhA gene was subcloned on a 2.8 kb MluI-MluI fragment into a multicopy vector and the region encompassing the gene was sequenced. The IdhA gene of E. coli was highly homologous to genes for other D-lactate-specific dehydrogenases but unrelated to those for the L-lactate-specific enzymes. We constructed a disrupted derivative of the ldhA gene by inserting a kanamycin resistance cassette into the unique KpnI site within the coding region. When transferred to the chromosome, the ldhA::Kan construct abolished the synthesis of the D-LDH completely. When present in high copy number, the ldhA gene was greatly overexpressed, suggesting escape from negative regulation. Cells expressing high levels of the D-LDH grew very poorly, especially in minimal medium. This poor growth was largely counteracted by supplementation with high alanine or pyruvate concentrations, suggesting that excess LDH converts the pyruvate pool to lactate, thus creating a shortage of 3-carbon metabolic intermediates. Using an ldhA-cat gene fusion construct we isolated mutants which no longer showed pH-dependent regulation of the ldhA gene. Some of these appeared to be in the pta gene, which encodes phosphotransacetylase, suggesting the possible involvement of acetyl phosphate in ldhA regulation.

The transcription initiation pathway of sigma 54 mutants that bypass the enhancer protein requirement. Implications for the mechanism of activation

In vitro transcription, DNase I footprinting, and abortive initiation assays were used to characterize transcription using mutant forms of sigma 54 shown previously to bypass certain enhancer requirements in vitro. The holoenzymes containing these sigma mutants produce low levels of open complexes at both the glnAp2 and glnHp2 promoters. The open complexes are unusual in that they are destroyed by heparin. Enhancer protein and ATP convert them into a stable heparin-resistant state. The enhancer response occurs over a similar range of NtrC concentration as occurs with the wild-type holoenzyme, indicating that the activation determinants have been largely preserved within these mutants. One-round transcription assays show that the mutant holoenzymes can be driven to transcribe both promoters without NtrC. The unstable opening induced by these mutations apparently serves as a conduit that can shuttle templates into transcriptionally competent complexes. The results lead to a model in which activation occurs in two steps. First, the enhancer complex overcomes an inhibitory effect of the sigma 54 leucine patch and unlocks the melting activity of the holoenzyme. Second, different sigma 54 determinants are used to drive stabilization of the open complexes, allowing the full transcription potential to be realized.

Complex regulatory activities associated with the histidine kinase PrrB in expression of photosynthesis genes in Rhodobacter sphaeroides 2.4.1

Rhodobacter sphaeroides 2.4.1 synthesizes a specialized photosynthetic membrane upon reduction of the O2 tension below threshold levels. The genes prrB and prrA encode a sensor kinase and a response regulator, respectively, of a two-component regulatory system that presumably is involved in transduction of the signal(s) that monitors alterations in oxygen levels. A third gene, prrC, is also involved in this cascade of events. Previously, we described a mutant form of PrrB, namely, PrrB78 (J. M. Eraso and S. Kaplan, J. Bacteriol. 177:2695-2706, 1995), which results in aerobic expression of the photosynthetic apparatus. Here we examine three mutated forms of the prrB gene that have the potential to encode truncated polypeptides containing the N-terminal 6, 63, or 163 amino acids, respectively. The resulting mutant strains showed residual levels of the light-harvesting spectral complexes and had diminished photosynthetic growth rates at high light intensities with no discernible growth under intermediate or low light conditions. When either lacZ transcriptional fusions or direct mRNA determinations were used to monitor specific photosynthesis gene expression, all the mutant strains showed unexpectedly high levels of gene expression when compared to mutant strains affected in prrA. Conversely, when translational fusions were used to monitor photosynthesis gene expression in these mutant strains, expression of both puc and puf operons was reduced, especially puf expression. In light of these studies and those of the PrrB78 mutant, the data suggest that PrrA can be activated in situ by something other than PrrB, and it also appears that PrrB can function as a negative regulator acting through PrrA. Finally, we consider the role of the Prr regulatory system in the posttranscriptional control of photosynthesis gene expression.

Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters

ArcA protein bearing an amino-terminal, oligohistidine extension has been purified, and its DNA binding activity has been characterized with or without prior incubation with carbamoyl phosphate. Electrophoretic mobility shift assays and DNase I protection assays indicate that where the phosphorylated form of the ArcA protein (ArcA-P) is expected to act as a transcriptional repressor (e.g., of lctPRD and gltA-sdhCDAB), the effect is likely to be mediated by sequestration of cis-controlling transcriptional regulatory elements. In contrast, in the case of cydAB, for which ArcA-P is expected to function as a transcriptional activator, two discrete binding sites have been identified upstream of a known promoter, and activation from these sites is likely to be mediated by a mechanism typical of the type I class of prokaryotic transcriptional activators. An additional ArcA-P binding site has also been located downstream of the known promoter, and a distinct role for this site in the regulation of the cydAB operon during anoxic growth transitions is suggested. These results are discussed within the framework of an overall model of signaling by the Arc two-component signal transduction system in response to changes in aerobiosis.

