Control of transcription elongation and DNA repair by alarmone ppGpp

Second messenger (p)ppGpp (collectively guanosine tetraphosphate and guanosine pentaphosphate) mediates bacterial adaptation to nutritional stress by modulating transcription initiation. More recently, ppGpp has been implicated in coupling transcription and DNA repair; however, the mechanism of ppGpp engagement remained elusive. Here we present structural, biochemical and genetic evidence that ppGpp controls Escherichia coli RNA polymerase (RNAP) during elongation via a specific site that is nonfunctional during initiation. Structure-guided mutagenesis renders the elongation (but not initiation) complex unresponsive to ppGpp and increases bacterial sensitivity to genotoxic agents and ultraviolet radiation. Thus, ppGpp binds RNAP at sites with distinct functions in initiation and elongation, with the latter being important for promoting DNA repair. Our data provide insights on the molecular mechanism of ppGpp-mediated adaptation during stress, and further highlight the intricate relationships between genome stability, stress responses and transcription.

Mechanisms of survival mediated by the stringent response in Pseudomonas aeruginosa under environmental stress in drinking water systems: Nitrogen deficiency and bacterial competition

Pseudomonas aeruginosa causes public health problems in drinking water systems. This study investigated the potential role of the stringent response in regulating the adaptive physiological metabolic behaviors of P. aeruginosa to low nitrogen stress and bacterial competition in drinking water systems. The results indicated that guanosine tetraphosphate (ppGpp) concentrations in P. aeruginosa increased to 135.5 pmol/g SS under short-term nitrogen deficiency. Meanwhile, the expression levels of the ppGpp synthesis genes (ppx, relA) and degradation gene (spoT) were upregulated by 37.0% and downregulated by 26.8%, respectively, indicating that the stringent response was triggered. The triggered stringent response inhibited the growth of P. aeruginosa and enhanced the metabolic activity of P. aeruginosa to adapt to nutrient deprivation. The interspecific competition significantly affected the regulation of the stringent response in P. aeruginosa. During short-term nitrogen deficiency, the extracellular polymeric substances concentration of P. aeruginosa decreased significantly, leading to desorption and diffusion of attached bacteria and increased ecological risks. The regulatory effect of stringent response on P. aeruginosa gradually weakened under long-term nitrogen deficiency. However, the expression of pathogenic genes (nalD/PA3310) and flagellar assembly genes (fliC) in P. aeruginosa was upregulated by the stringent response, which increased the risk of disease.

Regulation of ppGpp Synthesis and Its Impact on Chloroplast Biogenesis during Early Leaf Development in Rice

Guanosine tetraphosphate (ppGpp) is known as an alarmone that mediates bacterial stress responses. In plants, ppGpp is synthesized in chloroplasts from GTP and ATP and functions as a regulator of chloroplast gene expression to affect photosynthesis and plant growth. This observation indicates that ppGpp metabolism is closely related to chloroplast function, but the regulation of ppGpp and its role in chloroplast differentiation are not well understood. In rice, ppGpp directly inhibits plastidial guanylate kinase (GKpm), a key enzyme in GTP biosynthesis. GKpm is highly expressed during early leaf development in rice, and the GKpm-deficient mutant, virescent-2 (v2), develops chloroplast-deficient chlorotic leaves under low-temperature conditions. To examine the relationship between GTP synthesis and ppGpp homeostasis, we generated transgenic rice plants over-expressing RSH3, a protein known to act as a ppGpp synthase. When RSH3 was overexpressed in v2, the leaf chlorosis was more severe. Although the RSH3 overexpression in the wild type caused no visible effects, pulse amplitude modulation fluorometer measurements indicated that photosynthetic rates were reduced in this line. This finding implies that the regulation of ppGpp synthesis in rice is involved in the maintenance of the GTP pool required to regulate plastid gene expression during early chloroplast biogenesis. We further investigated changes in the expressions of RelA/SpoT Homolog (RSH) genes encoding ppGpp synthases and hydrolases during the same period. Comparing the expression of these genes with the cellular ppGpp content suggests that the basal ppGpp level is determined by the antagonistic action of multiple RSH enzymatic activities during early leaf development in rice.

Meta-Tyrosine Induces Cytotoxic Misregulation of Metabolism in Escherichia coli

The non-protein amino acid meta-Tyrosine (m-Tyr) is produced in cells under conditions of oxidative stress, and m-Tyr has been shown to be toxic to a broad range of biological systems. However, the mechanism by which m-Tyr damages cells is unclear. In E. coli, the quality control (QC) function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to m-Tyr. To determine the mechanism of m-Tyr toxicity, we utilitized a strain of E. coli that expresses a QC-defective PheRS. The global responses of E. coli cells to m-Tyr were assessed by RNA-seq, and >500 genes were differentially expressed after the addition of m-Tyr. The most strongly up-regulated genes are involved in unfolded-protein stress response, and cells exposed to m-Tyr contained large, electron-dense protein aggregates, indicating that m-Tyr destabilized a large fraction of the proteome. Additionally, we observed that amino acid biosynthesis and transport regulons, controlled by ArgR, TrpR, and TyrR, and the stringent-response regulon, controlled by DksA/ppGpp, were differentially expressed. m-Tyr resistant mutants were isolated and found to have altered a promoter to increase expression of the enzymes for Phe production or to have altered transporters, which likely result in less uptake or increased efflux of m-Tyr. These findings indicate that when m-Tyr has passed the QC checkpoint by the PheRS, this toxicity of m-Tyr may result from interfering with amino acid metabolism, destabalizing a large number of proteins, and the formation of protein aggregates.

Growth suppression by altered (p)ppGpp levels results from non-optimal resource allocation in Escherichia coli

Understanding how bacteria coordinate gene expression with biomass growth to adapt to various stress conditions remains a grand challenge in biology. Stress response is often associated with dramatic accumulation of cellular guanosine tetra- or penta-phosphate (p)ppGpp (also known as 'magic spot'), which is a key second messenger participating in regulating various biochemical and physiological processes of bacteria. Despite of the extensive studies on the mechanism of gene regulation by (p)ppGpp during stringent response, the connection between (p)ppGpp and bacterial steady-state exponential growth remains elusive. Here, we establish a versatile genetic approach to systematically perturb the (p)ppGpp level of Escherichia coli through titrating either the single-function (p)ppGpp synthetase or the singe-function (p)ppGpp hydrolase and quantitatively characterize cell growth and gene expression. Strikingly, increased and decreased (p)ppGpp levels both cause remarkable growth suppression of E. coli. From a coarse-grained insight, we demonstrate that increased (p)ppGpp levels limit ribosome synthesis while decreased (p)ppGpp levels limit the expression of metabolic proteins, both resulting in non-optimal resource allocation. Our study reveals a profound role of (p)ppGpp in regulating bacterial growth through governing global resource allocation. Moreover, we highlight the Mesh1 (p)ppGpp hydrolase from Drosophila melanogaster as a powerful genetic tool for interrogating bacterial (p)ppGpp physiology.

