Overlapping and separate controls on the phosphate regulon in Escherichia coli K12

Diversity in Starvation Survival Strategies and Outcomes among Heterotrophic Proteobacteria

Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial symbionts of plants and animals, and as ubiquitous organisms found free-living in many environments. Succeeding in these niches requires an ability to persist for potentially long periods of time in growth-arrested states when essential nutrients become limiting. The tendency of these bacteria to grow in dense biofilm communities frequently leads to the development of steep nutrient gradients and deprivation of interior cells even when the environment is nutrient rich. Surviving within host environments also likely requires tolerating growth arrest due to the host limiting access to nutrients and transitioning between hosts may require a period of survival in a nutrient-poor environment. Interventions to maximise plant-beneficial activities and minimise infections by bacteria will require a better understanding of metabolic and regulatory networks that contribute to starvation survival, and how these networks function in diverse organisms. Here we focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity. We first review models for studying bacterial starvation and known strategies that contribute to starvation survival. We then present the results of a survey of carbon starvation survival strategies and outcomes in ten bacterial strains, including representatives from the orders Enterobacterales and Pseudomonadales (both Gammaproteobacteria) and Burkholderiales (Betaproteobacteria). Finally, we examine differences in gene content between the highest and lowest survivors to identify metabolic and regulatory adaptations that may contribute to differences in starvation survival.

Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution

Neutral drift occurring over millions or billions of years results in substantial sequence divergence among enzymes that catalyze the same reaction. Although natural selection maintains the primary activity of orthologous enzymes, there is, by definition, no selective pressure to maintain physiologically irrelevant promiscuous activities. Thus, the levels and the evolvabilities of promiscuous activities may vary among orthologous enzymes. Consistent with this expectation, we have found that the levels of a promiscuous activity in nine gamma-glutamyl phosphate reductase (ProA) orthologs vary by about 50-fold. Remarkably, a single amino acid change from Glu to Ala near the active site appeared to be critical for improvement of the promiscuous activity in every ortholog. The effects of this change varied dramatically. The improvement in the promiscuous activity varied from 50- to 770-fold, and, importantly, was not correlated with the initial level of the promiscuous activity. The decrease in the original activity varied from 190- to 2,100-fold. These results suggest that evolution of a novel enzyme may be possible in some microbes, but not in others. Further, these results underscore the importance of using multiple orthologs as starting points for directed evolution of novel enzyme activities.

Induction of the Pho regulon suppresses the growth defect of an Escherichia coli sgrS mutant, connecting phosphate metabolism to the glucose-phosphate stress response

Some bacteria experience stress when glucose-6-phosphate or analogues like α-methyl glucoside-6-phosphate (αMG6P) accumulate in the cell. In Escherichia coli, the small SgrS RNA is vital to recovery from glucose-phosphate stress; the growth of sgrS mutants is strongly inhibited by αMG. SgrS helps to restore growth in part through inhibiting translation of the ptsG mRNA, which encodes the major glucose transporter EIICB(Glc). While the regulatory mechanism of SgrS has been characterized, little is known about how glucose-phosphate stress connects to other aspects of cell physiology. In the present study, we discovered that mutation of pitA, which encodes the low-affinity transporter of inorganic phosphate, partially suppresses the αMG growth defect of an sgrS mutant. Induction of the stress response was also reduced in the sgrS pitA mutant compared to its sgrS parent. Microarray analysis suggested that expression of phosphate (Pho) regulon genes is increased in the sgrS pitA mutant compared to the sgrS parent. Consistent with this, we found increased PhoA (alkaline phosphatase) activity in the sgrS pitA mutant compared to the sgrS strain. Further, direct induction of the Pho regulon (in a pitA(+) background) also resulted in partial suppression of the sgrS growth defect. The suppression was reversed when Pho induction was prevented by mutation of phoB, which encodes the Pho transcriptional activator. Deletion of individual Pho structural genes in suppressed strains did not identify a single gene responsible for suppression. Altogether, this work describes one of the first studies of glucose-phosphate stress physiology and suggests a novel connection of carbon and phosphate metabolism.

Bacterial solubilization of mineral phosphates: Historical perspective and future prospects

Maximum crop yields require sufficient phosphorus fertilization. Only phosphate in a soluble ionic form (Pi) is effective as a mineral nutrient. Current fertilizer technology supplies the soil solution with Pi via the application of large amounts of phosphate salts. Problems with this technology include energy-intensive production processes, the need for large scale mechanical application with associated environmental consequences, and reprecipitation of the phosphate into insoluble mineral complexes. It has been estimated that in some soils up to 75% of applied phosphate fertilizer may be lost to the plant because of mineral phase reprecipitation. Many approaches, ranging from cultural practices to biological inoculants such as mycorrhizal fungi, are being employed to enhance P-use efficiency. One area that is currently under-investigated is the ability of certain types of bacteria to solubilize mineral and organic phosphates. A review of the literature in the area of bacterial phosphate solubilization confirms that this trait is displayed by a wide range of bacteria. The phosphate starvation inducible (PSI) organic phosphate-solubilizing capability of E. coli is a component of a coordinately regulated gene system: the pho regulon. It has long been known that bacteria are also capable of solubilizing mineral phosphates such as hydroxyapatite. To date there has been no systematic study of the genetics of this phenomenon. Data from my laboratory indicate that the bacterial mineral phosphate-solubilizing (MPS) trait is regulated by the external level of Pi This conclusion is supported by results obtained from several types of molecular genetic studies. It is proposed that bacteria have mineral phosphate solubilizing (mps) genes. The potential agronomic applications of bacterial mineral and organic P solubilizing systems are discussed.

Uptake of glycerol-2-phosphate via the ugp-encoded transporter in Escherichia coli K-12

During phenotypic characterization of various Escherichia coli mutants, we observed that DeltaphoA strains are capable of using glycerol-2-phosphate (G2P) as a sole source of phosphorus. Mutations in the ugpBAECQ operon eliminated this phenotype, suggesting that G2P is a previously unrecognized substrate for the binding protein-dependent Ugp transporter.

Identification of the sequences recognized by the Bacillus subtilis response regulator YrkP

The Bacillus subtilis yrkP gene encodes a response regulator of a two-component regulatory system of unknown function. A previous DNA microarray experiment suggested that multicopy yrkP greatly enhanced the expression of yrkN, the ykcBC operon, and yrkO, which encodes a putative transporter. Here, lacZ fusion analysis confirmed these results and also revealed that YrkP autoregulates the putative yrkPQR operon, indicating that yrkPQR and yrkO form a divergon structure. In addition, real-time PCR analysis revealed that transcription of yrkO, yrkN, and ykcBC was significantly reduced in the yrkP strain. Hence, YrkP positively regulates the expression of these genes. Gel retardation analyses showed that YrkP bound to the promoter regions of yrkO, yrkN, and ykcB, albeit with lower binding affinities to the latter two promoters. The in vitro binding of YrkP to the promoter region of the yrkPQR and yrkO divergon was then analyzed by DNase I footprinting analysis. This revealed that YrkP recognizes three regions containing single-motifs or a direct repeat of the ten-base sequence [T/G]TCA[T/C]AAATT. lacZ fusion analysis of deleted and mutagenized promoter regions of yrkO and yrkPQR divergon confirmed that the three YrkP-binding regions are needed for the YrkP-mediated activation of yrkO and/or yrkPQR.

Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli

Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap the gyrase molecule at the DNA cleavage stage. Owing to this interaction, double-stranded DNA breaks are introduced and replication machinery is arrested at blocked replication forks. This immediately results in bacteriostasis and ultimately induces cell death. Here we demonstrate, through a series of phenotypic and gene expression analyses, that superoxide and hydroxyl radical oxidative species are generated following gyrase poisoning and play an important role in cell killing by gyrase inhibitors. We show that superoxide-mediated oxidation of iron–sulfur clusters promotes a breakdown of iron regulatory dynamics; in turn, iron misregulation drives the generation of highly destructive hydroxyl radicals via the Fenton reaction. Importantly, our data reveal that blockage of hydroxyl radical formation increases the survival of gyrase-poisoned cells. Together, this series of biochemical reactions appears to compose a maladaptive response, that serves to amplify the primary effect of gyrase inhibition by oxidatively damaging DNA, proteins and lipids.

Interdomain linkers of homologous response regulators determine their mechanism of action

OmpR and PhoB are response regulators that contain an N-terminal phosphorylation domain and a C-terminal DNA binding effector domain connected by a flexible interdomain linker. Phosphorylation of the N terminus results in an increase in affinity for specific DNA and the subsequent regulation of gene expression. Despite their sequence and structural similarity, OmpR and PhoB employ different mechanisms to regulate their effector domains. Phosphorylation of OmpR in the N terminus stimulates the DNA binding affinity of the C terminus, whereas phosphorylation of the PhoB N terminus relieves inhibition of the C terminus, enabling it to bind to DNA. Chimeras between OmpR and PhoB containing either interdomain linker were constructed to explore the basis of the differences in their activation mechanisms. Our results indicate that effector domain regulation by either N terminus requires its cognate interdomain linker. In addition, our findings suggest that the isolated C terminus of OmpR is not sufficient for a productive interaction with RNA polymerase.

Cloning and expression of the phosphotriesterase gene hocA from Pseudomonas monteilii C11

The cloning of a gene encoding the novel phosphotriesterase from Pseudomonas monteilii C11, which enabled it to use the organophosphate (OP) coroxon as its sole phosphorus source, is described. The gene, called hocA (hydrolysis of coroxon) consists of 501 bp and encodes a protein of 19 kDa. This protein had no sequence similarity to any proteins in the SWISS-PROT/GenBank databases. When a spectinomycin-resistance cassette was placed in this gene, phosphotriesterase activity was abolished and P. monteilii C11 could no longer grow with coroxon as the sole phosphorus source. Overexpression and purification of HocA as a maltose-binding protein fusion produced a protein having a broad substrate specificity across oxon and thion OPs. Michaelis-Menten kinetics were observed with the oxon OPs, but not with the thion OPs. End-product inhibition was observed for coroxon-hydrolytic activity. Increased expression of hocA was observed from an integrative hocA-lacZ fusion when cultures were grown in the absence of phosphate, suggesting that it might be part of the Pho regulon, but the phosphate-regulated promoter was not cloned in this study. This is believed to be the first study in which a gene required for an organism to grow with OP pesticides as a phosphorus source has been isolated.

Isolation of a Pseudomonas monteilli strain with a novel phosphotriesterase

A Pseudomonas monteilli strain (designated C11) that uses the phosphotriester coroxon as its sole phosphorus source has been isolated. Native PAGE and activity staining identified a single isozyme with significant phosphotriesterase activity in the soluble fraction of the cell. This phosphotriesterase could hydrolyse both coumaphos and coroxon. The hydrolysis product of coroxon, diethylphosphate, and the thion analogue, coumaphos, could not serve as phosphorus sources when added to the growth medium. The majority of the phosphotriesterase and phosphatase activity was contained in the soluble fraction of the cell. Phosphatase activity was inhibited by vanadate as well as by dialysis against the metal chelator, EDTA. Phosphotriesterase activity was not affected by either vanadate or dialysis with EDTA or 1,10-phenanthroline. Phosphotriesterase activity was regulated by the amounts of both phosphate and coroxon in the medium, whereas total phosphatase activity was regulated by phosphate but not coroxon. A lack of hybridisation using a probe against the opd (organophosphate degradation) gene encoding a phosphotriesterase from Flavobacterium sp. ATCC27551 against bulk DNA from P. monteilli C11 suggested that this strain does not contain opd. The work presented here indicates the presence of a novel phosphotriesterase in P. monteilli C11.

Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria

We have developed a series of powerful and versatile conditional-replication, integration, and modular (CRIM) plasmids. CRIM plasmids can be replicated at medium or high copy numbers in different hosts for making gene (or mutant) libraries. They can be integrated in single copies into the chromosomes of Escherichia coli and related bacteria to study gene function under normal physiological conditions. They can be excised from the chromosome, e.g., to verify that phenotypes are caused by their presence. Furthermore, they can be retrieved singly or en masse for subsequent molecular analyses. CRIM plasmids are integrated into the chromosome by site-specific recombination at one of five different phage attachment sites. Integrants are selected as antibiotic-resistant transformations. Since CRIM plasmids encode different forms of resistance, several can be used together in the same cell for stable expression of complex metabolic or regulatory pathways from diverse sources. Following integration, integrants are stably maintained in the absence of antibiotic selection. Each CRIM plasmid has a polylinker or one of several promoters for ectopic expression of the inserted DNA. Their modular design allows easy construction of new variants with different combinations of features. We also report a series of easily curable, low-copy-number helper plasmids encoding all the requisite Int proteins alone or with the respective Xis protein. These helper plasmids facilitate integration, excision ("curing"), or retrieval of the CRIM plasmids.

Dual transcriptional regulation of the Escherichia coli phosphate-starvation-inducible psiE gene of the phosphate regulon by PhoB and the cyclic AMP (cAMP)-cAMP receptor protein complex

We have shown that the Escherichia coli phosphate-starvation-inducible psiE gene is regulated by both phosphate and the carbon source by using both lacZ and chloramphenicol acetyltransferase gene (cat) fusions. Yet, under all conditions tested, a single transcriptional start site lying 7 bp downstream of a predicted -10 region was revealed by primer extension analysis. DNase I footprinting showed that the PhoB transcriptional-activator protein protects two predicted pho boxes lying upstream of and near the -35 promoter region. Similar analysis showed that the cyclic AMP (cAMP)-cAMP receptor protein (cAMP-CRP) complex binds a region that overlaps with the downstream pho box. These results, together with measurements of the in vivo psiE promoter activity under various conditions, show that expression of the psiE gene is under direct positive and negative control by PhoB and cAMP-CRP, respectively.