Involvement of the sensor kinase EnvZ in the in vivo activation of the response-regulator PhoB by acetyl phosphate

Three signalling pathways lead to activation of the phosphate (Pho) regulon by phosphorylation of the response-regulator PhoB in Escherichia coli. One pathway responds to the extracellular inorganic phosphate (PI) level and leads to activation by the Pi sensor kinase, PhoR. The other two pathways are Pi independent and are apparent in the absence of PhoR. One Pi-independent pathway responds to the level of an unknown catabolite and leads to activation by the catabolite regulatory sensor kinase, CreC (originally called PhoM); the other Pi-independent pathway responds to acetyl phosphate and leads to activation by a process requiring acetyl phosphate. Here we show that activation of PhoB by acetyl phosphate can require the sensor kinase EnvZ. Accordingly, we propose that the in vivo activation of PhoB by acetyl phosphate (and perhaps other two-component response-regulators as well) probably always requires a certain kinase that can vary depending upon the growth conditions.

Bacterial defense against aging: role of the Escherichia coli ArcA regulator in gene expression, readjusted energy flux and survival during stasis

Using two-dimensional gel electrophoresis and N-terminal amino acid sequencing analysis, we demonstrate that a mutant of the global regulatory protein ArcA fails to decrease the synthesis of the TCA cycle enzymes malate dehydrogenase, isocitrate dehydrogenase, lipoamide dehydrogenase E3 and succinate dehydrogenase in response to stasis, while the increased production of the glycolysis enzymes phosphoglycerate mutase and pyruvate kinase is unaffected. Microcalorimetric and respiratory measurements show that the continued production of TCA cycle enzymes in the (delta)arcA mutant is manifested as an elevated rate of respiration and total metabolic activity during starvation. The (delta)arcA mutant is severely impaired in surviving prolonged periods of exogenous carbon starvation, a phenotype that can be alleviated by overproducing the superoxide dismutase SodA. In addition, flow cytometry demonstrates that starving (delta)arcA mutant cells, in contrast to wild-type cells, fail to perform reductive division, remain large and contain multiple chromosomal copies. We suggest that the ArcA-dependent reduced production of electron donors and the decreased level and activity of the aerobic respiratory apparatus during growth arrest is an integral part of a defense system aimed at avoiding the damaging effects of oxygen radicals and controlling the rate of utilization of endogenous reserves.

The activation of PhoB by acetylphosphate

PhoB is a response-regulator protein from Escherichia coli that controls an adaptive response to limiting phosphate. It is activated by autophosphorylation of a conserved aspartate residue within its regulatory domain. Its primary phospho-donor is its cognate histidine kinase PhoR; however, it also becomes phosphorylated when incubated with acetylphosphate. To further characterize its activation, PhoB was considered to be an acetylphosphatase whose enzymatic mechanism involves a phospho-enzyme intermediate. The kinetic constants for autophosphorylation were determined using 32P-and fluorescence-based assays and indicated that PhoB has a K(m) for acetylphosphate of between 7 and 8 mM. These constants are not consistent with an in vivo role for acetylphosphate in the normal control of the Pho regulon. In addition, when PhoB was phosphorylated by acetylphosphate it eluted from a high-performance liquid chromatography (HPLC) size-exclusion column in two peaks. The larger form of PhoB eluted from the column in a similar manner to a chemically cross-linked dimer of PhoB. The smaller form of PhoB is a monomer. Phosphorylated PhoB bound pho-box DNA approximately 10 times tighter than PhoB. These observations show that PhoB forms a dimer when phosphorylated and suggest that the characteristics of activated PhoB result from its dimerization.

In vitro reconstitution and characterization of the Rhodobacter capsulatus NtrB and NtrC two-component system

Enhancer-dependent transcription in enteric bacteria depends upon an activator protein that binds DNA far upstream from the promoter and an alternative sigma factor (sigma 54) that binds with the core RNA polymerase at the promoter. In the photosynthetic bacterium Rhodobacter capsulatus, the NtrB and NtrC proteins (RcNtrB and RcNtrC) are putative members of a two-component system that is novel because the enhancer-binding RcNtrC protein activates transcription of sigma 54-independent promoters. To reconstitute this putative two-component system in vitro, the ReNtrB protein was overexpressed in Escherichia coli and purified as a maltose-binding protein fusion (MBP-RcNtrB). MBP-RcNtrB autophosphorylates in vitro to the same steady state level and with the same stability as the Salmonella typhimurium NtrB (StNtrB) protein but at a lower initial rate. MBP-RcNtrB autophosphorylates the S.typhimurium NtrC (St-NtrC) and RcNtrC proteins in vitro. The enteric NtrC protein is also phosphorylated in vivo by RcNtrB because plasmids that encode either RcNtrB or MBP-Rc-NtrB activate transcription of an NtrC-dependent nifL-lacZ fusion. The rate of phosphotransfer to RcNtrC and autophosphatase activity of phosphorylated RcNtrC (RcNtrC---P) are comparable to the StNtrC protein. However, the RcNtrC protein appears to be a specific RcNtrB P phosphatase since RcNtrC is not phosphorylated by small molecular weight phosphate compounds or by the StNtrB protein. RcNtrC forms a dimer in solution, and RcNtrC - P binds the upstream tandem binding sites of the g1nB promoter 4-fold better than the unphos-phorylated RcNtrC protein, presumably due to oligomerization of RcNtrC -P. Therefore, the R. capsulatus NtrB and NtrC proteins form a two-component system similar to other NtrC-like systems, where specific Rc- NtrB phosphotransfer to the RcNtrC protein results in increased oligoinerization at the enhancer but with subsequent activation of a sigma 54-independent promoter.