Gene Transfer Agent Promotes Evolvability within the Fittest Subpopulation of a Bacterial Pathogen

The Bartonella gene transfer agent (BaGTA) is an archetypical example for domestication of a phage-derived element to permit high-frequency genetic exchange in bacterial populations. Here we used multiplexed transposon sequencing (TnSeq) and single-cell reporters to globally define the core components and transfer dynamics of BaGTA. Our systems-level analysis has identified inner- and outer-circle components of the BaGTA system, including 55 regulatory components, as well as an additional 74 and 107 components mediating donor transfer and recipient uptake functions. We show that the stringent response signal guanosine-tetraphosphate (ppGpp) restricts BaGTA induction to a subset of fast-growing cells, whereas BaGTA particle uptake depends on a functional Tol-Pal trans-envelope complex that mediates outer-membrane invagination upon cell division. Our findings suggest that Bartonella evolved an efficient strategy to promote genetic exchange within the fittest subpopulation while disfavoring exchange of deleterious genetic information, thereby facilitating genome integrity and rapid host adaptation.

Cytosolic ppGpp accumulation induces retarded plant growth and development

In bacteria a second messenger, guanosine 5'-diphosphate 3'-diphosphate (ppGpp), synthesized upon nutrient starvation, controls many gene expressions and enzyme activities, which is necessary for growth under changeable environments. Recent studies have shown that ppGpp synthase and hydrolase are also conserved in eukaryotes, although their functions are not well understood. We recently showed that ppGpp-overaccumulation in Arabidopsis chloroplasts results in robust growth under nutrient-limited conditions, demonstrating that the bacterial-like stringent response at least functions in plastids. To test if ppGpp also functions in the cytosol, we constructed the transgenic Arabidopsis expressing Bacillus subtilis ppGpp synthase gene yjbM. Upon induction of the gene, the mutant synthesizes ∼10-20-fold higher levels of ppGpp, and its fresh weight was reduced to ˜80% that of the wild type. These results indicate that cytosolic ppGpp negatively regulates plant growth and development.

Elevated guanosine 5'-diphosphate 3'-diphosphate level inhibits bacterial growth and interferes with FtsZ assembly

FtsZ, a protein essential for prokaryotic cell division, forms a ring structure known as the Z-ring at the division site. FtsZ has a GTP binding site and is assembled into linear structures in a GTP-dependent manner in vitro. We assessed whether guanosine 5'-diphosphate 3'-diphosphate (ppGpp), a global regulator of gene expression in starved bacteria, affects cell division in Salmonella Paratyphi A. Elevation of intracellular ppGpp levels by using the relA expression vector induced repression of bacterial growth and incorrect FtsZ assembly. We found that FtsZ forms helical structures in the presence of ppGpp by using the GTP binding site; however, ppGpp levels required to form helical structures were at least 20-fold higher than the required GTP levels in vitro. Furthermore, once formed, helical structures did not change to the straight form even after GTP addition. Our data indicate that elevation of the ppGpp level leads to inhibition of bacterial growth and interferes with FtsZ assembly.

Recent functional insights into the role of (p)ppGpp in bacterial physiology

The alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppGpp) are involved in regulating growth and several different stress responses in bacteria. In recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppGpp metabolism and (p)ppGpp-mediated regulation. In this Review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the RelA/SpoT homologue (RSH) proteins, which are key players that regulate the cellular levels of (p)ppGpp. We also discuss the structural basis of transcriptional regulation by (p)ppGpp and the role of (p)ppGpp in GTP metabolism and in the emergence of bacterial persisters.

Signalling by the global regulatory molecule ppGpp in bacteria and chloroplasts of land plants

The hyperphosphorylated guanine ribonucleotide ppGpp mediates the stringent response in bacteria. Biochemical and genetic studies of this response in Escherichia coli have shown that the biosynthesis of ppGpp is catalysed by two homologous enzymes, RelA and SpoT. RelA is activated in response to amino acid starvation, and SpoT responds to abiotic physical stress beside nutritional stress. All free-living bacteria, including Gram-positive firmicutes, contain RelA-SpoT homologues (RSH). Further, novel ppGpp biosynthetic enzymes, designated small alarmone synthetases (SASs), were recently identified in a subset of bacteria, including the Gram-positive organism Bacillus subtilis, and were shown to consist only of a ppGpp synthetase domain. Studies suggest that these SAS proteins contribute to ppGpp signalling in response to stressful conditions in a manner distinct from that of RelA-SpoT enzymes. SAS proteins currently appear to always occur in addition to RSH enzymes in various combinations but never alone. RSHs have also been identified in chloroplasts, organelles of photosynthetic eukaryotes that originated from endosymbiotic photosynthetic bacteria. These chloroplast RSHs are exclusively encoded in nuclear DNA and targeted into chloroplasts. The findings suggest that ppGpp may regulate chloroplast functions similar to those regulated in bacteria, including transcription and translation. In addition, a novel ppGpp synthetase that is regulated by Ca²⁺ as a result of the presence of two EF-hand motifs at its COOH terminus was recently identified in chloroplasts of land plants. This finding indicates the existence of a direct connection between eukaryotic Ca²⁺ signalling and prokaryotic ppGpp signalling in chloroplasts. The new observations with regard to ppGpp signalling in land plants suggest that such signalling contributes to the regulation of a wider range of cellular functions than previously anticipated.

ppGpp-mediated stationary phase induction of the genes encoded by horizontally acquired pathogenicity islands and cob/pdu locus in Salmonella enterica serovar Typhimurium

Salmonella enterica is highly diverse in terms of genome structure, which is at least partly due to the horizontal transfer of genetic elements from various sources. In this study, we examined the expression profiles of such genes in Salmonella Pathogenicity Islands (SPIs) and the cob/pdu locus, horizontally acquired large DNA segments, during growth under standard growth conditions. Transcripts from exponentially growing and early stationary phase Salmonellae were compared using various methods including cDNA microarray analysis. Nearly all genes encoded by SPIs and the cob/pdu locus were induced at the onset of the stationary phase in a stringent molecule ppGpp-dependent but stationary phase sigma, sigma38-independent manner. Although, it has been suggested that ppGpp acts in concert with DksA, we found the stationary phase induction of those SPI genes was not DksA dependent. It is suggested that ppGpp stimulates the expression of these stress-inducible genes encoded by horizontally acquired DNA, by itself or in concert with DksA.

A pathway and genetic factors contributing to elevated gene expression noise in stationary phase

Previous studies have identified factors associated with transcription and translation efficiency, such as promoter strength and mRNA sequences, that can affect stochasticity in gene expression. Here we present evidence for a pathway and associated genetic factors (namely, the ribosome modulation factor RMF and ppGpp) in Escherichia coli that contribute to heightened levels of gene expression noise during stationary phase. Endogenous cellular mechanisms that globally affect gene expression noise, such as those identified in this study, could provide phenotypic diversity under adverse conditions such as stationary phase.