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage lambda Red recombinase, which is synthesized under the control of an inducible promoter on an easily curable, low copy number plasmid. To demonstrate the utility of this approach, we generated PCR products by using primers with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites. By using the respective PCR products, we made 13 different disruptions of chromosomal genes. Mutants of the arcB, cyaA, lacZYA, ompR-envZ, phnR, pstB, pstCA, pstS, pstSCAB-phoU, recA, and torSTRCAD genes or operons were isolated as antibiotic-resistant colonies after the introduction into bacteria carrying a Red expression plasmid of synthetic (PCR-generated) DNA. The resistance genes were then eliminated by using a helper plasmid encoding the FLP recombinase which is also easily curable. This procedure should be widely useful, especially in genome analysis of E. coli and other bacteria because the procedure can be done in wild-type cells.

Hyperalkaline and thermostable phosphatase in Thermus thermophilus

The phosphatases existing in the extreme thermophilic bacterium Thermus thermophilus have been studied. Utilizing ion exchange, hydrophobic, pseudoaffinity, and affinity chromatography, a number of distinct phosphatase activities were identified. At least four phosphatases, with optimum pH ranging between 5.0 and 11.5, were assayed with p-nitrophenylphosphate, and two with optimum pH between 7.0 and 11.0, with 32P-casein as substrate. The authors have focused on the hyperalkaline phosphatase and have tried to purify and characterize it. This hyperalkaline phosphatase reaches a maximal level at the stationary phase of the growth, and is co-purified with alkaline phosphatase with optimum pH of 10.2. The enzymes present a relative mol wt of 65 and 58 kDa, respectively, as judged by SDS-PAGE and Sephadex G-150 column, and possess similar properties, indicating that they are isoforms. These enzymes barely function in the presence of tartrate, and are inhibited by EDTA, pyrophosphate, and molybdate. Among the metals tested, Hg2+ appeared as the strongest inhibitor of the hyperalkaline phosphatase. The two enzymes are thermostable and, upon treatment at 90 degrees C for 10 min, 75% of their activity remains. The physiological role and function of these phosphatases need further investigation.

Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon

Escherichia coli genes regulated by environmental inorganic phosphate (Pi) levels form the phosphate (Pho) regulon. This regulation requires seven proteins, whose synthesis is under autogenous control, including response regulator PhoB, its partner, histidine sensor kinase PhoR, all four components of the Pi-specific transport (Pst) system (PstA, PstB, PstC, and PstS), and a protein of unknown function called PhoU. Here we examined the effects of uncoupling PhoB synthesis and PhoR synthesis from their normal controls by placing each under the tight control of the arabinose-regulated P(araB) promoter or the rhamnose-regulated P(rhaB) promoter. To do this, we made allele replacement plasmids that may be generally useful for construction of P(araB) or P(rhaB) fusions and for recombination of them onto the E. coli chromosome at the araCBAD or rhaRSBAD locus, respectively. Using strains carrying such single-copy fusions, we showed that a P(rhaB) fusion is more tightly regulated than a P(araB) fusion in that a P(rhaB)-phoR+ fusion but not a P(araB)-phoR+ fusion shows a null phenotype in the absence of its specific inducer. Yet in the absence of induction, both P(araB)-phoB+ and P(rhaB)-phoB+ fusions exhibit a null phenotype. These data indicate that less PhoR than PhoB is required for transcriptional activation of the Pho regulon, which is consistent with their respective modes of action. We also used these fusions to study PhoU. Previously, we had constructed strains with precise delta phoU mutations. However, we unexpectedly found that such delta phoU mutants have a severe growth defect (P. M. Steed and B. L. Wanner, J. Bacteriol. 175:6797-6809, 1993). They also readily give rise to compensatory mutants with lesions in phoB, phoR, or a pst gene, making their study particularly difficult. Here we found that, by using P(araB)-phoB+, P(rhaB)-phoB+, or P(rhaB)-phoR+ fusions, we were able to overcome the extremely deleterious growth defect of a Pst+ delta phoU mutant. The growth defect is apparently a consequence of high-level Pst synthesis resulting from autogenous control of PhoB and PhoR synthesis in the absence of PhoU.

Cloning and characterization of a Pseudomonas aeruginosa gene involved in the negative regulation of phosphate taxis

Pseudomonas aeruginosa PAO1 exhibited a positive chemotactic response to P(i). The chemotactic response was induced by P(i) limitation. An alkaline phosphatase (AP) constitutive mutant showed a chemotactic response to P(i), regardless of whether the cells were starved for P(i). Sequence analysis and complementation studies showed that the P. aeruginosa phoU gene was involved both in the regulation of AP expression and in the induction of P(i) taxis. However, unlike AP expression, P(i) taxis was not regulated by the phoB gene product.

Hyper-invasive mutants define a novel Pho-regulated invasion pathway in Escherichia coli

We have isolated two transposon insertion mutations of the pst-phoU operon which result in the constitutive expression of the phoA gene product, alkaline phosphatase. The two mutations also render Escherichia coli invasive towards cultured HEp-2 cells and define a novel Pho-regulated invasion pathway. The presence of the large 'invasion' plasmid derived from an entero-invasive E. coli (EIEC) clinical isolate in these mutants leads to enhanced invasiveness toward cultured HEp-2 cells, a phenomenon referred to as the 'hyper-invasive' phenotype. Transduction of a pst-phoU insertion mutation into clinical isolates of EIEC and Shigella flexneri results in constitutive PhoA expression and coupled hyper-invasiveness in the former but not the latter. We speculate that the Pho-regulated invasion pathway described here, while silent in bacteria grown in standard laboratory rich media, may become functional in the host when invasive bacteria encounter nutrient starvation and/or other related stress conditions.

Use of the rep technique for allele replacement to construct mutants with deletions of the pstSCAB-phoU operon: evidence of a new role for the PhoU protein in the phosphate regulon

The phosphate regulon is negatively regulated by the PstSCAB transporter and PhoU protein by a mechanism that may involve protein-protein interaction(s) between them and the Pi sensor protein, PhoR. In order to study such presumed interaction(s), mutants with defined deletions of the pstSCAB-phoU operon were made. This was done by construction of M13 recombinant phage carrying these mutations and by recombination of them onto the chromosome by using a rep host (which cannot replicate M13) for allele replacement. These mutants were used to show that delta (pstSCAB-phoU) and delta (pstB-phoU) mutations abolished Pi uptake by the PstSCAB transporter, as expected, and that delta phoU mutations had no effect on uptake. Unexpectedly, delta phoU mutations had a severe growth defect, and this growth defect was (largely) alleviated by a compensatory mutation in the pstSCAB genes or in the phoBR operon, whose gene products positively regulate expression of the pstSCAB-phoU operon. Because delta phoU mutants that synthesize a functional PstSCAB transporter constitutively grew extremely poorly, the PhoU protein must have a new role, in addition to its role as a negative regulator. A role for the PhoU protein in intracellular Pi metabolism is proposed. Further, our results contradict those of M. Muda, N. N. Rao, and A. Torriani (J. Bacteriol. 174:8057-8064, 1992), who reported that the PhoU protein was required for Pi uptake.