A phosphotransferase activity of the Bacillus subtilis sporulation protein Spo0F that employs phosphoramidate substrates

Transient phosphorylation at an aspartate residue on the Spo0F protein is a central step in the phosphorelay signal transduction pathway controlling sporulation in Bacilli. The response regulator Spo0F-P is stable to hydrolysis (t1/2 > 24 h at 23 degrees C in the absence of Mg2+), allowing the use of nondenaturing PAGE to separate the phosphorylated and non-phosphorylated forms of Spo0F. Using this novel assay, phosphoramidate containing compounds were found to specifically phosphorylate Spo0F, a reaction that requires the presence of a divalent metal, but mixed phosphate-carboxylate compounds did not act as phospho donors. Rapid hydrolysis of Spo0F-P generated with phosphoramidate by proteins downstream in the phosphorelay (Spo0B and Spo0A) is consistent with phosphorylation at the active site of Spo0F. The initial rate of Spo0F-P formation from phosphoramidate displays Michaelis-Menten kinetics, providing evidence for the proposal that response regulators, such as Spo0F, function as phosphoryl transferase enzymes (McCleary et al., 1993). The results establish that Spo0F functions as a phosphoryl transferase that uses exclusively a phosphoramidate rather than an acyl phosphate as substrate during autophosphorylation.

Dual function of PilS during transcriptional activation of the Pseudomonas aeruginosa pilin subunit gene

The polar pili of Pseudomonas aeruginosa are composed of subunits encoded by the pilA gene. Expression of pilA requires the alternative sigma factor RpoN and a pair of regulatory elements, PilS and PilR. These two proteins are members of the two-component regulatory family, in which PilS is the sensory component and PilR is the response regulator. By using expression and localization analyses, in this work we show that PilS is synthesized as a 59-kDa polypeptide located in the P. aeruginosa cytoplasmic membrane. When the pilS gene is expressed in Escherichia coli, aberrant translational initiation results in a smaller, 40-kDa polypeptide. Unexpectedly, overexpression of pilS in P. aeruginosa results in decreased transcription of the pilA gene. Moreover, fully functional PilS was not required for this inhibitory effect. A mutation in the histidine residue essential for kinase activity resulted in a protein unable to activate transcription, yet when overexpressed in the presence of the wild-type PilS protein, this protein still repressed pilin synthesis. A shorter form of PilS, lacking its transmembrane segments, was active and fully capable of stimulating pilA transcription but when overexpressed did not show the inhibitory effect on pilin expression seen with full-length PilS. We also show that overexpression of pilR can activate transcription of pilA even in the absence of PilS. On the basis of our studies, we propose a complex mechanism of regulation of PilS function, involving other cellular factors that control PilS and its activities during the phosphorelay mechanism of signal transduction.

Phosphorylated BvgA is sufficient for transcriptional activation of virulence-regulated genes in Bordetella pertussis

In Bordetella pertussis the expression of virulence factors is coordinately regulated by the BvgS and BvgA proteins, members of the bacterial two-component signal transduction family, BvgS being the transmembrane sensor and BvgA the regulator. Activation of virulence gene expression requires phosphorylation of BvgA. On the basis of observed differences in the regulation of individual genes, the existence of accessory regulators has been postulated. They were supposed to be necessary for expression of genes encoding adenylate cyclase toxin (cya) and pertussis toxin (ptx), but not required for the expression of fha, encoding filamentous hemagglutinin. To clarify this issue we investigated the mechanism of activation of the BvgAS-controlled genes by performing in vitro run-off transcription experiments. We show, using purified RNA polymerase of B.pertussis, that phosphorylated BvgA is sufficient for transcriptional activation of the major virulence genes, thus providing good evidence that BvgA regulation operates directly with the transcription initiation machinery at the promoters of the virulence genes without a requirement for accessory activators. In addition, our results indicate that activation of the different promoters may involve distinct mechanisms. We suggest that the previously observed differences in regulation of individual virulence-associated genes reflect differences in the phosphorylation state of BvgA.

Nitrogen control in bacteria

Nitrogen metabolism in prokaryotes involves the coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds. The control of this expression is determined by the availability of fixed nitrogen to the cell and is effected by complex regulatory networks involving regulation at both the transcriptional and posttranslational levels. While the most detailed studies to date have been carried out with enteric bacteria, there is a considerable body of evidence to show that the nitrogen regulation (ntr) systems described in the enterics extend to many other genera. Furthermore, as the range of bacteria in which the phenomenon of nitrogen control is examined is being extended, new regulatory mechanisms are also being discovered. In this review, we have attempted to summarize recent research in prokaryotic nitrogen control; to show the ubiquity of the ntr system, at least in gram-negative organisms; and to identify those areas and groups of organisms about which there is much still to learn.

Converting Escherichia coli RNA polymerase into an enhancer-responsive enzyme: role of an NH2-terminal leucine patch in sigma 54

The protein sigma 54 associates with Escherichia coli core RNA polymerase to form a holoenzyme that binds promoters but is inactive in the absence of enhancer activation. Here, mutants of sigma 54 enabled polymerases to transcribe without enhancer protein and adenosine triphosphate. The mutations are in leucines within the NH2-terminal glutamine-rich domain of sigma 54. Multiple leucine substitutions mimicked the effect of enhancer protein, which suggests that the enhancer protein functions to disrupt a leucine patch. The results indicate that sigma 54 acts both as an inhibitor of polymerase activity and as a receptor that interacts with enhancer protein to overcome this inhibition, and that these two activities jointly confer enhancer responsiveness.