(p)ppGpp regulates type 1 fimbriation of Escherichia coli by modulating the expression of the site-specific recombinase FimB

In this report we have examined the role of the regulatory alarmone (p)ppGpp on expression of virulence determinants of uropathogenic Escherichia coli strains. The ability to form biofilms is shown to be markedly diminished in (p)ppGpp-deficient strains. We present evidence (i) that (p)ppGpp tightly regulates expression of the type 1 fimbriae in both commensal and pathogenic E. coli isolates by increasing the subpopulation of cells that express the type 1 fimbriae; and (ii) that the effect of (p)ppGpp on the number of fimbrial expressing cells can ultimately be traced to its role in transcription of the fimB recombinase gene, whose product mediates inversion of the fim promoter to the productive (ON) orientation. Primer extension analysis suggests that the effect of (p)ppGpp on transcription of fimB occurs by altering the activity of only one of the two fimB promoters. Furthermore, spontaneous mutants with properties characteristic of ppGpp(0) suppressors restore fimB transcription and consequent downstream effects in the absence of (p)ppGpp. Consistently, the rpoB3770 allele also fully restores transcription of fimB in a ppGpp(0) strain and artificially elevated levels of FimB bypass the need for (p)ppGpp for type 1 fimbriation. Our findings suggest that the (p)ppGpp-stimulated expression of type 1 fimbriae may be relevant during the interaction of pathogenic E. coli with the host.

The stringent response mediator Rsh is required for Brucella melitensis and Brucella suis virulence, and for expression of the type IV secretion system virB

Physiological adaptation of intracellular bacteria is critical for timely interaction with eukaryotic host cells. One mechanism of adaptation, the stringent response, is induced by nutrient stress via its effector molecule (p)ppGpp, synthesized by the action of RelA/SpoT homologues. The intracellular pathogen Brucella spp., causative agent of brucellosis, possesses a gene homologous to relA/spoT, named rsh, encoding a (p)ppGpp synthetase as confirmed by heterologous complementation of a relA mutant of Sinorhizobium meliloti. The Rsh deletion mutants in Brucella suis and Brucella melitensis were characterized by altered morphology, and by reduced survival under starvation conditions and in cellular and murine models of infection. Most interestingly, we evidenced that expression of virB, encoding the type IV secretion system, a major virulence factor of Brucella, was Rsh-dependent. All mutant phenotypes, including lack of VirB proteins, were complemented with the rsh gene of Brucella. In addition, RelA of S. meliloti functionally replaced Brucella Rsh, describing the capacity of a gene from a plant symbiont to restore virulence in a mammalian pathogen. We therefore concluded that in the intramacrophagic environment encountered by Brucella, Rsh might participate in the adaptation of the pathogen to low-nutrient environments, and indirectly in the VirB-mediated formation of the final replicative niche.

A Vibrio cholerae relaxed (relA) mutant expresses major virulence factors, exhibits biofilm formation and motility, and colonizes the suckling mouse intestine

We have constructed a relaxed mutant of El Tor biotype Vibrio cholerae strain C7258 by disruption of the RelA catalytic domain. The ability of the V. cholerae relaxed mutant to biosynthesize guanosine tetraphosphate and pentaphosphate was severely affected; the mutant showed a reduced growth rate in minimal medium that could be reversed by the addition of Casamino Acids, and it was thermosensitive. Contrary to published findings, the new relA mutant still produced significant cholera toxin and toxin-coregulated pilus. The V. cholerae relA mutant was motile, produced normal biofilms, and colonized the suckling mouse intestine. Our data suggest that levels of basal guanosine nucleotides pppGpp and ppGpp, rather than the availability of a stringent response, could influence expression of virulence factors, depending on strain and culture conditions. Production of hemagglutinin (HA)/protease, which requires HapR, RpoS, and the cyclic AMP receptor protein, was not strongly affected. Nevertheless, overexpression of RelA protein from an isopropyl-beta-d-thiogalactopyranoside-inducible promoter posttranscriptionally diminished production of HA/protease.

[The stringent response--bacterial mechanism of an adaptive stress response]

The stringent response is a key regulatory reaction exhibited by bacteria in response to amino acid deprivation or carbon, nitrogen and phosphate limitation. In E. coli, the products of the relA and spoT genes regulate accumulation of the effector molecules of the stringent response--guanosine tetra- and pentaphosphates (ppGpp and pppGpp respectively). These unusual hyperphosphorylated nucleotides bind directly to the bacterial RNA polymerase and change transcriptional activity of some genes--transcription repression of genes associated with the translational apparatus and the simultaneous upregulation of genes encoding metabolic enzymes, especially those involved in amino acid biosynthesis, protein hydrolysis and coding for the sigma S factor. Sigma S factor binds to the core of the bacterial RNA polymerase and induce stationary-phase-specific and stress-response-specific genes expression.

Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation

Rickettsia conorii is an obligate intracellular bacterium transmitted to humans by Rhipicephalus sanguineus ticks. The success of this microorganism at surviving in nature implicates the ability to efficiently adapt to different environments, including the arthropod vector and the mammalian host. Numerous bacterial species possess a highly evolved system for stress adaptation. This so-called stringent response is mediated by guanosine 3',5'-bispyrophosphate and guanosine 3'-diphosphate 5'-triphosphate which are under spoT control in some Gram-negative bacteria. Interestingly, annotation of the R. conorii genome evidenced 5 spoT paralogs. We hypothesized that these spoT genes play a role in adaptation to environmental changes specifically encountered by rickettsiae during their different life cycles. Transcription of the spoT paralogs was examined by RT-PCR from infected Vero cells maintained in rich or deficient culture media, from infected C6/36 insect cells cultured at various temperatures and from infected ticks. Our results demonstrated that the 5 spoT genes can be transcribed. SpoT1 (RC0374) is only transcribed upon stringent response. Transcription of spoT3 (RC0888) was never observed in arthropod cells or ticks, but was specific to R. conorii RNA extracted from infected Vero cells. These results indicate that rickettsial spoT paralogs are independently transcribed, depending on the different infected hosts and the adaptive capacity of the pathogen. Bioinformatics analysis of these possibly encoded proteins is also reported.

ppGpp-dependent stationary phase induction of genes on Salmonella pathogenicity island 1

We have examined expression of the genes on Salmonella pathogenicity island 1 (SPI1) during growth under the physiologically well defined standard growth condition of Luria-Bertani medium with aeration. We found that the central regulator hilA and the genes under its control are expressed at the onset of stationary phase. Interestingly, the two-component regulatory genes hilC/hilD, sirA/barA, and ompR, which are known to modulate expression from the hilA promoter (hilAp) under so-called "inducing conditions" (Luria-Bertani medium containing 0.3 m NaCl without aeration), acted under standard conditions at the stationary phase induction level. The induction of hilAp depended not on RpoS, the stationary phase sigma factor, but on the stringent signal molecule ppGpp. In the ppGpp null mutant background, hilAp showed absolutely no activity. The stationary phase induction of hilAp required spoT but not relA. Consistent with this requirement, hilAp was also induced by carbon source deprivation, which is known to transiently elevate ppGpp mediated by spoT function. The observation that amino acid starvation elicited by the addition of serine hydroxamate did not induce hilAp in a RelA(+) SpoT(+) strain suggested that, in addition to ppGpp, some other alteration accompanying entry into the stationary phase might be necessary for induction. It is speculated that during the course of infection Salmonella encounters various stressful environments that are sensed and translated to the intracellular signal, ppGpp, which allows expression of Salmonella virulence genes, including SPI1 genes.