The loss of culturability by Escherichia coli cells in seawater depends on availability of phosphate ions and phosphate transport systems

Using strains with or without the PhoE porin or different components of the phosphate regulon, we determined that maintenance of the culturability of Escherichia coli in seawater depended significantly on the presence of structures allowing access of phosphate ions to the periplasm, then to the cytoplasm of cells. Cells totally deprived of the two main phosphate transport systems (Pit, Pst) exhibited the highest loss of culturability. Most of this effect resulted from the loss of the high-affinity Pst system, and more specifically that of the periplasmic phosphate-binding protein PhoS. Survival was enhanced in seawater supplemented with phosphate (0.5 mM), whether or not these structures were present. From an ecological point of view, it is assumed that the presence of phosphate ions, even at low concentrations, can influence the behavior of E. coli cells in seawater.

Cyclic AMP in prokaryotes

Cyclic AMP (cAMP) is found in a variety of prokaryotes including both eubacteria and archaebacteria. cAMP plays a role in regulating gene expression, not only for the classic inducible catabolic operons, but also for other categories. In the enteric coliforms, the effects of cAMP on gene expression are mediated through its interaction with and allosteric modification of a cAMP-binding protein (CRP). The CRP-cAMP complex subsequently binds specific DNA sequences and either activates or inhibits transcription depending upon the positioning of the complex relative to the promoter. Enteric coliforms have provided a model to explore the mechanisms involved in controlling adenylate cyclase activity, in regulating adenylate cyclase synthesis, and in performing detailed examinations of CRP-cAMP complex-regulated gene expression. This review summarizes recent work focused on elucidating the molecular mechanisms of CRP-cAMP complex-mediated processes. For other bacteria, less detail is known. cAMP has been implicated in regulating antibiotic production, phototrophic growth, and pathogenesis. A role for cAMP has been suggested in nitrogen fixation. Often the only data that support cAMP involvement in these processes includes cAMP measurement, detection of the enzymes involved in cAMP metabolism, or observed effects of high concentrations of the nucleotide on cell growth.

Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S

The novel sigma factor (sigma S) encoded by rpoS (katF) is required for induction of many growth phase-regulated genes and expression of a variety of stationary-phase phenotypes in Escherichia coli. Here we demonstrate that wild-type cells exhibit spherical morphology in stationary phase, whereas rpoS mutant cells remain rod shaped and are generally larger. Size reduction of E. coli cells along the growth curve is a continuous and at least biphasic process, the second phase of which is absent in rpoS-deficient cells and correlates with induction of the morphogene bolA in wild-type cells. Stationary-phase induction of bolA is dependent on sigma S. The "gearbox" a characteristic sequence motif present in the sigma S-dependent growth phase- and growth rate-regulated bolAp1 promoter, is not recognized by sigma S, since stationary-phase induction of the mcbA promoter, which also contains a gearbox, does not require sigma S, and other sigma S-controlled promoters do not contain gearboxes. However, good homology to the potential -35 and -10 consensus sequences for sigma S regulation is found in the bolAp1 promoter.

Identification of a central regulator of stationary-phase gene expression in Escherichia coli

During carbon-starvation-induced entry into stationary phase, Escherichia coli cells exhibit a variety of physiological and morphological changes that ensure survival during periods of prolonged starvation. Induction of 30-50 proteins of mostly unknown function has been shown under these conditions. In an attempt to identify C-starvation-regulated genes we isolated and characterized chromosomal C-starvation-induced csi::lacZ fusions using the lambda placMu system. One operon fusion (csi2::lacZ) has been studied in detail. csi2::lacZ was induced during transition from exponential to stationary phase and was negatively regulated by cAMP. It was mapped at 59 min on the E. coli chromosome and conferred a pleiotropic phenotype. As demonstrated by two-dimensional gel electrophoresis, cells carrying csi2::lacZ did not synthesize at least 16 proteins present in an isogenic csi2+ strain. Cells containing csi2::lacZ or csi2::Tn10 did not produce glycogen, did not develop thermotolerance and H2O2 resistance, and did not induce a stationary-phase-specific acidic phosphatase (AppA) as well as another csi fusion (csi5::lacZ). Moreover, they died off much more rapidly than wild-type cells during prolonged starvation. We conclude that csi2::lacZ defines a regulatory gene of central importanc e for stationary phase E. coli cells. These results and the cloning of the wild-type gene corresponding to csi2 demonstrated that the csi2 locus is allelic with the previously identified regulatory genes katF and appR. The katF sequence indicated that its gene product is a novel sigma factor supposed to regulate expression of catalase HPII and exonuclease III (Mulvey and Loewen, 1989). We suggest that this novel sigma subunit of RNA polymerase defined by csi2/katF/appR is a central early regulator of a large starvation/stationary phase regulon in E. coli and propose 'rpoS' ('sigma S') as appropriate designations.

Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi

The phn (psiD) gene cluster is induced during Pi limitation and is required for the use of phosphonates (Pn) as a phosphorus (P) source. Twelve independent Pn-negative (Pn-) mutants have lesions in the phn gene cluster which, as determined on the basis of recombination frequencies, is larger than 10 kbp. This distance formed the basis for determining the complete DNA sequence of a 15.6-kbp BamHI fragment, the sequences of which suggested an operon with 17 open reading frames, denoted (in alphabetical order) the phnA to phnQ genes (C.-M. Chen, Q.-Z. Ye, Z. Zhu, B. L. Wanner, and C. T. Walsh, J. Biol. Chem. 265:4461-4471, 1990) Ten Pn- lesions lie in the phnD, phnE, phnH, phnJ, phnK, phnO, and phnP genes. We propose a smaller gene cluster with 14 open reading frames, phnC to phnP, which probably encode transporter and regulatory functions, in addition to proteins needed in Pn biodegradation. On the basis of the effects on phosphite (Pt), Pi ester, and Pi use, we propose that PhnC, PhnD, and PhnE constitute a binding protein-dependent Pn transporter which also transports Pt, Pi esters, and Pi. We propose that PhnO has a regulatory role because a phnO lesion affects no biochemical function, except for those due to polarity. Presumably, the 10 other phn gene products mostly act in an enzyme complex needed for breaking the stable carbon-phosphorus bond. Interestingly, all Pn- mutations abolish the use not only of Pn but also of Pt, in which P is in the +3 oxidation state. Therefore, Pn metabolism and Pt metabolism are related, supporting a biochemical mechanism for carbon-phosphorus bond cleavage which involves redox chemistry at the P center. Furthermore, our discovery of Pi-regulated genes for the assimilation of reduced P suggests that a P redox cycle may be important in biology.