Abortive cycling and the release of polymerase for elongation at the sigma 54-dependent glnAp2 promoter

Transcription initiation at the sigma 54-dependent glnAp2 promoter was studied to follow the state of polymerase as RNA synthesis begins. Sigma 54 polymerase begins transcription in abortive cycling mode, i.e. after the first bond is made, approximately 75% of the time the short RNA is aborted and synthesis must be restarted. Polymerase is capable of abortive initiation until it reaches a position beyond +3 and before +7, at which stage polymerase is released from its promoter contacts and an elongation complex is formed. INitial elongation is accompanied by two transcription bubbles, one moving with the polymerase and the other remaining at the transcription start site. The sigma 54-associated polymerase shows an earlier and more efficient transition out of abortive initiation mode than prior studies of sigma 70-associated polymerase.

Activation of transcription initiation from the nac promoter of Klebsiella aerogenes

The nac gene of Klebsiella aerogenes encodes a bifunctional transcription factor that activates or represses the expression of several operons under conditions of nitrogen limitation. In experiments with purified components, transcription from the nac promoter was initiated by sigma 54 RNA polymerase and was activated by the phosphorylated form of nitrogen regulator I (NRI) (NtrC). The activation of the nac promoter required a higher concentration of NRI approximately P than did the activation of the Escherichia coli glnAp2 promoter, and both the promoter and upstream enhancer element contributed to this difference. The nac promoter had a lower affinity for sigma 54 RNA polymerase than did glnAp2, and uninitiated competitor-resistant transcription complexes formed at the nac promoter decayed to competitor-sensitive complexes at a greater rate than did similar complexes formed at the glnAp2 promoter. The nac enhancer, consisting of a single high-affinity NRI-binding site and an adjacent site with low affinity for NRI, was less efficient in stimulating transcription than was the glnA enhancer, which consists of two adjacent high-affinity NRI-binding sites. When these binding sites were exchanged, transcription from the nac promoter was increased and transcription from the glnAp2 promoter was decreased at low concentrations of NRI approximately P. Another indication of the difference in the efficiency of these enhancers is that although activation of a nac promoter construct containing the glnA enhancer was relatively insensitive to subtle alterations in the position of these sites relative to the position of the promoter, activation of the natural nac promoter or a nac promoter construct containing only a single high-affinity NRI approximately P binding site was strongly affected by subtle alterations in the position of the NRI approximately P binding site(s), indicating a face-of-the-helix dependency for activation.

A novel bacterial transcription cycle involving sigma 54

sigma 54 is the promoter recognition subunit of the form of bacterial RNA polymerase that transcribes from promoters with enhancer elements. DNase footprinting experiments show that sigma 54 is attached selectively to the template strand, which must be single-stranded for transcription initiation. sigma 54 remains bound at the promoter after core polymerase begins elongation, in contrast to the well-established sigma 70-holoenzyme transcription cycle. Permanganate footprinting experiments show that the bound sigma 54 and the elongating core RNA polymerase downstream of it are each associated with a single-strand DNA region. Template commitment assays show that the promoter-bound sigma 54 must be reconfigured before reinitiation of transcription can occur. This unexpected pathway raises interesting possibilities for transcriptional regulation, especially with regard to control at the level of reinitiation.

Phosphorylation-dependent conformational changes in OmpR, an osmoregulatory DNA-binding protein of Escherichia coli

Osmoregulated porin gene expression in Escherichia coli is controlled by the two-component regulatory system EnvZ and OmpR. EnvZ, the osmosensor, is an inner membrane protein and a histidine kinase. EnvZ phosphorylates OmpR, a cytoplasmic DNA-binding protein, on an aspartyl residue. Phospho-OmpR binds to the promoters of the porin genes to regulate the expression of ompF and ompC. We describe the use of limited proteolysis by trypsin and ion spray mass spectrometry to characterize phospho-OmpR and the conformational changes that occur upon phosphorylation. Our results are consistent with a two-domain structure for OmpR, an N-terminal phosphorylation domain joined to a C-terminal DNA-binding domain by a flexible linker region. In the presence of acetyl phosphate, OmpR is phosphorylated at only one site. Phosphorylation induces a conformational change that is transmitted to the C-terminal domain via the central linker. Previous genetic analysis identified a region in the C-terminal domain that is required for transcriptional activation. Our results indicate that this region is within a surface-exposed loop. We propose that this loop contacts the alpha subunit of RNA polymerase to activate transcription. Mass spectrometry also reveals an unusual dephosphorylated form of OmpR, the potential significance of which is discussed.

Mechanism of activation of a response regulator: interaction of NtrC-P dimers induces ATPase activity

NtrC is the transcriptional activator for nitrogen-regulated promoters and, as a response regulator, belongs to the protein family of two-component systems. The activity of all response regulators is modulated by phosphorylation of the conserved N-terminal receiver domain. Phosphorylation of the dimeric NtrC has two consequences: (i) a strong increase in the cooperative binding of NtrC to two adjacent binding sites and (ii) activation of NtrC as an ATPase. Here we show that phosphorylation of NtrC is not sufficient for activation of NtrC. At low protein concentrations (50 nM), phosphorylated NtrC was only active as an ATPase upon cooperative binding to DNA. At high protein concentrations (above 50 nM), NtrC was active in the absence of DNA, and activation occurred in parallel with the formation of high-molecular-weight aggregates. We infer that activation of NtrC involves an interaction between two NtrC-P dimers and proceeds in two steps. The first step is the phosphorylation of NtrC. The second step is the interaction between two NtrC-P dimers. This interaction induces the conformational change in NtrC-P to the active conformation.