Fusidic acid-resistant mutants of Salmonella enterica serovar Typhimurium with low fitness in vivo are defective in RpoS induction

Mutants of Salmonella enterica serovar Typhimurium resistant to fusidic acid (Fusr) have mutations in fusA, the gene encoding translation elongation factor G (EF-G). Most Fusr mutants have reduced fitness in vitro and in vivo, in part explained by mutant EF-G slowing the rate of protein synthesis and growth. However, some Fusr mutants with normal rates of protein synthesis still suffer from reduced fitness in vivo. As shown here, Fusr mutants could be similarly ranked in their relative fitness in mouse infection models, in a macrophage infection model, in their relative hypersensitivity to hydrogen peroxide in vivo and in vitro, and in the amount of RpoS production induced upon entry into the stationary phase. We identify a reduced ability to induce production of RpoS (sigmas) as a defect associated with Fusr strains. Because RpoS is a regulator of the general stress response, and an important virulence factor in Salmonella, an inability to produce RpoS in appropriate amounts can explain the low fitness of Fusr strains in vivo. The unfit Fusr mutants also produce reduced levels of the regulatory molecule ppGpp in response to starvation. Because ppGpp is a positive regulator of RpoS production, we suggest that a possible cause of the reduced levels of RpoS is the reduction in ppGpp production associated with mutant EF-G. The low fitness of Fusr mutants in vivo suggests that drugs that can alter the levels of global regulators of gene expression deserve attention as potential antimicrobial agents.

Mutations in rpoBC suppress the defects of a Sinorhizobium meliloti relA mutant

The nitrogen-fixing symbiosis between Sinorhizobium meliloti and Medicago sativa requires complex physiological adaptation by both partners. One method by which bacteria coordinately control physiological adaptation is the stringent response, which is triggered by the presence of the nucleotide guanosine tetraphosphate (ppGpp). ppGpp, produced by the RelA enzyme, is thought to bind to and alter the ability of RNA polymerase (RNAP) to initiate and elongate transcription and affect the affinity of the core enzyme for various sigma factors. An S. meliloti relA mutant which cannot produce ppGpp was previously shown to be defective in the ability to form nodules. This mutant also overproduces a symbiotically necessary exopolysaccharide called succinoglycan. The work presented here encompasses the analysis of suppressor mutants, isolated from host plants, that suppress the symbiotic defects of the relA mutant. All suppressor mutations are extragenic and map to either rpoB or rpoC, which encode the beta and beta' subunits of RNAP. Phenotypic, structural, and gene expression analyses reveal that suppressor mutants can be divided into two classes; one is specific in its effect on stringent response-regulated genes and shares striking similarity with suppressor mutants of Escherichia coli strains that lack ppGpp, and another reduces transcription of all genes tested in comparison to that in the relA parent strain. Our findings indicate that the ability to successfully establish symbiosis is tightly coupled with the bacteria's ability to undergo global physiological adjustment via the stringent response.

Control of rRNA expression by small molecules is dynamic and nonredundant

The control of ribosomal RNA transcription is one of the most enduring issues in molecular microbiology, having been subjected to intense scrutiny for over 50 years. Rapid changes in rRNA expression occur during transitions in the bacterial growth cycle and following nutritional shifts during exponential growth. Genetic approaches and measurements of initiating nucleoside triphosphate (iNTP) and guanosine 5'-diphosphate, 3'-diphosphate (ppGpp) concentrations and of rRNA promoter activities showed that rapid changes in the concentrations of iNTPs and ppGpp account for the rapid changes in rRNA expression. The two regulatory signals are nonredundant: changes in iNTP concentration dominate regulation during outgrowth from stationary phase, whereas changes in ppGpp concentration are responsible for regulation following upshifts and downshifts during exponential phase. The results suggest a molecular logic for the use of two homeostatic regulatory mechanisms to monitor different aspects of ribosome activity and provide general insights into the nature of overlapping regulatory circuits.

Essential steps in the ppGpp-dependent regulation of bacterial ribosomal RNA promoters can be explained by substrate competition

Transcription of stable RNA genes is known to be dramatically reduced in the presence of guanosine tetraphosphate (ppGpp), the mediator of the stringent response. Using in vitro transcription systems with ribosomal RNA P1 promoters, we have analyzed which step of the initiation cycle is inhibited by the effector ppGpp. We show that formation of the ternary transcription initiation complex consisting of RNA polymerase holoenzyme, the promoter DNA, and the first initiating nucleotide triphosphate is the major step at which ppGpp exerts its regulation. Neither primary binding of RNA polymerase to the promoter nor isomerization to the open binary complexes or the subsequent promoter clearance steps contributes notably to the observed inhibition. The effect of ppGpp-dependent inhibition in the formation of the ternary transcription initiation complex could be mimicked by nucleotide derivatives known to bind to the RNA polymerase active center. Using these model compounds, almost identical inhibition characteristics were observed as seen with ppGpp. The results support the previously published model, which suggests that ppGpp-dependent inhibition is based on competition between the inhibitor molecules and NTP substrates for access to the active center of RNA polymerase.

Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli

The bacterial sigma factor RpoS is strongly induced under a variety of stress conditions and during growth into stationary phase. Here, we used rpoS-lac fusions in Escherichia coli to investigate control acting at the level of RpoS synthesis, which is especially evident when cells approach stationary phase in rich medium. Previous work has shown that the small molecule ppGpp is required for normal levels of RpoS in stationary phase. Despite the attraction of a model in which the ppGpp level controls stationary-phase induction of RpoS, careful measurement of rpoS-lac expression in a mutant lacking ppGpp showed similar effects during both exponential growth and stationary phase; the main effect of ppGpp was on basal expression. In addition, a modest regulatory defect was associated with the mutant lacking ppGpp, delaying the time at which full expression was achieved by 2 to 3 h. Deletion analysis showed that the defect in basal expression was distributed over several sequence elements, while the regulatory defect mapped to the region upstream of the rpoS ribosome-binding site (RBS) that contains a cis-acting antisense element. A number of other genes that have been suggested as regulators of rpoS were tested, including dksA, dsrA, barA, ppkx, and hfq. With the exception of the dksA mutant, which had a modest defect in Luria-Bertani medium, none of these mutants was defective for rpoS stationary-phase induction. Even a short rpoS segment starting at 24 nucleotides upstream of the AUG initiation codon was sufficient to confer substantial stationary-phase regulation, which was mainly posttranscriptional. The effect of RBS-proximal sequence was independent of all known trans-acting factors, including ppGpp.

Regulation of sigma factor competition by the alarmone ppGpp

Many regulons controlled by alternative sigma factors, including sigma(S) and sigma(32), are poorly induced in cells lacking the alarmone ppGpp. We show that ppGpp is not absolutely required for the activity of sigma(S)-dependent promoters because underproduction of sigma(70), specific mutations in rpoD (rpoD40 and rpoD35), or overproduction of Rsd (anti-sigma(70)) restored expression from sigma(S)-dependent promoters in vivo in the absence of ppGpp accumulation. An in vitro transcription/competition assay with reconstituted RNA polymerase showed that addition of ppGpp reduces the ability of wild-type sigma(70) to compete with sigma(32) for core binding and the mutant sigma(70) proteins, encoded by rpoD40 and rpoD35, compete less efficiently than wild-type sigma(70). Similarly, an in vivo competition assay showed that the ability of both sigma(32) and sigma(S) to compete with sigma(70) is diminished in cells lacking ppGpp. Consistently, the fraction of sigma(S) and sigma(32) bound to core was drastically reduced in ppGpp-deficient cells. Thus, the stringent response encompasses a mechanism that alters the relative competitiveness of sigma factors in accordance with cellular demands during physiological stress.