Role of Escherichia coli heat shock proteins DnaK and HtpG (C62.5) in response to nutritional deprivation

Because of the highly conserved pattern of expression of the eucaryotic heat shock genes hsp70 and hsp84 or their cognates during sporulation in Saccharomyces cerevisiae and development in higher organisms, the role of the Escherichia coli homologs dnaK and htpG was examined during the response to starvation. The htpG deletion mutant was found to be similar to its wild-type parent in its ability to survive starvation for essential nutrients and to induce proteins specific to starvation conditions. The dnaK103 mutant, however, was highly susceptible to killing by starvation for carbon and, to a lesser extent, for nitrogen and phosphate. Analysis of proteins induced under starvation conditions on two-dimensional gels showed that the dnaK103 mutant was defective for the synthesis of some proteins induced in wild-type cells by carbon starvation and of some proteins induced under all starvation conditions, including the stationary phase in wild-type cells. In addition, unique proteins were synthesized in the dnaK103 mutant in response to starvation. Although the synthesis of some proteins under glucose starvation control was drastically affected by the dnaK103 mutation, the synthesis of proteins specifically induced by nitrogen starvation was essentially unaffected. Similarly, the dnaK103 mutant was able to grow, utilizing glutamine or arginine as a source of nitrogen, at a rate approximate to that of the wild-type parent, but it inefficiently utilized glycerol or maltose as carbon sources. Several differences between the protein synthetic pattern of the dnaK103 mutant and the wild type were observed after phosphate starvation, but these did not result in a decreased ability to survive phosphate starvation, compared with nitrogen starvation.

The leucine regulon of Escherichia coli K-12: a mutation in rblA alters expression of L-leucine-dependent metabolic operons

We have isolated and characterized a highly pleiotropic Escherichia coli mutant affected in the activity of a number of enzymes involved in different metabolic pathways, all of which are regulated by leucine. Selected for its ability to grow with L-serine as sole carbon source, the rbl-1::Tn10 mutant had high levels of L-serine deaminase activity (due to increased transcription of the structural gene) and of another amino acid-degrading enzyme, L-threonine dehydrogenase, and decreased transcription of the operons serA and ilvIH, coding for biosynthetic enzymes. The rbl mutation suppressed the slow growth of a metK mutant, deficient in S-adenosylmethionine synthetase. Furthermore, metK mutants spontaneously accumulated faster-growing rbl-like derivatives, and a commonly used metK strain, RG62, carries such a mutation. The rbl gene is located near 20 min on the E. coli genetic map. All phenotypes of the rbl mutant could be observed in rbl+ strains cultivated in the presence of L-leucine, and exogenous L-leucine had little further effect on the rbl strains. We propose that the rbl gene product is the regulator of a global response to leucine.

Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions

Twenty-four independent phosphate starvation-inducible (psi) transcriptional fusions made with Mu d1(lacZbla) were analyzed by sequencing the psi::lacZ(Mu d1) chromosomal junctions by using DNAs amplified with the polymerase chain reaction or mini-Mu cloning. Our DNA sequence analysis showed that the MuR DNA in Mu d1 has an unexpected structure that is comprised of 104 bases of MuR DNA in the form of a large inverted repeat, which we denoted Mu d1-R. Also, Mu d1s in the phoA and phn (psiD) loci of the phosphate regulon showed regional specificities for the insertion sites despite the randomness of Mu d1 insertions into the genome as a whole. Gene products or open reading frames were identified for seven unknown psi::lacZ(Mu d1) transcriptional fusions by searching DNA data bases with the sequences adjacent and upstream of the Mu d1s. One psiC::lacZ(Mu d1) lies in the ugpB gene of the ugpBAEC operon, which encodes a periplasmic sn-glycerol-3-phosphate-binding protein; two psiQ::lacZ(Mu d1)s lie in the gltB gene, and one psiQ::lacZ(Mu d1) lies in the gltD gene of the gltBDF operon, encoding the large and small subunits of glutamate synthase, respectively; and the psi-51::lacZ(Mu d1) lies in the glpB gene of the glpABC operon, which codes for the anaerobically regulated glycerol-3-phosphate dehydrogenase. psiE and psiF::lacZ(Mu d1)s lie in uncharacterized open reading frames near the xylE and phoA genes, respectively. Six other psi::lacZ(Mu d1)s lie in yet unreported Escherichia coli sequences.

A phoA structural gene mutation that conditionally affects formation of the enzyme bacterial alkaline phosphatase

The phoA503 mutant was identified as a mutant that shows a novel phoA regulatory phenotype. The phoA503 allele dramatically reduces the synthesis of bacterial alkaline phosphatase activity during Pi starvation in an otherwise wild-type host and during the logarithmic growth phase in a phoR or phoU background. Near-normal amounts of enzyme activity are found in phoR phoA503 or phoU phoA503 mutants when starved for carbon, nitrogen, or sulfur or during the stationary phase, however. Marker rescue and DNA sequence analysis located the phoA503 mutation to the phoA coding region. It is a C-to-T transition that would cause a substitution of Val for Ala-22 in the mature protein. Transcriptional and translational lacZ fusions to both wild-type and mutant alleles demonstrated that phoA gene expression is unaltered. Also, the mutant protein was secreted and processed as efficiently as the wild type. Furthermore, the subunits appeared to dimerize and to be stable in the periplasm. But, greater than 98% of the dimers were inactive and found exclusively as isozyme 1. An activation of preformed phoA503 dimers occurred during the stationary phase with the concomitant conversion into isozymes 2 and 3. We propose that the phoA503 mutation affects a late stage in the formation of active enzyme. An unknown change when Pi is present during stationary-phase growth leads to formation of active dimers, which is responsible for this new conditional phenotype.

Protein phosphorylation and regulation of adaptive responses in bacteria

Bacteria continuously adapt to changes in their environment. Responses are largely controlled by signal transduction systems that contain two central enzymatic components, a protein kinase that uses adenosine triphosphate to phosphorylate itself at a histidine residue and a response regulator that accepts phosphoryl groups from the kinase. This conserved phosphotransfer chemistry is found in a wide range of bacterial species and operates in diverse systems to provide different regulatory outputs. The histidine kinases are frequently membrane receptor proteins that respond to environmental signals and phosphorylate response regulators that control transcription. Four specific regulatory systems are discussed in detail: chemotaxis in response to attractant and repellent stimuli (Che), regulation of gene expression in response to nitrogen deprivation (Ntr), control of the expression of enzymes and transport systems that assimilate phosphorus (Pho), and regulation of outer membrane porin expression in response to osmolarity and other culture conditions (Omp). Several additional systems are also examined, including systems that control complex developmental processes such as sporulation and fruiting-body formation, systems required for virulent infections of plant or animal host tissues, and systems that regulate transport and metabolism. Finally, an attempt is made to understand how cross-talk between parallel phosphotransfer pathways can provide a global regulatory curcuitry.

