A gene involved in the metabolic control of ppGpp synthesis

Summary A genetic locus has been identified which controls the basal synthesis of ppGpp in growing E. coli. Cells carrying a recessive allele of the relX gene have a very low concentration of ppGpp during balanced growth, and fail to accumulate ppGpp in response to carbon/energy source downshift. Moreover, the recessive relX allele renders the cells unable to grow at 42° C and, when coupled with relA, makes the cells sensitive to the presence of leucine in minimal medium. RelX is cotransduced with fuc and relA and located at approximately 59.4 min on the E. coli genetic map.     

Regulation of stable RNA synthesis and ppGpp levels in growing cells of Escherichia coli

Under the balanced condition of growth of E. coli cells, no distinct difference is observed in stable RNA and protein synthesis between CP78 (rel⁺) and CP79 (rel⁻), whereas a considerable difference is present in RNA accumulation between NF161 (rel⁺) and NF162 (rel⁻), where NF161 < NF162. The RNA content of NF161 is lower than that of NF162 in four different cultures with different growth rates. These two sets of isogenic pairs of rel⁺ and rel⁻ strains are commonly used in the study of rel gene function; however, NF161 is a mutant in the spoT gene whose product may be responsible for the degradation of ppGpp. The basal levels of ppGpp in these four strains growing with three different growth rates were examined: NF161 (rel⁺spoT⁻) has a much higher content of ppGpp than do other strains. Furthermore, the contents of ppGpp tend to be lower when the above four strains are growing at a faster rate. Thus a close correlation seems to exist between the content of RNA and the basal level of ppGpp under the condition of balanced growth.     

Factors enhancing l-valine production by the growth-limited l-isoleucine auxotrophic strain Corynebacterium glutamicum ΔilvA ΔpanB ilvNM13 (pECKAilvBNC)

Cell growth limitation is known to be an important condition that enhances l-valine synthesis in Corynebacterium glutamicum recombinant strains with l-isoleucine auxotrophy. To identify whether it is the limited availability of l-isoleucine itself or the l-isoleucine limitation-induced rel-dependent ppGpp-mediated stringent response that is essential for the enhancement of l-valine synthesis in growth-limited C. glutamicum cells, we deleted the rel gene, thereby constructing a relaxed (rel ⁻ ) C. glutamicum ΔilvA ΔpanB Δrel ilvNM13 (pECKAilvBNC) strain. Variations in enzyme activity and l-valine synthesis in rel ⁺ and rel ⁻ strains under conditions of l-isoleucine excess and limitation were investigated. A sharp increase in acetohydroxy acid synthase (AHAS) activity, a slight increase in acetohydroxyacid isomeroreductase (AHAIR) activity, and a dramatic increase in l-valine synthesis were observed in both rel ⁺ and rel ⁻ cells exposed to l-isoleucine limitation. Although the positive effect of induction of the stringent response on AHAS and AHAIR upregulation in cells was not confirmed, we found the stringent response to be beneficial for maintaining increased AHAS, dihydroxyacid dehydratase, and transaminase B activity and l-valine synthesis in cells during the stationary growth phase.     

Thermolability of the stringent factor in rel mutants of Escherichia coli

The stringent factor extracted from several independently isolated rel^- mutants is more thermolabile than the stringent factor extracted from the parental rel⁺ strain. This thermolability is characteristically different in each of the mutants. This strongly suggests that the stringent factor is the product of the rel gene.     

Anti-tyrosinase antibodies in malignant melanoma

 Anti-tyrosinase antibodies were measured by enzyme-linked immunosorbent assay in sera of patients with malignant melanoma with either metastatic disease or no evidence of disease, in patients with melanoma and associated hypopigmentation (MAH), in patients with vitiligo and in healthy volunteers. The mean relative absorbance (A _rel) was calculated by dividing the absorbance of each sample by the mean value for the control group. Using this method, the A _rel of the control group was 1.000(SE 0.083). A _rel of patients with metastatic disease (1.516; SE 0.225) was significantly higher (P = 0.03) than the value for the controls, but insignificantly higher than that for patients with no evidence of disease (1.216; SE 0.148). Patients with no evidence of disease, in whom the primary lesion originated in the lower limb, had a significantly higher (P = 0.01) A _rel than the healthy volunteers. Patients with metastatic disease showed higher A _rel if their primary lesions were confined to the area of the head and neck or to the lower limb. Patients with vitiligo had higher A _rel values for their anti-tyrosinase antibody than any of the other groups. However, those with melanoma and MAH (vitiligo-like) had the same A _rel of anti-tyrosinase antibodies as the controls or the patients with metastatic melanoma. This observation reflected the possible absorption of anti-tyrosinase antibodies to melanoma antigens, and pointed to the participation of anti-tyrosinase antibodies in the destruction of normal melanocytes in patients with melanoma, as part of the immune reaction towards this disease. Received: 4 January 1996 / Accepted: 11 April 1996     