Charging levels of four tRNA species in Escherichia coli Rel(+) and Rel(-) strains during amino acid starvation: a simple model for the effect of ppGpp on translational accuracy

Escherichia coli strains mutated in the relA gene lack the ability to produce ppGpp during amino acid starvation. One consequence of this deficiency is a tenfold increase in misincorporation at starved codons compared to the wild-type. Previous work had shown that the charging levels of tRNAs were the same in Rel(+) and Rel(-) strains and reduced, at most, two- to fivefold in both strains during starvation. The present reinvestigation of the charging levels of tRNA(2)(Arg), tRNA(1)(Thr), tRNA(1)(Leu) and tRNA(His) during starvation of isogenic Rel(+) and Rel(-) strains showed that starvation reduced charging levels tenfold to 40-fold. This reduction corresponds much better with the decreased rate of protein synthesis during starvation than that reported earlier. The determination of the charging levels of tRNA(2)(Arg) and tRNA(1)(Thr) during starvation were accurate enough to demonstrate that charging levels were at least fivefold lower in the Rel(-) strain compared to the Rel(+) strain. Together with other data from the literature, these new data suggest a simple model in which mis-incorporation increases as the substrate availability decreases and that ppGpp has no direct effect on enhancing translational accuracy at the ribosome.

Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor

The uspA promoter, driving production of the universal stress protein A in response to diverse stresses, is demonstrated to be under dual control. One regulatory pathway involves activation of the promoter by the alarmone guanosine 3',5'-bisphosphate, via the beta-subunit of RNA polymerase, whereas the other consists of negative control by the FadR repressor. In contrast to canonical dual control by activation and repression circuits, which depends on concomitant activation and derepression for induction to occur, the ppGpp-dependent activation of the uspA promoter overrides repression by an active FadR under conditions of severe cellular stress (starvation). The ability of RNA polymerase to overcome repression during stringency depends, in part, on the strength of the FadR operator. This emergency derepression is operative on other FadR-regulated genes induced by starvation and is argued to be an essential regulatory mechanism operating during severe stress.

Regulation of bacteriophage lambda development by guanosine 5'-diphosphate-3'-diphosphate

On infection of its host, Escherichia coli, bacteriophage lambda can follow one of two alternative developmental pathways: lytic or lysogenic. Here we demonstrate that the "lysis-versus-lysogenization" decision is influenced by guanosine tetraphosphate (ppGpp), a nucleotide that is synthesized in E. coli cells in response to amino acid or carbon source starvation. We found that the efficiency of lysogenization is the highest at ppGpp concentrations somewhat higher than the basal level; too low and too high levels of ppGpp result in less efficient lysogenization. Maintenance of the already integrated lambda prophage and phage lytic development were not significantly influenced in the host lacking ppGpp. We found that the level of HflB/FtsH protease, responsible for degradation of the CII protein, an activator of "lysogenic" promoters, depends on ppGpp concentration. The highest levels of HflB/FtsH was found in bacteria lacking ppGpp and in cells bearing increased concentrations of this nucleotide. Using lacZ fusions, we investigated the influence of ppGpp on activities of lambda promoters important at the stage of the lysis-versus-lysogenization decision. We found that each promoter is regulated differentially in response to the abundance of ppGpp. Moreover, our results suggest that the cAMP level may influence ppGpp concentration in cells. The mechanism of the ppGpp-mediated control of lambda development at the stage of the lysis-versus-lysogenization decision may be explained on the basis of differential influence of guanosine tetraphosphate on activities of p(L), p(R), p(E), p(I), and p(aQ) promoters and by dependence of HflB/FtsH protease level on ppGpp concentration.

Activities of constitutive promoters in Escherichia coli

The in vivo activities of seven constitutive promoters in Escherichia coli have been determined as functions of growth rate in wild-type relA+ spoT+ strains with normal levels of guanosine tetraphosphate (ppGpp) and in ppGpp-deficient DeltarelADeltaspoT derivatives. The promoters include (i) the spc ribosomal protein operon promotor Pspc; (ii) the beta-lactamase gene promotor Pblaof plasmid pBR322; (iii) the PLpromoter of phage lambda; (iv) and (v) the replication control promoters PRNAIand PRNAIIof plasmid pBR322; and (vi) and (vii) the P1 and P2 promoters of the rrnB ribosomal RNA operon. Each strain carried an operon fusion consisting of one of the respective promoter regions linked to lacZ and recombined into the chromosome at the mal locus of a lac deletion strain. The amount of 5'-terminal lacZ mRNA and of beta-galactosidase activity expressed from these promoters were determined by standard hybridization or enzyme activity assays, respectively. In addition, DNA, RNA and protein measurements were used to obtain information about gene dosage, rRNA synthesis and translation rates. By combining lacZ mRNA hybridization data with gene dosage and rRNA synthesis data, the absolute activity of the different promoters, in transcripts/minute per promoter, was determined. In ppGpp-proficient (relA+ spoT+) strains, the respective activities of rrnB P1 and P2 increased 40 and fivefold with increasing growth rate between 0.7 and 3.0 doublings/hour. The activities of Pspc, PL, Pbla, and PRNAIincreased two- to threefold and reached a maximum at growth rates above 2.0 doublings/hour. In contrast, PRNAIIactivity decreased threefold over this range of growth rates. In ppGpp-deficient (DeltarelA DeltaspoT) bacterial strains, the activities of rrnB P1 and P2 promoters both increased about twofold between 1.6 and 3.0 doublings/hour, whereas the activities of Pspc, PL, Pbla, and PRNAI, and PRNAIIwere about constant. To explain these observations, we suggest that the cellular concentration of free RNA polymerase increases with increasing growth rate; for saturation the P1 and P2 rRNA promoters require a high RNA polymerase concentration that is approached only at the highest growth rates, whereas the other promoters are saturated at lower polymerase concentrations achieved at intermediate growth rates. In addition, the data indicate that the respective rrnB P1 and PRNAIIpromoters were under negative and positive control by ppGpp. This caused a reduced activity of rrnB P1 and an increased activity of PRNAIIduring slow growth in wild-type (relA+ spoT+) relative to ppGpp-deficient (DeltarelA DeltaspoT) bacterial strains.