Isolation of two glycosylated forms of membrane-bound alkaline phosphatase from avian growth plate cartilage matrix vesicle-enriched microsomes

Isolation of two membrane-bound alkaline phosphatase (AP) species from avian growth plate cartilage matrix vesicle (MV) fractions is described. AP was first released from the membranes by phosphatidylinositol-specific phospholipase C (PIase C), followed by chromatography on DEAE-Bio-Gel A and Reactive-Red agarose. Two AP species having apparent Mr of 81.5 and 77 kDa by SDS-PAGE were purified in high yield and specific activity by this simple method. Treatment with neuraminidase to remove sialic acid residues reduced their size slightly, but did not diminish the difference in Mr between the two species. Digestion with N-glycanase, however, decreased both AP species to a common size of 59 kDa. This reveals that both enzymes are highly glycosylated and suggests that the two forms may result from differences in degree of glycation. The amino acid compositions of the two avian enzyme forms are very similar, but are markedly enriched in serine, glycine and glutamate when compared to those reported for mammalian liver-kidney-bone AP. Possible differences in amino acid sequence between the two avian forms have not been excluded. The cross-reactivity of polyclonal antibodies to these enzymes with bovine kidney, but not intestinal AP, indicate that the avian cartilage APs are of the liver-kidney-bone isozyme type.

Nostoc commune UTEX 584 gene expressing indole phosphate hydrolase activity in Escherichia coli

A gene encoding an enzyme capable of hydrolyzing indole phosphate was isolated from a recombinant gene library of Nostoc commune UTEX 584 DNA in lambda gt10. The gene (designated iph) is located on a 2.9-kilobase EcoRI restriction fragment and is present in a single copy in the genome of N. commune UTEX 584. The iph gene was expressed when the purified 2.9-kilobase DNA fragment, free of any vector sequences, was added to a cell-free coupled transcription-translation system. A polypeptide with an Mr of 74,000 was synthesized when the iph gene or different iph-vector DNA templates were expressed in vitro. When carried by different multicopy plasmids and phagemids (pMP005, pBH6, pB8) the cyanobacterial iph gene conferred an Iph+ phenotype upon various strains of Escherichia coli, including a phoA mutant. Hydrolysis of 5-bromo-4-chloro-3-indolyl phosphate was detected in recombinant E. coli strains grown in phosphate-rich medium, and the activity persisted in assay buffers that contained phosphate. In contrast, indole phosphate hydrolase activity only developed in cells of N. commune UTEX 584, when they were partially depleted of phosphorus, and the activity associated with these cells was suppressed partially by the addition of phosphate to assay buffers. Indole phosphate hydrolase activity was detected in periplasmic extracts from E. coli (Iph+) transformants.

Cyclic AMP-cyclic AMP receptor protein as a repressor of transcription of the spf gene of Escherichia coli

The spf gene of Escherichia coli encodes an unstable 109-nucleotide RNA, spot 42 RNA; the level of this RNA was reduced three- to fivefold when cells were grown in the presence of 3',5'-cyclic AMP (cAMP). We show that this regulation occurs through reduction in transcription and depends on both cAMP and the cAMP receptor protein (CRP) but is independent of the de novo protein synthesis. Through deletion analysis of the spf gene promoter, we have identified sequences that are important in the synthesis of spot 42 RNA. Deletion of sequences upstream of -77 completely eliminated the negative control of cAMP-CRP and resulted in high constitutive levels of transcription. This region contained a sequence that both conformed to the consensus binding site for cAMP-CRP in positively regulated promoters and acted as a cAMP-CRP binding site in a gel retardation assay. Deletion of sequences between positions -77 and -60 greatly reduced the level of transcription in the presence or absence of cAMP-CRP, indicating that at least part of this region is a binding site for a positive-acting transcription factor (or RNA polymerase itself). We propose that the proximity of the two sites defined here allows for the negative control of spf gene transcription by cAMP-CRP. In particular, if only one site at a time can be occupied, the binding of cAMP-CRP would interfere with the binding of a transcription factor.

Control of bacterial alkaline phosphatase synthesis and variation in an Escherichia coli K-12 phoR mutant by adenyl cyclase, the cyclic AMP receptor protein, and the phoM operon

Mutant phoR cells show a clonal variation phenotype with respect to bacterial alkaline phosphatase (BAP) synthesis. BAP clonal variation is characterized by an alternation between a Bap+ and Bap- phenotype. The switching is regulated by the phoM operon and the presence of glucose; the pho-510 mutant form of the phoM operon abolishes both BAP clonal variation and the effect of glucose (B.L. Wanner, J. Bacteriol. 169:900-903, 1987). In this paper we show that a mutation of the adenyl cyclase (cya) and the cyclic AMP receptor protein (crp) gene also abolish BAP clonal variation; either simultaneously reduces the amount of BAP made in phoR mutants. Also, the pho-510 mutation is epistatic; it increases BAP synthesis in delta cya phoR and delta crp phoR mutants. These data are consistent with the wild-type phoM operon having a negative, as well as a positive, regulatory role in gene expression. Furthermore, the data suggest that adenyl cyclase and Crp indirectly regulate BAP synthesis in a phoR mutant via an interaction with the phoM operon or its gene products. However, phoM operon expression was unaffected when tested with phoM operon lacZ transcriptional fusions. In addition, the switching Bap phenotype was not associated with an alternation in phoM operon expression.

Identification and characterization of starvation-regulated genetic loci in Salmonella typhimurium by using Mu d-directed lacZ operon fusions

We used the technique of Mu d-directed lac operon fusion formation in an effort to identify loci in Salmonella typhimurium which are transcriptionally regulated by nutrient starvation conditions. We identified lacZ operon fusions in eight genetic loci, all of which exhibited increased transcription when starved for two or more of the following nutrients: nicotinate, phosphate, ammonium, glucose, and sulfate. The loci have been designated stiA to stiH for starvation-inducible loci. Mutations in two sti loci (stiC and stiD) significantly decreased cell viability during prolonged periods of nicotinate starvation, stiA and stiD are linked and map at 30 min. The stiC, stiE, stiG, and stiH loci mapped at approximately 77, 43, 88, and 56 min, respectively, on the S. typhimurium linkage map.