Phenotypic heterogeneity in mycobacterial stringent response

Background  

A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to survive under stress. In a recent study, a mycobacterial population of M. smegmatis was shown to develop phenotypic heterogeneity under nutrient depletion. The observed heterogeneity is in the form of a bimodal distribution of the expression levels of the Green Fluorescent Protein (GFP) as reporter with the gfp fused to the promoter of the rel gene. The stringent response pathway is initiated in the subpopulation with high rel activity.     

Cell volume change of Escherichia coli under stringent control apparent increase of K in rel cells

With several pairs of rel⁺ and rel⁻ strains of Escherichia coli, the effects of amino acid starvation on the intracellular concentration of K⁺ and the rate of uptake of ⁴²K⁺ were investigated. In the early phase of the experiments, the intracellular concentration of K⁺ was estimated by the conventional method in which the cell volume per A₆₆₀ value of the culture was assumed to be constant, being not influenced by the variation of growth condition and strain. Apparently, the K⁺ concentration of rel⁺ cells was kept almost constant, while that of rel⁻ cells increased about 1.5-fold 2 h after the exposure to amino acid starvation. Unexpectedly, however, the above assumption was found not to be valid in the present study. The cell volume per A₆₆₀ changed only slightly in CP78 (rel⁺) cells, while it increased markedly in CP79 (rel⁻) cells after the exposure to amino acid starvation. Reestimation of the K⁺ concentrations based on the estimated respective values of cell volumes per A₆₆₀ revealed no significant difference between both strains. After all, the above apparent phenomenon was found to be due to the fact that the increase in cell volume of the rel⁺ cells was arrested upon amino acid starvation whereas that in the rel⁻ cells was not. The ⁴²K⁺ uptake by the rel⁺ cells was depressed upon amino acid starvation, whereas that by the rel⁻ cells increased. Some regulatory mechanism was suggested to operate in both strains to keep their K⁺ concentrations constant. When intracellular concentration of a metabolite is to be determined, importance of measurement of cell volume under the respective conditions, without assuming the constancy of the cell volume per A₆₆₀ of the culture, was pointed out.     

Specificity of the amino acid transfer reaction inE. coli strains carrying different alleles of the RNA control (RC) gene

Summary The idea has been tested here that the aberration in amino acid controlled regulation of RNA synthesis in a mutant strain ofE. coli might reflect a major breakdown in the specificity of transfer of amino acids to S-RNA. For this purpose, S-RNA and amino acid activating enzymes were extracted from bacteria carrying either the normalRC ^st or the aberrantRC ^rel allele of the RNA control gene. The purified S-RNA preparations were first charged enzymatically with one or more of the 20 standard amino acids, then oxidized with periodate, and finally reisolated and retested for their residual capacity to accept an amino acid that was absent from the preliminary charging mixture. If preliminary charging transferred an amino acid to a non-cognate S-RNA species belonging to an absent amino acid, then the acceptor capacity for the missing amino acid would survive periodate oxidation and reveal its presence on recharging with that amino acid after post-periodate reisolation of the S-RNA. The results presented here show that there does not appear to exist any such major breakdown of transfer specificity in eitherRC ^st orRC ^rel bacteria: preliminary charging of the S-RNA fromRC ^rel bacteria with 19 of the 20 standard amino acids by use of the homologous amino acid activating enzymes does not afford protection against periodate oxidation for any appreciable fraction of the acceptor capacity for the absent 20th amino acid (when that amino acid is either methionine or arginine). It is unlikely, therefore, that thecatholic inducer, postulated to explain the continued RNA synthesis ofRC ^rel amino acid auxotrophs in the absence of their growth requirement, is one of the 20 standard amino acids.This investigation was supported by Public Health Service Research Grant CA 02129, from the National Cancer Institute.     