Autophosphorylation and activation of transcriptional activator PhoB of Escherichia coli by acetyl phosphate in vitro

The PhoB protein, the transcriptional activator for the genes belonging to the phosphate regulon in Escherichia coli, was autophosphorylated in the presence of acetyl phosphate (acP) in vitro. The properties of phospho-PhoB, such as stability upon acid or alkali treatment and activating pstS transcription by RNA polymerase holoenzyme, were the same as those of phospho-PhoB produced from phospho-PhoR or phospho-PhoM. These results indicate that PhoB is an enzyme that catalyzes its own phosphorylation using acP, a low-molecular-weight metabolic intermediate.

Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR

During the search for unknown factors involved in motility, we have found that expression of the flagellar master operon flhDC is affected by mutations of the pta and ackA genes, encoding phosphotransacetylase and acetate kinase, respectively (S. Shin, J. Sheen, and C. Park, Korean J. Microbiol. 31:504-511, 1993). Here we describe results showing that this effect is modulated by externally added acetate, except when both pta and ackA are mutated, suggesting the role of acetyl phosphate, an intermediate of acetate metabolism, as a regulatory effector. Furthermore, the following evidence indicates that the phosphorylation of OmpR, a trans factor for osmoregulation, regulates flagellar expression. First, in a strain lacking ompR, the expression of flhDC is no longer responsive to a change in the level of acetyl phosphate. Second, an increase in medium osmolarity does not decrease flhDC expression in an ompR mutant. It is known that such an increase normally enhances OmpR phosphorylation. Third, OmpR protein binds to the DNA fragment containing the flhDC promoter, and its affinity is increased with phosphorylation by acetyl phosphate. DNase I footprinting revealed the regions of the flhDC promoter protected by OmpR in the presence or absence of phosphorylation. Therefore, we propose that the phosphorylated OmpR, generated by either osmolarity change or the internal level of acetyl phosphate, negatively regulates the expression of flagella.

The Escherichia coli PII signal transduction protein is activated upon binding 2-ketoglutarate and ATP

Nitrogen regulation of transcription in Escherichia coli requires sensation of the intracellular nitrogen status and control of the dephosphorylation of the transcriptional activator NRI-P. This dephosphorylation is catalyzed by the bifunctional kinase/phosphatase NRII in the presence of the dissociable PII protein. The ability of PII to stimulate the phosphatase activity of NRII is regulated by a signal transducing uridylyltransferase/uridylyl-removing enzyme (UTase/UR), which converts PII to PII-UMP under conditions of nitrogen starvation; this modification prevents PII from stimulating the dephosphorylation of NRI approximately P. We used purified components to examine the binding of small molecules to PII, the effect of small molecules on the stimulation of the NRII phosphatase activity by PII, the retention of PII on immobilized NRII, and the regulation of the uridylylation of PII by the UTase/UR enzyme. Our results indicate that PII is activated upon binding ATP and either 2-ketoglutarate or glutamate, and that the liganded form of PII binds much better to immobilized NRII. We also demonstrate that the concentration of glutamine required to inhibit the uridylyltransferase activity is independent of the concentration of 2-ketoglutarate present. We hypothesize that nitrogen sensation in E. coli involves the separate measurement of glutamine by the UTase/UR protein and 2-ketoglutarate by the PII protein.

Glutamine synthetase/glutamate synthase ammonium-assimilating pathway in Schizosaccharomyces pombe

Kinetic parameters of glutamine synthetase (GS) and glutamate synthase (glutamine-oxoglutarate aminotransferase) (GOGAT) activities, including initial velocity, pH, and temperature optima, as well as Km values, were estimated in Schizosaccharomyces pombe crude cell-free extracts. Five glutamine auxotrophic mutants of S. pombe were isolated following MNNG treatment. These were designated gln1-1,2,3,4,5, and their growth could be repaired only by glutamine. Mutants gln1-1,2,3,4,5 were found to lack GS activity, but retained wild-type levels of NADP-glutamate dehydrogenase (GDH), NAD-GDH, and GOGAT. One further glutamine auxotrophic mutant, gln1-6, was isolated and found to lack both GS and GOGAT but retained wild-type levels of NADP-GDH and NAD-GDH activities. Fortuitously, this isolate was found to harbor an unlinked second mutation (designated gog1-1), which resulted in complete loss of GOGAT activity but retained wild-type GS activity. The growth phenotype of mutant gog1-1 (in the absence of the gln1-6 mutation) was found to be indistinguishable from the wild type on various nitrogen sources, including ammonium as a sole nitrogen source. Double-mutant strains containing gog1-1 and gdh1-1 or gdh2-1 (mutations that result specifically in the abolition of NADP-GDH activity) result in a complete lack of growth on ammonium as sole nitrogen source in contrast to gdh or gog mutants alone.