Mu d-directed lacZ fusions regulated by low pH in Escherichia coli

Methods were devised to isolate strains of Escherichia coli containing Mu d (lacZ Kmr) operon fusions regulated by external pH and by internal pH. External acid-inducible fusions (exa) were detected by plating a Mu d fusion pool on Luria broth with 5-bromo-4-chloro-3-indolyl-beta-D-galactoside, buffered at pH 7.4, and then replica plating on the same medium buffered at pH 5.5. Two exa strains showed induction by external acidification, up to 800-fold and 90-fold. Induction of both fusions was maximal at pH 5.6 and minimal over pH 7.0 to 8.3. There was no induction by membrane-permeable weak acids which depress internal pH at constant external pH. Anaerobiosis increased the steady-state level of transcription of exa-1 5-fold and of exa-2 2.5-fold at low external pH. Internal acid-inducible fusions (ina) were detected by plating a Mu d fusion pool on MacConkey medium, pH 6.8, and then replica plating with 15 mM benzoate. Two ina strains showed 10-fold induction by 20 mM benzoate at external pH 7.0. Similar results were obtained with other weak acids; their relative potency (salicylate greater than benzoate greater than dimethoxazoledinedione) was consistent with their relative ability to depress internal pH. In the absence of a weak acid, external pH had almost no effect over the pH range 5.5 to 8.0. Anaerobiosis did not affect ina induction. To our knowledge, this is the first report of E. coli genes induced specifically by internal but not external acidification and the first report of gene fusions induced by external acidification but not by weak acids.

Molecular cloning of Mu d(bla lacZ) transcriptional and translational fusions

The vector pBW2 was made to selectively clone chimeric plasmids with chromosomal Mu d(bla lacZ) transcriptional or translational fusions. It was tetracycline resistant and had the carboxyl-terminal end of bla distal to its PstI site. Because ligation of PstI-digested chromosomal DNA of a Mu d(bla lacZ) insertion with pBW2 restored bla, ampicillin-resistant chimeric plasmids were selectable. These plasmids had the Mu d bla amino terminus and simultaneously acquired other Mu d sequences including lacZ, the chromosomal fusion joint, and the DNA adjacent to the nearest chromosomal PstI site. The plasmid pBW2 was useful in the molecular cloning of several psi and pho::lacZ(Mu d) fusions, as well as chromosomal genes located near Mu d insertions.

Involvement of the phosphate regulon and the psiD locus in carbon-phosphorus lyase activity of Escherichia coli K-12

Escherichia coli K-12 can readily mutate to use methylphosphonic acid as the sole phosphorus source by a direct carbon-to-phosphorus (C-P) bond cleavage activity that releases methane and Pi. The in vivo C-P lyase activity is both physiologically and genetically regulated as a member of the phosphate regulon. Since psiD::lacZ(Mu d1) mutants cannot metabolize methylphosphonic acid, psiD may be the structural gene(s) for C-P lyase.

Rat alkaline phosphatase. I. Purification and characterization of the enzyme from osteosarcoma: generation of monoclonal and polyclonal antibodies

Alkaline phosphatase (AP) was purified to over 90% homogeneity from rat osteosarcoma by acetone precipitation followed by chromatography on DEAE-cellulose, Sephacryl S-200, and hydroxyapatite. The purified enzyme had a specific activity of 759 units/mg protein at its optimal pH (10.5), and a Km of 0.8 mM for p-nitrophenylphosphate. The enzyme's apparent subunit molecular mass on sodium dodecyl sulfate-polyacrylamide gel electrophoresis was 82,000 Da. The heat-inactivation profile and homoarginine inhibition were characteristic of the bone-liver-kidney AP isoenzyme. Monoclonal and polyclonal anti-AP antibodies were prepared and characterized. Polyclonal rabbit antiserum quantitatively precipitated the activity from purified AP preparations and tissue extracts but did not inhibit AP catalytic activity. This antiserum was almost 10-fold less active against heat-inactivated enzyme when tested in a competition assay using 125I-AP. Two distinct monoclonal antibodies were each partly effective in immunoprecipitating AP when tested individually; however, together they precipitated over 90% of the AP activity.

Analysis of transcription of the exotoxin A gene of Pseudomonas aeruginosa

Analysis of RNA isolated from Pseudomonas aeruginosa PA103 and PAKS grown under Fe2+-limiting (0.08 microgram/ml) and Fe2+-sufficient (10 micrograms/ml) conditions demonstrated that exotoxin A (ETA) expression is regulated by Fe2+ at the level of transcription. S1 nuclease mapping revealed two 5' termini of the tox transcript, 89 base pairs (bp) (S1A) and 62 bp (S1B) 5' to the ETA initiation codon. There appeared to be no consensus promoter sequence for either tox transcript. An 8-bp direct repeat was found 5' to the start of transcript S1A. Transcript S1B mapped 8 bp upstream of a dodecamer sequence conserved between the ETA and phospholipase C genes of P. aeruginosa. Multicopy plasmids in which the expression of ETA is directed from the Escherichia coli trp promoter (ptrpETA-RSF1010) or the tox promoter (pCMtox) were constructed and mobilized into a Tox-P. aeruginosa strain, WR5. WR5 synthesized and secreted high levels of ETA when it was expressed from the E. coli trp promoter; however, the synthesis of ETA from its own promoter in this strain was very low. These and other data suggest that the expression of ETA is under a positive control mechanism. A fusion of the ETA promoter fragment to lacZ was constructed. Use of this fusion plasmid revealed that this DNA fragment directed the synthesis of beta-galactosidase in E. coli at very low levels and that the synthesis of beta-galactosidase from this fusion in E. coli was not regulated by Fe2+.

Bacterial alkaline phosphatase clonal variation in some Escherichia coli K-12 phoR mutant strains

Several phoR alleles (phoR19, phoR20, phoR68, phoR69, phoR70, and phoR78) led to either a bacterial alkaline phosphatase (BAP)-constitutive phenotype or a variable behavior, depending upon the strain tested. Whereas Escherichia coli K10, MC1000, and XPh4 phoR mutants were constitutive, AB1157, BD792, MC4100, and W3110 phoR mutants displayed the metastable character. For the latter strains, constitutive mutants regularly segregated BAP-negative clones which yielded constitutive variants again at a high frequency. Indeed, the pattern of variation observed in BAP-variable phoR strains is phenotypically analogous to phase variation of the H1/H2 flagellum antigen type in Salmonella typhimurium and the molecular switch between the immune and sensitive states in bacteriophage lambda. The metastable behavior was not a general property of BAP-constitutive mutants, since several phosphate-specific transport-phoU mutations led to a constitutive (stable) phenotype regardless of the strain tested. But in phoR phosphate-specific transport-phoU mutants, the metastable character was epistatic (dominant), and such double mutants showed clonal variation in BAP-variable strains.

Starvation proteins in Escherichia coli: kinetics of synthesis and role in starvation survival

Starvation proteins synthesized by Escherichia coli at the onset of carbon starvation (R. G. Groat and A. Matin, J. Indust. Microbiol. 1:69-73, 1986) exhibited four temporal classes of synthesis in response to glucose or succinate starvation, indicating sequential expression of carbon starvation response (cst) genes. A cst mutant of E. coli showed greatly impaired carbon starvation survival. Thus, it appears that E. coli undergoes a significant molecular realignment in response to starvation, which increases its resistance to this stress. New polypeptides were also synthesized by E. coli in response to phosphate or nitrogen starvation. Some of these polypeptides were unique to a given starvation regimen, but at least 13 appeared to be synthesized regardless of the nutrient deprivation causing the starvation.