The relA locus and the regulation of lysine biosynthesis in Escherichia coli

Summary The allelic state of relA influences the phenotype of Escherichia coli strains carrying the lysA22 mutation: lysA22 relA strains are Lys^– where lysA22 relA ⁺ strains grow (slowly) in the absence of lysine. This physiological effect has been related to an effect of the expression of the relA locus on the regulation of lysine biosynthesis. The fully derepressed levels of some lysine enzymes (aspartokinase III, aspartic semialdehyde dehydrogenase, dihydrodipicolinate reductase) are observed under lysine limitation only in rel ⁺ strains. And the induction of DAP-decarboxylase by DAP is much higher in rel ⁺ than in rel ^– strains when an amino acid limitation of growth is also realised. These results are in agreement with the hypothesis of Stephens et al. (1975) on a possible role of the stringent regulation as a general signal for amino acid deficiency.     

The regulation of the ammonia assimilatory enzymes in Rel+ and Rel- strains of Salmonella typhimurium

Summary The influence of the relA1 mutation on the regulation of the ammonia assimilatory enzymes, glutamate dehydrogenase (EC 1.4.1.4), glutamine synthetase (EC 6.3.1.2), and glutamate synthase (EC 1.4.1.3), was examined. When cells grown in rich media (either Luria broth or glucose-ammonia plus casamino acids) were transferred to a glucose-ammonia medium, the relA mutant failed to resume growth and did not have the same increase in any of the assimilatory enzyme activities as the rel ⁺ strain. This effect was particularly dramatic for glutamate dehydrogenase, which increased 6-fold in the rel ⁺ strain. Measurements of the guanosine nucleotide concentrations showed that the rel ⁺ strain had a ppGpp concentration about 9 times that of the relA mutant 5 min after the shift to minimal medium. These results are consistent with those for other biosynthetic enzymes and show that the ammonia assimilatory enzymes require a relA product for their synthesis during shifts from rich to minimal media. In addition, we examined the response of these strains to a change in nitrogen source. The relA mutant again failed to resume growth after a shift from glucose-ammonia to glucose-arginine medium. Even though the ppGpp concentration did not increase, the rel ⁺ strain grew and increased glutamine synthetase activities about 2-fold. These changes in the absence of increased ppGpp levels suggest that some other relA-mediated function is important during this change in nitrogen source.     

Movement of ribosomes over messenger RNA in polysomes of rel + and rel - Escherichia coli strains

The in vitro movement of ribosomes over messenger RNA was studied in both the presence and the absence of protein synthesis. For this purpose, labeled polysomes were extracted from rel⁺ and rel^? strains of Escherichia coli grown in the presence of radioactive uracil and incubated in a cell-free system containing tRNA, amino acids, soluble enzymes and a source of energy. The gradual conversion of the labeled polysomes into monosomes and ribosomal subunits was followed by subjecting the reaction mixture to sucrose gradient sedimentation after various incubation times and measuring the radioactivity present in the three relevant ribosomal fractions.It was found that when the conditions of incubation allow protein synthesis to occur, polysomes extracted from rel⁺ and rel^? cells are converted mainly into free monosomes, which can be made to dissociate into subunits by high-sodium or low-magnesium ion concentrations. Under conditions in which protein synthesis cannot occur because a mutant aminoacyl-tRNA synthetase has been rendered inactive, polysome conversion still occurs, though to a reduced extent. When the products of such residual run-off are examined, however, a difference is manifest between polysomes extracted from rel⁺ and from rel^? strains: whereas the polysomes from the rel^? strain are still converted into free monosomes even in the absence of protein synthesis, the polysomes from the rel⁺ strain are now converted mainly into subunits. It can be inferred, therefore, that ribosomes from rel^? bacteria, but not those from rel⁺ bacteria, continue movement over messenger RNA in the absence of protein synthesis.Studies of mixed extracts from rel^? and rel⁺ bacteria have shown that the character of the run-off process does not depend on the source of tRNA and soluble enzymes; the proportions of monosomes and subunits among the run-off products formed in the absence of protein synthesis depend only on the source of the polysomes. It is suggested that the mutation of the rel gene alters the functional architecture of ribosomes.     