The nitrogen assimilation control protein, NAC, is a DNA binding transcription activator in Klebsiella aerogenes

A 32-kDa polypeptide corresponding to NAC, the product of the Klebsiella aerogenes nac gene, was overexpressed from a plasmid carrying a tac'-'nac operon fusion and purified to near homogeneity by taking advantage of its unusual solubility properties. NAC was able to shift the electrophoretic migration of DNA fragments carrying the NAC-sensitive promoters hutUp, putPp1, and ureDp. The interaction between NAC and hutUp was localized to a 26-bp region centered approximately 64 bp upstream of the hutUp transcription initiation site. Moreover, NAC protected this region from DNase I digestion. Mobility shift and DNase I protection studies utilizing the putP and ureD promoter regions identified NAC-binding regions of sizes and locations similar to those found in hutUp. Comparison of the DNA sequences which were protected from DNase I digestion by NAC suggests a minimal NAC-binding consensus sequence: 5'-ATA-N9-TAT-3'. In vitro transcription assays demonstrated that NAC was capable of activating the transcription of hutUp by sigma 70-RNA polymerase holoenzyme when this promoter was presented as either a linear or supercoiled DNA molecule. Thus, NAC displays the in vitro DNA-binding and transcription activation properties which have been predicted for the product of the nac gene.

Active contribution of two domains to cooperative DNA binding of the enhancer-binding protein nitrogen regulator I (NtrC) of Escherichia coli: stimulation by phosphorylation and the binding of ATP

Activation by the prokaryotic activator nitrogen regulator I (NRI, or NtrC) of Escherichia coli requires an interaction between two NRI dimers. ATP-dependent phosphorylation stimulates this tetramerization, which can be detected as cooperative binding to DNA. A polypeptide containing only the DNA-binding carboxyl-terminal domain has been previously shown to bind noncooperatively to DNA. Our primary purpose was to determine whether the highly conserved N-terminal domain or the ATP-binding central domain is required for cooperative DNA binding. Because ATP was present in the experiments that showed that phosphorylation enhances cooperative bindings, it is possible that ATP and not phosphorylation stimulated cooperative binding. Our secondary purpose was to separately assess the effects of ATP and phosphorylation on cooperative binding. We showed that a variant with a deletion of the central domain, NRI-(delta 143-398), binds cooperatively as well as unphosphorylated wild-type NRI, implying that the N-terminal domain mediates phosphorylation-independent cooperative binding. Phosphorylation of NRI-(delta 143-398) did not further stimulate this binding, suggesting that the ATP-binding central domain may be required for the phosphorylation-dependent enhancement. Cooperative binding was enhanced by either acetyl-phosphate-dependent (i.e., ATP-independent) phosphorylation of NRI or the specific binding of ATP to the central domain. Their effects were not additive, a finding which is consistent with the interpretation that each promotes a similar dimer-dimer interaction. We discuss these results within the context of the hypothesis that the highly conserved N-terminal domain mediates phosphorylation-independent cooperativity and the central domain is required for cooperativity stimulated by ATP binding or phosphorylation.

Effector-mediated stimulation of ATPase activity by the sigma 54-dependent transcriptional activator FHLA from Escherichia coli

The FHLA protein is the transcriptional regulator of the genes of the formate regulon from Escherichia coli. The protein shares homology with the sigma 54-dependent regulators of the NTRC family in the central and C-terminal domains but differs in possessing an extended N terminus lacking the aspartate residue which is the site of phosphorylation. Purified FHLA displays intrinsic ATPase activity which is stimulated weakly by formate and DNA. The presence of both formate and DNA carrying the upstream regulatory sequence to which FHLA binds leads to a large increase in the rate of ATP hydrolysis. Hypophosphite, a structural analog of formate, and azide, a transition state analog of formate, also stimulate ATPase activity, supporting the conclusion that formate is a direct ligand of FHLA. Half-maximal saturation of FHLA with formate took place at around 5 mM, and half-maximal saturation with target DNA took place at around 50 nM. The stimulation of ATPase activity by formate was conferred by a decrease in the apparent Km for ATP, whereas the effect of the DNA binding site also affected the Kcat of the reaction. The other nucleoside triphosphates, GTP, UTP, and CTP, competed with ATP cleavage by FHLA, suggesting at least their binding to FHLA. The specific ATPase activity of FHLA was dependent on the concentration of FHLA in the assay, especially in the presence of DNA and formate. Direct liganding of the effector, therefore, leads to the same consequence as phosphorylation for the NTRC-type regulators, namely, stimulation of ATPase activity.

A carbon starvation survival gene of Pseudomonas putida is regulated by sigma 54

By using mini-Tn5 transposon mutagenesis, two mutants of Pseudomonas putida ATCC 12633 were isolated which showed a marked increase in their sensitivity to carbon starvation; these mutants are presumably affected in the Pex type of proteins that P. putida induces upon carbon starvation (M. Givskov, L. Eberl, and S. Molin, J. Bacteriol. 176:4816-4824, 1994). The affected genes in our mutants were induced about threefold upon carbon starvation. The promoter region of the starvation gene in the mutant MK107 possessed a strong sigma 54-type-promoter sequence, and deletion analysis suggested that this was the major promoter regulating expression; this was confirmed by transcript mapping in rpoN+ and rpoN mutant backgrounds. The deletion analysis implicated a sequence upstream of the sigma 54 promoter, as well as a region downstream of the transcription start site, in the functioning of the promoter. Two sigma 70-type Pribnow boxes were also detected in the promoter region, but their transcriptional activity in the wild type was very weak. However, in a sigma 54-deficient background, these promoters became stronger. The mechanism and possible physiological role of this phenomenon and the possibility that the sequence upstream of the sigma 54 promoter may have a role in carbon sensing are discussed.

Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains

In the presence of toluene, xylenes and other structural analogues, the regulatory protein XylR, of the family of transcriptional regulators which act in concert with the sigma 54 factor, activate the promoter Pu of the TOL (toluene degradation) plasmid pWWO of Pseudomonas putida. Amino acid changes Val-219-Asp and Ala-220-Pro, introducing a proline kink at the hinge region between the N-terminal A domain and the central portion of XylR, resulted in a semi-constitutive phenotype which mimicked the activating effect of aromatic inducers. This phenotype was further exacerbated by inserting extra amino acid residues within the same inter-domain region. A truncated XylR protein devoid of the signal-receiving, amino-terminal portion of the protein stimulated the cognate promoter Pu at high levels independently of inducer addition, both in Escherichia coli and in Pseudomonas putida. Replacement of the amino-terminal domain by a heterologous peptide derived from the MS2 virus polymerase resulted in a hybrid protein still able to bind DNA to the same extent in vivo as XylR, but unable to stimulate transcription. These data indicate that a key event in the activation of XylR by toluene/xylenes is the release of the repression caused by the A domain of the protein on surfaces located at the central domain of the regulator.

A sequence-induced superhelical DNA segment serves as transcriptional enhancer

The initiation of transcription at the sigma 54-dependent promoter glnAp2 of Escherichia coli is activated by the protein NR1(NTRC)-phosphate, which binds to two sites located upstream of the promoter that together constitute an enhancer. The cooperative binding facilitates the oligomerization of NR1-phosphate endowing it with the ATPase activity required for its ability to serve as transcriptional activator. We show here that these sites can be replaced by sequence-dependent superhelical inserts, lacking any homology to the nucleotide sequence of the enhancers. These superhelical inserts, irrespective of their chirality, are as effective as the paired sites in binding NR1-phosphate and in stimulating its oligomerization. We conclude that a specific sequence of nucleotides and the three-dimensional structure of DNA can determine its affinity for the NR1 activator protein capable of binding to DNA.

Activation of the dephosphorylation of nitrogen regulator I-phosphate of Escherichia coli

The transcription of sigma 54 RNA polymerase-dependent nitrogen-regulated genes is activated by nitrogen regulator I (NRI)-phosphate. The kinase NRII is responsible for the phosphorylation of NRI. It has been shown that NRII also has the ability to dephosphorylate NRI-phosphate but only when PII is present at a concentration greatly in excess of that of NRII. We have now shown that glutamate enables PII to stimulate the dephosphorylation of NRI-phosphate when present in equimolar concentration with NRII. This effect of glutamate appears to be a backup control that becomes effective when the normal regulation of PII activity is disabled.

Phosphorylation and functional analysis of PilA, a protein involved in the transcriptional regulation of the pilin gene in Neisseria gonorrhoeae

The transcriptional regulation of the pilE gene, coding for the pilin in Neisseria gonorrhoeae, by PilA/PilB proteins is quite complex. Sequence analysis of PilA suggested that it has multiple domains. PilA appears to have in its N-terminal half a DNA-binding site followed by a region showing sequence similarity with other bacterial transcriptional regulators. In its C-terminal half, PilA has extensive homology with the 54 kDa protein of the eukaryotic signal-recognition particle which is involved in protein secretion. A transcriptional fusion between the promoter of pilE and the lacZ gene was constructed and integrated into the gonococcal chromosome. We show that transcription of the pilE-lacZ fusion is affected in pilA mutants in the absence of any possible interference with pilin secretion. Moreover, pilE transcription depends on a -24/-12-type promoter which could be a member of a family of promoters recognized by the alternative sigma subunit, RpoN, of the RNA polymerase. We also show that PilA binds specifically to the promoter region of pilE and that it is phosphorylated in a manner dependent on acidic residues Glu-59, Asp-149 and Asp-186. The functional organization of PilA suggests that it may be an unusual transcriptional regulator different from other RpoN-dependent activators.

Preliminary X-ray diffraction analysis of crystals of the PII protein from Escherichia coli

PII protein, which carries metabolic signals regulating the transcription and activity of glutamine synthetase in nitrogen assimilation in Escherichia coli, has been crystallized in space group P2(1) with a = 47.8 A, b = 62.9 A, c = 52.8 A and beta = 100.3 degrees and space group P2(1)2(1)2(1) with a = 52.2 A. b = 64.9 A and c = 100.1 A. Both the monoclinic crystals, which diffract beyond 3.0 A, and the orthorhombic crystals, which diffract beyond 2.5 A, probably have three molecules of 12,400 Da each in the crystallographic asymmetric unit.

NarL-phosphate must bind to multiple upstream sites to activate transcription from the narG promoter of Escherichia coli

The stimulation of Fnr-dependent transcription from the narG promoter by NarL-phosphate is known to require a cis-acting sequence, the NarL box, located approximately 195 bp upstream from the transcription start site, and the interaction of integration host factor (IHF) with a binding site in the intervening region (positions -110 to -140) between the NarL box and the transcription start site. By gel retardation and DNase I protection studies, we have demonstrated that NarL-phosphate, produced by the reaction of purified NarL with acetyl phosphate, specifically binds to a fragment derived from the upstream region of the narG promoter. The fragment was protected by NarL-phosphate binding to two distinct regions. One was an extended sequence of approximately 40 bp surrounding the NarL box at -195; the second was located downstream from the IHF-binding region and included a sequence extending from positions -80 to -120. Alteration by site-directed mutagenesis of a putative inverted NarL box sequence identified within the downstream protected region in a plasmid containing a narG-lacZ fusion eliminated the NarL-phosphate-mediated stimulation of transcription. NarL-phosphate bound to the two regions independently from IHF binding and it bound to each site independently when the two sites were separated by cleavage of the promoter fragment. Stimulation of transcription from the narG promoter by NarL-phosphate appears to result from the formation of a folded protein-DNA structure created by the binding of NarL-phosphate to multiple sites on either side of an IHF-induced bend in the upstream region of the promoter.