The replication checkpoint control in Bacillus subtilis: identification of a novel RTP-binding sequence essential for the replication fork arrest after induction of the stringent response

We have shown previously that induction of the stringent response in Bacillus subtilis resulted in the arrest of chromosomal replication between 100 and 200 kb either side of oriC at distinct stop sites, designated LSTer and RSTer, left and right stringent terminators respectively. This replication checkpoint was also shown to involve the RTP protein, normally active at the chromosomal terminus. In this study, we show that the replication block is absolutely dependent upon RelA, correlated with high levels of ppGpp, but that efficient arrest at STer sites also requires RTP. DNA-DNA hybridization data indicated that one or more such LSTer sites mapped to gene yxcC (-128 kb from oriC). A 7.75 kb fragment containing this gene was cloned into a theta replicating plasmid, and plasmid replication arrest, requiring both RelA and RTP, was demonstrated. This effect was polar, with plasmid arrest only detected when the fragment was orientated in the same direction with respect to replication, as in the chromosome. This LSTer2 site was further mapped to a 3.65 kb fragment overlapping the next40 probe. Remarkably, this fragment contains a 17 bp sequence (B'-1) showing 76% identity with an RTP binding site (B sequence) present at the chromosomal terminus. This B'-1 sequence, located in the gene yxcC, efficiently binds RTP in vitro, as shown by DNA gel retardation studies and DNase I footprinting. Importantly, precise deletion of this sequence abolished the replication arrest. We propose that this modified B site is an essential constituent of the LSTer2 site. The differences between arrest at the normal chromosomal terminus and arrest at LSTer site are discussed.

Changes in conserved region 3 of Escherichia coli sigma 70 mediate ppGpp-dependent functions in vivo

In Escherichia coli, deletion of relA and spoT results in an inability to synthesize ppGpp, guanosine-3',5'-bis(pyrophosphate), and a loss in the ability to grow on amino acid-free minimal media. Two spontaneous missense suppressor alleles, rpoD(P504L) and rpoD(S506F), able to confer complete prototrophy without the reappearance of ppGpp, were localized to that portion of rpoD coding for conserved region 3.1 of sigma 70. Characterization of these mutants revealed distinct physiological effects. Both mutations cause growth rate defects exacerbated in the presence of ppGpp and paralleled by reductions in rrnB P1-lacZ reporter gene expression, as if growth of these mutants is limited by rrn P1 promoter activity. Levels of ppGpp, as a function of growth rate, are lowered by a constant fraction (75%) in the rpoD(P504L) strain and by a decreasing fraction at lower growth rates in the rpoD(S506F) strain. Comparisons of rrnB P1-lacZ expression at different ppGpp levels is interpreted for the rpoD(P504L) mutant as resulting from a hypersensitivity to ppGpp. For the rpoD(S506F) mutant there is a normal sensitivity to ppGpp but the action of ppGpp is functionally mimicked; that is, a low intrinsic rrnB P1 promoter activity is manifested even in the absence of ppGpp. In addition to effects on rrnB P1 promoters, the accumulation of the stationary phase-specific sigma factor (sigma s), which is normally ppGpp-dependent, was assayed in the rpoD mutants and in one, rpoD(S506F), found to be restored in the absence of ppGpp. The behavior of these mutants thus seems consistent with a unitary effect of ppGpp on transcription resulting in both negative and positive regulation of gene expression. In addition, the cellular fraction of sigma 70 associated with holoenzyme appears reduced by both rpoD mutations as judged by comparison with wild-type and ppGpp-deficient strains. Interestingly, the amount of holoenzyme-associated sigma 70 was higher in the ppGpp-deficient than in the wild-type strain, possibly indicating that sigma 70-core RNA polymerase interactions are decreased by ppGpp.

Direct correlation between overproduction of guanosine 3',5'-bispyrophosphate (ppGpp) and penicillin tolerance in Escherichia coli

The penicillin tolerance exhibited by amino acid-deprived Escherichia coli has been previously proposed to be a consequence of the stringent response. Evidence indicating that penicillin tolerance is directly attributable to guanosine 3',5'-bispyrophosphate (ppGpp) overproduction and not to some other effect of amino acid deprivation is now presented. Accumulation of ppGpp in the absence of amino acid deprivation was achieved by the controlled overexpression of the cloned relA gene, which encodes ppGpp synthetase I. The overproduction of ppGpp resulted in the inhibition of both peptidoglycan and phospholipid synthesis and in penicillin tolerance. The minimum concentration of ppGpp required to establish these phenomena was determined to be 870 pmol per mg (dry weight) of cells. This represented about 70% of the maximum level of ppGpp accumulated during the stringent response. Penicillin tolerance and the inhibition of peptidoglycan synthesis were both suppressed when ppGpp accumulation was prevented by treatment with chloramphenicol, an inhibitor of ppGpp synthetase I activation. Glycerol-3-phosphate acyltransferase, the product of plsB, was recently identified as the main site of ppGpp inhibition in phospholipid synthesis (R. J. Health, S. Jackowski, and C. O. Rock, J. Biol. Chem. 269:26584-26590, 1994). The overexpression of the cloned plsB gene reversed the penicillin tolerance conferred by ppGpp accumulation. This result supports previous observations indicating that the membrane-associated events in peptidoglycan metabolism were dependent on ongoing phospholipid synthesis. Interestingly, treatment with beta-lactam antibiotics by itself induced ppGpp accumulation, but the maximum levels attained were insufficient to confer penicillin tolerance.

Lysis of Escherichia coli by beta-lactams which bind penicillin-binding proteins 1a and 1b: inhibition by heat shock proteins

The heat shock proteins (HSPs) of Escherichia coli were artificially induced in cells containing the wild-type rpoH+ gene under control of a tac promoter. At 30 degrees C, expression of HSPs produced cells that were resistant to lysis by cephaloridine and cefsulodin, antibiotics that bind penicillin-binding proteins (PBPs) 1a and 1b. This resistance could be reversed by the simultaneous addition of mecillinam, a beta-lactam that binds PBP 2. However, even in the presence of mecillinam, cells induced to produce HSPs were resistant to lysis by ampicillin, which binds all the major PBPs. Lysis of cells induced to produce HSPs could also be effected by imipenem, a beta-lactam known to lyse nongrowing cells. These effects suggest the existence of at least two pathways for beta-lactam-dependent lysis, one inhibited by HSPs and one not. HSP-mediated lysis resistance was abolished by a mutation in any one of five heat shock genes (dnaK, dnaJ, grpE, GroES, or groEL). Thus, resistance appeared to depend on the expression of the complete heat shock response rather than on any single HSP. Resistance to lysis was significant in the absence of the RelA protein, implying that resistance could not be explained by activation of the stringent response. Since many environmental stresses promote the expression of HSPs, it is possible that their presence contributes an additional mechanism toward development in bacteria of phenotypic tolerance to beta-lactam antibiotics.

Protein sequences encoded by the relA and the spoT genes of Escherichia coli are interrelated

relA and spoT are designations for two unlinked Escherichia coli genes whose products function in the synthesis and degradation of guanosine 3',5'-bispyrophosphate during the stringent regulatory response to amino acid deprivation. The RelA protein catalyzes an ATP:GTP 3'-pyrophosphoryl group transfer reaction, and the SpoT protein has a guanosine 3',5'-bispyrophosphate 3'-pyrophosphohydrolyase activity. Both genes have been sequenced recently; the relA gene produces an 84-kDa protein, and the spoT gene is deduced to encode a 79-kDa protein. We report here that the protein sequences of the relA and spoT genes are extensively interrelated.