Nucleotide sequence of the phoM region of Escherichia coli: four open reading frames may constitute an operon

The phoM gene is one of the positive regulatory genes for the phosphate regulon of Escherichia coli. We analyzed the nucleotide sequence of a 4.7-kilobase chromosomal DNA segment that encompasses the phoM gene and its flanking regions. Four open reading frames (ORFs) were identified in the order ORF1-ORF2-ORF3 (phoM)-ORF4-dye clockwise on the standard E. coli genetic map. Since these ORFs are preceded by a putative promotor sequence upstream of ORF1 and followed by a putative terminator distal to ORF4, they seem to constitute an operon. The 157-amino-acid ORF1 protein contains highly hydrophobic amino acids in the amino-terminal portion, which is a characteristic of a signal peptide. The 229-amino-acid ORF2 protein is highly homologous to the PhoB protein, a positive regulatory protein for the phosphate regulon. The ORF3 (phoM gene) protein contains two stretches of highly hydrophobic residues in the amino-terminal and central regions and, therefore, may be a membrane protein. The 450-amino-acid ORF4 protein contains long hydrophobic regions and is likely to be a membrane protein.

Novel regulatory mutants of the phosphate regulon in Escherichia coli K-12

New pleiotropic mutants were isolated that express either the phoA, psiE or psiO promoter constitutively and simultaneously alter bacterial alkaline phosphatase regulation, carbon utilization or ultraviolet light sensitivity. To do this, Lac+ mutants were isolated from strains with the appropriate lacZ transcriptional fusions. Over 300 independent mutants were characterized, and all that constitutively express phoA map in phoR, phoU, the phosphate-specific transport system or a new locus called phoF. However, only phoU mutants express both phoA and psiE constitutively. Carbohydrate-utilizing mutants that show constitutive expression of psiE and psiO map in cya, crp and, possibly, crr. Also, numerous ultraviolet-light-sensitive mutants were discovered that show increased psiO expression and map in lon. Some other mutations that lead to constitutive psiO expression (which is normally induced either by phosphate, nitrogen or carbon starvation or anoxia) show decreased expression of phoA. Also, several mutants were found that show an unusual metastable character affecting psiO or phoA transcription. In these, colonies spontaneously switch between an induced and repressed "state" with respect to lac or bacterial alkaline phosphatase expression. In some, the clonal variation of the lactose phenotype or bacterial alkaline phosphatase synthesis is recA-independent and phenotypically resembles phase variation in Salmonella typhimurium. The latter class are called "phase mutants". The mutants are discussed in terms of protein-nucleic acid interactions and/or possible changes in the DNA, i.e. modifications or rearrangements, within the phosphate gene system, that are physiologically regulated.

Molecular cloning of the phosphate (inorganic) transport (pit) gene of Escherichia coli K12. Identification of the pit+ gene product and physical mapping of the pit-gor region of the chromosome

The pit+ gene, encoding the phosphate (inorganic) transport system of Escherichia coli, was isolated from a library of E. coli genes inserted in the cosmid vector pHC79. A 25.5-kb chromosomal DNA fragment was shown also to carry the gor locus encoding glutathione oxidoreductase. Physical mapping placed the two genes about 10 kb apart, confirming bacteriophage P1 mapping of the 77-min region. Subcloning and deletion analysis indicated that the entire pit+ gene was located within a 2.2-kb Sal1-Ava1 fragment. The pit+ gene product was identified by SDS-polyacrylamide gel electrophoresis as a 39-kdal inner membrane protein by two methods: 35S-methionine-labelling of minicells carrying pit+ plasmids or plasmids from which all or part of the pit+ gene was deleted. Overproduction of the Pit protein using a thermoinducible "runaway" replication plasmid. Complementation of the pit-1 mutant allele using a unit-copy-number pit+ plasmid indicated that the pit-1 mutation is recessive. Strains carrying a multicopy pit+ plasmid show a 10-fold increase in the initial rate of phosphate uptake; however there is no change in the steady-state level of 32Pi accumulation.

Contrasting mechanisms of envZ control of mal and pho regulon genes in Escherichia coli

The envZ11 missense mutation in the regulatory gene envZ pleiotropically repressed synthesis of OmpF, alkaline phosphatase, and several proteins of the maltose regulon. Procaine treatment of wild-type cells resulted in the same phenotype through an envZ+-mediated mechanism. Here we show that envZ11-procaine act differently on the mal and pho regulons. In the mal system, the expression of the positive regulator gene malT, measured as beta-galactosidase activity of a malT-lac+ operon fusion, was drastically reduced by procaine treatment or by the envZ11 mutation. In contrast, expression of the positive regulator of the pho regulon phoB was not reduced by procaine treatment. The products of the regulatory genes phoM, phoR, and phoU were also not required for procaine action. Procaine and envZ11 inhibited expression of only two products of the pho regulon, alkaline phosphatase and the PhoE porin. The conclusion that envZ11-procaine act differently on the mal and the pho regulons is supported by our ability to isolate second-site mutations with a Mal+ PhoA- phenotype in an envZ11 strain.

Phosphate starvation regulon of Salmonella typhimurium

Several phosphate-starvation-inducible (psi) genetic loci in Salmonella typhimurium were identified by fusing the lacZ gene to psi promoters by using the Mu d1 and Mu d1-8 bacteriophages. Although several different starvation conditions were examined, the psi loci responded solely to phosphate deprivation. A regulatory locus, psiR, was identified as controlling the psiC locus. The psiR locus did not affect the expression of the Escherichia coli phoA locus or any of the other psi loci described.

Does secA mediate coupling between secretion and translation in Escherichia coli?

An amber mutation in the secA gene of Escherichia coli causes a pleiotropic decrease in the synthesis of secreted proteins, including maltose-binding protein (MBP) and alkaline phosphatase. Reversal of the inhibition of MBP synthesis in secA(Am) strains by signal sequence mutations in the malE gene has been reported. These results suggest a coupling between secretion and translation which involves an interaction between the signal sequence of nascent polypeptides and a cellular secretion machinery. Further analysis reported here indicated that signal sequence mutations of MBP or alkaline phosphatase did not selectively overcome the inhibition of MBP or alkaline phosphatase synthesis in secA(Am) strains. Rather, at a given time in parallel experiments there was substantial variability among closely isogenic secA(Am) strains in the magnitude of the synthesis block; this variability could account for the earlier results. Further experiments suggested that the inhibition of MBP synthesis in secA(Am) strains was caused by depletion of cyclic AMP, leading to decreased transcription of the malE gene. However, the secretion defects in secA(Am) strains were not affected by cyclic AMP levels. Therefore, we conclude that the reduction in MBP synthesis was a secondary consequence of the primary export defect in the secA(Am) strains.