Nucleotide sequence of the phosphotransacetylase gene of Escherichia coli strain K12

The phosphotransacetylase gene (pta) from Escherichia coli strain K-12 1100 was identified in a cloned fragment of chromosomal DNA (Yamamoto-Otake, H., Matsuyama, A. and Nakano, A. (1990) Appl. Microbiol. Biotechnol. 33, 680-682). Overexpression in E. coli confirmed the presence of the pta gene within the cloned fragment. DNA sequence analysis of the cloned pta gene indicates that the predicted phosphotransacetylase polypeptide chain is 713 amino acids in length. The carboxyterminal region of the E. coli phosphotransacetylase shows 42.6% sequence identity with the corresponding enzyme from Methanosarcina thermophila (142 out of 333 residues in corresponding positions are identical). Several short regions of high sequence identity may be structurally or functionally important for enzymic activity.

Multiple copies of the proB gene enhance degS-dependent extracellular protease production in Bacillus subtilis

Bacillus subtilis secretes extracellular proteases whose production is positively regulated by a two-component regulatory system, DegS-DegU, and other regulatory factors including DegR. To identify an additional regulatory gene(s) for exoprotease production, we performed a shotgun cloning in the cell carrying multiple copies of degR and found a transformant producing large amounts of the exoproteases. The plasmid in this transformant, pLC1, showed a synergistic effect with multiple copies of degR on the production of the extracellular proteases, and it required degS for its enhancing effect. The DNA region responsible for the enhancement contained the proB gene, as shown by restriction analyses and sequence determination. The proB gene encoding gamma-glutamyl kinase was followed by the proA gene encoding glutamyl-gamma-semialdehyde dehydrogenase at an interval of 39 nucleotides, suggesting that the genes constitute an operon. pLC1 contained the complete proB gene and a part of proA lacking the proA C-terminal region. It was also found that proB on the chromosome showed a synergistic effect with multiple copies of degR. We consider on the basis of these results that the metabolic intermediate, gamma-glutamyl phosphate, would transmit a signal to DegS, resulting in a higher level of phosphorylated DegU. Possible involvement of DegR in this process is discussed.

The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli

The leucine-responsive regulatory protein (Lrp) regulates the expression of more than 40 genes and proteins in Escherichia coli. Among the operons that are positively regulated by Lrp are operons involved in amino acid biosynthesis (ilvIH, serA)), in the biosynthesis of pili (pap, fan, fim), and in the assimilation of ammonia (glnA, gltBD). Negatively regulated operons include operons involved in amino acid catabolism (sdaA, tdh) and peptide transport (opp) and the operon coding for Lrp itself (lrp). Detailed studies of a few members of the regulon have shown that Lrp can act directly to activate or repress transcription of target operons. A substantial fraction of operons regulated by Lrp are also regulated by leucine, and the effect of leucine on expression of these operons requires a functional Lrp protein. The patterns of regulation are surprising and interesting: in some cases activation or repression mediated by Lrp is antagonized by leucine, in other cases Lrp-mediated activation or repression is potentiated by leucine, and in still other cases leucine has no effect on Lrp-mediated regulation. Current research is just beginning to elucidate the detailed mechanisms by which Lrp can mediate such a broad spectrum of regulatory effects. Our view of the role of Lrp in metabolism may change as more members of the regulon are identified and their regulation characterized, but at this point Lrp seems to be important in regulating nitrogen metabolism and one-carbon metabolism, permitting adaptations to feast and to famine.

Why does Escherichia coli have two primary pathways for synthesis of glutamate?

Escherichia coli has two primary pathways for glutamate synthetase-glutamate synthase pathway is known to be essential for synthesis at low ammonium concentrations and for regulation of the glutamine pool, but the necessity for glutamate dehydrogenase (GDH) has been uncertain. The results of competition experiments between the wild type and a GDH-deficient mutant during nutrient-limited growth and of direct enzyme measurements suggest that GDH is used in glutamate synthesis when the cell is limited for energy (and carbon) but ammonium and phosphate are present in excess, while the glutamine synthetase-glutamate synthase pathway is used when the cell is not under energy limitation. The use of alternative routes for glutamate synthesis implies that the energy cost of biosynthesis may be less when energy is limited than when energy is unlimited.

Chemosensing and signal transduction in bacteria

Major advances have been made over the past year in understanding the molecular mechanisms involved in membrane receptor function, and in resolving the global organization of intracellular signaling pathways. Crystallographic and biochemical studies are revealing details of transmembrane signaling mechanisms and the phosphorylation reactions of the two-component regulatory systems. In addition, the discovery of new signal transduction pathways and new inputs into known pathways are providing a clearer view of the basic architecture of the signal transduction networks within the bacterial cell.