Expression of a cloned beta-glucanase gene from Bacillus amyloliquefaciens in an Escherichia coli relA strain after plasmid amplification

Amino acid starvation of cells of the Escherichia coli relA strain, CP79, which cannot accumulate guanosine tetraphosphate (ppGpp) in response to amino acid limitation, increased the pEG1 plasmid content about 5- to 7-fold in comparison with exponentially growing cells (pEG1:pBR322 with an insertion of Bacillus amyloliquefaciens DNA coding for beta-glucanase). In contrast, no pEG1 amplification occurred in E. coli CP78, the stringently controlled counterpart, after amino acid starvation. In order to verify these results, the plasmid DNA content was monitored by measuring the expression of pEG1-encoded beta-glucanase from B. amyloliquefaciens both before and after plasmid amplification. When amino acid starved CP79 cells were given an additional dose of amino acids, a more than 10-fold increase in pEG1-encoded beta-glucanase activity (per cell mass) was measured. This increase in enzyme activity correlates with pEG1 amplification during amino acid limitation. Under comparable conditions the activity of beta-glucanase was not increased in strain CP78, which did not amplify the plasmid. We suggest that the replication of pEG1 in amino acid starved E. coli cells is somehow under negative control by ppGpp. Moreover, we found the Bacillus beta-glucanase in E. coli relA cells to be excreted into the growth medium after starvation and overexpression.

Near-UV stress in Salmonella typhimurium: 4-thiouridine in tRNA, ppGpp, and ApppGpp as components of an adaptive response

We have examined the role of 4-thiouridine in the responses of Salmonella typhimurium to near-UV irradiation. Mutants lacking 4-thiouridine (nuv) and mutants defective in the synthesis of ppGpp (guanosine 5'-diphosphate-3'-diphosphate) (relA) were found to be sensitive to killing by near-UV. Near-UV induced the synthesis of a set of proteins that were not induced in the nuv mutant. Some of these proteins were identified as oxidative defense proteins, and others were identified as ppGpp-inducible proteins. Over 100-fold increases in ApppGpp (adenosine 5', 5"'-triphosphoguanosine-3"'-diphosphate, the adenylylated form of ppGpp) were observed in wild-type cells after near-UV irradiation but not in the 4-thiouridine-deficient mutant. These data support a model in which ppGpp and ApppGpp, a dinucleotide proposed to be synthesized by tRNA-aminoacyl synthetases as a response to the cross-linking of 4-thiouridine in tRNA by near-UV, induce the synthesis of proteins necessary for resistance to near-UV irradiation.

High temperature induction of a stringent response in the dnaK(Ts) and dnaJ(Ts) mutants of Escherichia coli

The cellular concentrations of ppGpp in the dnaK(Ts) and dnaJ(Ts) mutants of Escherichia coli were examined, since the thermosensitive RNA synthesis of these mutants is relaxed by an additional mutation in the relA gene. The results showed that ppGpp accumulated extensively in the dnaK(Ts) and dnaJ(Ts) mutants after a temperature shift up, reaching levels of 5 mM and 0.5 mM, respectively. This unusual accumulation of ppGpp was suppressed by the relA1 mutation, implying that it results from induction of a stringent response in these mutants at a nonpermissive temperature.

[The role of ppGpp in the coordination of transcription of the ribosomal protein genes rplKAJL and RNA-polymerase rpoBC genes in Escherichia coli cells]

Transcription of the ribosomal protein genes rplKAJL and of the RNA polymerase genes proBC in the E. coli cells depends on the level of regulatory nucleotide ppGpp. The ppGpp acts as a negative regulator of transcription of the rpoBC genes in conditions of moderate deficiency of amino acids (after the cells were shifted down from amino acid rich to minimal media) or after incomplete deacylation of tRNA exerted by addition of serine-hydroxamate, or by partial inactivation of valyl-tRNA synthetase. Rifampicin of low concentrations, which inhibit total transcription not more than to 50%, stimulates transcription of the genes rpoBC and rplKAJL. It was estimated that stimulatory effect of rifampicin results from the ability of this antibiotic to decrease synthesis of ppGpp--the negative regulator of transcription of genes rplKAJL and rpoBC.

[Synthesis of alkaline phosphatase in a stringent and a relaxed strain of Escherichia coli under amino acid and phosphate limitation]

Synthesis of alkaline phosphatase in Escherichia coli is derepressed under phosphate starvation in the stringent strain CP78 as well as in its relaxed counterpart CP79. During limitation of phosphate as well as of amino acids a decrease of enzyme activity is observed, especially in the relaxed strain, which can not produce ppGpp under this conditions. After phosphate limitation synthesis of ppGpp is not stimulated and the kinetics of RNA synthesis is similar in both strains. We suggest that ppGpp is not directly involved in the regulation of gene expression during phosphate starvation.

Optimization of near ultraviolet irradiation conditions for isolation of relaxed mutants of Escherichia coli

We describe optimized conditions for isolation of relaxed mutants of bacteria with 4-thiouridine-containing tRNAs. The results presented here imply that besides the knowledge of the action spectra for near UV-induced growth inhibition of stringent and relaxed cells the fluence--fluence rate dependence of growth inhibition is an essential factor for optimizing the enrichment of relaxed mutants. We investigated systematically the dependence of growth inhibition of both stringent and relaxed strains of E. coli on the wavelength lambda, on the fluence F and on the fluence rate I within the ranges lambda = 301-365 nm, F = 0-48 kJ X m-2 and I = 0-60 W X m-2. The optimized conditions for selection of relaxed mutants of E. coli are lambda = 334 nm, F = 48 kJ X m-2 and I = 60 W X m-2. These optimized parameters determined for E. coli may be used in general to select relaxed mutants of other bacterial species by combining the turbidostat technique with near UV irradiation (Riesenberg et al. 1983).

Mixed culture kinetics of stringent and relaxed Escherichia coli cells in glucose-limited chemostat

The mixed culture kinetics of stringent and relaxed Escherichia coli cells were investigated in a glucose-limited chemostat at different dilution rates. Independent of the dilution rate the stringent cells competed out the relaxed cells. But the number of generations necessary for displaying the relaxed cells by the stringent ones increased with increasing dilution rate. The results are discussed as a consequence of the regulatory role of guanosine-5'-diphosphate-3'-diphosphate (ppGpp) which is known to be present at different concentrations in stringent and relaxed cells under conditions of nutrient limitation. In addition, it is postulated that the coefficient of the maintenance metabolism according to PIRT (1965) is slower in stringent cells than in relaxed cells of E. coli.

Functional interrelationship between two tandem E. coli ribosomal RNA promoters

The Escherichia coli chromosome carries seven cistrons encoding ribosomal RNA sequences. In all cases studied, in vitro and in vivo, it has been established that transcription is initiated from two tandem promoters. The expression of the rRNA cistrons is regulated in response to growth rate as well as to aminoacyl tRNA availability. In the present study, a plasmid (pPS1) carrying the promoter region of the rrnA cistron fused to the terminator region of rrnB has been used for in vitro transcription experiments. The presence of the terminators (T1 and T2) together with the fact that supercoiled DNA is found to be a highly efficient template, provide an ideal in vitro system in which to study the functional interrelationship between the two tandem promoters of E. coli rRNA cistrons. The results suggest that the rate of rRNA synthesis in E. coli cells growing in various conditions, as reflected by the availability of RNA polymerase, is primarily dependent on the properties of the two tandem rRNA promoters.

[Role of spot gene product in the degradation of pppGpp in bacteria]

In Baccillus subtilis cells, in contrast to Escherichia coli cells, chelating agent 1,10-phenanthroline induces the expansion of guanosine-5'-diphosphate,3'-diphosphate( (ppGpp) pool, as well as the pool of its precursor guanosine-5'-triphosphate,3'-diphosphate (pppGpp). Under these conditions the degradation rate of both nucleotides decreases greatly, which is the main cause of their accumulation in the cells. In E. coli phenanthroline inactivates the product of spoT gene, which is responsible for ppGpp degradation, as a result of combining Mn2+ ions necessary for the activity of this enzyme. The addition of Mn2+ ions to B. subtilis cells, treated with phenanthroline, leads to the decline in (p)ppGpp pools. Antibiotic tetracycline, which has the chelating properties at the concentration of 1 mg/ml, also inactivates spoT gene product in E. coli and slows down the decay of ppGpp, but not of pppGpp. The addition of high concentrations of tetracycline to B. subtilis cells leads to severe inhibition of the degradation of both nucleotides. Therefore in B. subtilis spoT gene product is involved in the degradation of pppGpp, as well as ppGpp. In E. coli cells with defective gpp gene product, taking part in the conversion of pppGpp to ppGpp, phenanthroline and tetracycline also inhibit the breakdown of both nucleotides. The similarity of B. subtilis and E. coli gpp cells in respect of spoT gene product functions and of enhanced pppGpp fraction in the total amount of guanosine polyphosphates during aminoacyl-tRNA limitation makes it plausible that in B. subtilis cells the product of gpp gene is missing or has low activity.

[Dependence of threonine operon expression on the relA gene allelic state and the level of guanosine tetraphosphate in E. coli]

The expression of threonine operon in Rel+ and Rel- E. coli cells was studied at the transcriptional level. The rel+ genotype and the lack of a specific amino acid--threonine--are necessary for the stimulation of threonine operon transcription. Under these conditions the RNA fraction, which is thr-mRNA, is increased 2-fold. The lack of arginine or histidine in Rel+ strain does not lead to derepression of the threonine operon. It is shown that in a cell-free system 0.1 mM ppGpp stimulate the synthesis of thr-mRNA on phage DNA lambda dthr and plasmid DNA PYN1107, containing total threonine operon 1.5--2-fold. It is assumed that ppGpp stimulates the initiation of transcription. Studies on the strain carrying spoT- mutation, which significantly lowers the rate of ppGpp degradation and results in suppression of rel- phenotype, revealed positive correlation between the intracellular level of ppGpp and the thr-mRNA fraction in the total transcript.

Isolation and characterization of prototrophic relaxed mutants of Klebsiella pneumoniae

A new selection procedure has been developed for isolating prototrophic relaxed mutants of Klebsiella pneumoniae. Two mutants were isolated. One of them showed a fully relaxed phenotype, while the other one behaved in a semi-relaxed way. The wild-type strain, as well as the rel mutants exerted similar patterns to their E. coli counterparts in RNA, protein, ppGpp and pppGpp accumulation during amino starvation, carbon source shift-down and nitrogen starvation. Both mutants became stringent after introducing an F'-factor carrying the relA+ allele from Escherichia coli. The relaxed phenotype could be recovered by curing the F'-factor. Some of the pleiotropic consequences of rel mutations found in E. coli are present in the Klebsiella mutants also while some of them are absent. The mutants are defective in dinitrogen fixation after the exhaustion of limiting ammonium from the culture medium. However, their merodiploid derivatives, carrying the E. coli relA+ allele, showed the wild-type level of nitrogenase activity under the same conditions.

Translational accuracy enhanced in vitro by (p)ppGpp

The effect of (p)ppGpp on the accuracy of translation in vitro was studied with a system that has a missense error frequency similar to that of living bacteria. When poly (U) is translated, limitation of the system in Phe increases the Leu missense error frequency. The introduction of (p)ppGpp to the Phe-limited mixtures reduces significantly the missense errors as well as reduces the rate of translation. The introduction of (p)ppGpp to a full system has no effect on the accuracy of translation but does reduce its rate. The effects of (p)ppGpp on rate and accuracy of translation can be simulated in part by other inhibitors of translation such as GDPCP, fusidic acid and tetracycline. Furthermore, the presence of ppGpp or GDPCP in a Phe-limited system leads to an accumulation of Phe-tRNA, while a Phe-limited system that contains only GTP has negligibly small concentrations of Phe-tRNA. We conclude that one way in which (p)ppGpp improves the accuracy of translation is by permitting the system to maintain a favorable Phe-tRNA/Leu-tRNA ratio.

Escherichia coli mutant containing a large deletion from relA to argA

A mutant of Escherichia coli has been isolated that contains a large deletion (about 3 X 10(7) daltons of deoxyribonucleic acid) encompassing argA, fuc, and relA. This mutant strain (AA-787) is also cold sensitive for growth at 18 degrees C. Strain AA-787 was obtained fortuitously as a cold-sensitive pseudorevertant of a strain having a heat-sensitive peptidyl-transfer ribonucleic acid hydrolase. Genetic analysis, using transduction and interrupted mating, showed the cold sensitivity mutation to be located adjacent to relA. Further analysis demonstrated loss of relA, fuc, and argA gene functions but retention of eno and recB, closely linked genes adjacent to relA and argA, respectively. Unusually high cotransduction of flanking markers (cysC and thyA) indicated loss of approximately 1 min of the E. coli genetic map in strain AA-787. Guanosine 3'-diphosphate 5'-diphosphate (ppGpp) was synthetized in mutant strain AA-787 at basal levels, and ppGpp synthesis was stimulated by carbon-source downshift. No ppGpp synthesis could be obtained using ribosomes isolated from strain AA-787. These findings, taken together, show that deletion of relA in E. coli does not completely abolish ppGpp synthesis and suggests that another enzyme system must also be responsible for ppGpp synthesis.

Mutants of Escherichia coli defective in the degradation of guanosine 5'-triphosphate, 3'-diphosphate (pppGpp)

A new class of mutants of E. coli exhibiting altered metabolism of ppGpp and pppGpp has been isolated, and mapped at a locus designated gpp, near min 83 on the genetic map. These mutants accumulate elevated levels of pppGpp during amino acid starvation or carbon source downshift, and exhibit a reduced rate of pppGpp degradation in vivo. The in vitro evidence suggests that the gpp mutants are defective in a 5'-nucleotidase, which specifically hydrolyzes pppGpp to ppGpp. Certain combinations of gpp and spoT mutations are inviable. A gpp spoT double mutant, constructed by employing a leaky spoT mutation, was found to have a slower rate of pppGpp degradation than the gpp mutant alone. This result indicates that spoT also participates in pppGpp degradation. The inviability of certain gpp spoT combinations is attributed to the inability of the double mutants to degrade pppGpp. This is supported by the observation that selection for increased growth rate on the double mutant results in the recovery of relA mutations. Various effects of the gpp mutation upon the pppGpp and ppGpp pools provide additional support for a scheme in which pppGpp is the major precursor of ppGpp.