Reduction of Methionine Sulfoxide by Plants

A relaxed (rel) mutant was found among thirty spontaneous thiopeptin-resistant isolates of Streptomyces antibioticus strain 3720, an actinomycin-producing strain, which showed severely reduced ability to accumulate ppGpp during a nutritional shift-down. The pool size of GTP decreased markedly in the parental strain, but to a lesser extent in the rel mutant. The rel mutant did not show the induction of an enzyme, phenoxazinone synthase, which is involved in the biosynthesis of actinomycin. No negative effect of the rel mutation was observed on a constitutive enzyme, kynurenine formamidase, which also plays a role in actinomycin synthesis. The mutant also failed to produce melanin, but still retained the ability to form aerial mycelium and spores, although the onset of the formation of aerial mycelium was markedly delayed. Neither the phenoxazinone synthase activity nor the kynurenine formamidase activity was affected by ppGpp in vitro. It is suggested tha the stringent response (ppGpp) may be generally essential for the induction of enzymes involved in secondary metabolism.     

The relA/spoT-Homologous Gene in Streptomyces coelicolor Encodes Both Ribosome-Dependent (p)ppGppSynthesizing and -Degrading Activities

Streptomyces coelicolor (p)ppGpp synthetase (Rel protein) belongs to the RelA and SpoT (RelA/SpoT) family, which is involved in (p)ppGpp metabolism and the stringent response. The potential functions of the rel gene have been examined. S. coelicolor Rel has been shown to be ribosome associated, and its activity in vitro is ribosome dependent. Analysis in vivo of the active recombinant protein in well-defined Escherichia coli relA and relA/spoT mutants provides evidence that S. coelicolor Rel, like native E. coli RelA, is functionally ribosome associated, resulting in ribosome-dependent (p)ppGpp accumulation upon amino acid deprivation. Expression of an S. coelicolor C-terminally deleted Rel, comprised of only the first 489 amino acids, catalyzes a ribosome-independent (p)ppGpp formation, in the same manner as the E. coli truncated RelA protein (1 to 455 amino acids). An E. coli relA spoT double deletion mutant transformed with S. coelicolor rel gene suppresses the phenotype associated with (p)ppGpp deficiency. However, in such a strain, a rel-mediated (p)ppGpp response apparently occurs after glucose depletion, but only in the absence of amino acids. Analysis of ppGpp decay in E. coli expressing the S. coelicolor rel gene suggests that it also encodes a (p)ppGpp-degrading activity. By deletion analysis, the catalytic domains of S. coelicolor Rel for (p)ppGpp synthesis and degradation have been located within its N terminus (amino acids 267 to 453 and 93 to 397, respectively). In addition, E. coli relA in an S. coelicolor rel deletion mutant restores actinorhodine production and shows a nearly normal morphological differentiation, as does the wild-type rel gene, which is in agreement with the proposed role of (p)ppGpp nucleotides in antibiotic biosynthesis.     

Involvement of cyclic AMP and its receptor protein in the sensitivity of Escherichia coli K 12 toward serine: excretion of 2-ketobutyrate, a precursor of isoleucine.

Summary A relationship between serine-induced growth sensitivity and the cAMP-CAP complex is established. Mutants of Escherichia coli K 12 deficient either in the cya or crp gene function exhibit a resistant phenotype on serine media although they harbor a relA allele normally leading to sensitivity toward serine. The presence of a crp ^* allele in a cya rela background restores the sensitivity phenotype, while the analysis of serine resistant mutants selected from a crp ^* cya relA strains shows that the mutation leading to resistance is located at, or very near, the crp gene, giving a more or less Crp^- phenotype. In addition crp ^* cya relA strains excrete large quantities of 2-ketobutyrate when grown on glucose M63 medium. This excretion is unambiguously linked to the presence of the crp ^* allele and is correlated with an enhanced threonine deaminase activity. Besides, the complex regulation exerted on the acetolactate synthase activities is discussed.     

Nonsense suppression in aminoacyl-t-RNA limited cells

Summary A number of nonsense alleles of lacZ exhibit phenotypic suppression (as much as a sixteen-fold increase in leakiness) during partial limitation for certain aminoacyl-tRNA species in relA mutant cells. Each responsive allele has its individual pattern of response to limitation for one or more amino acids or aminoacyl-tRNA's. The phenotypic suppression occurs only during limitation, and ceases once limitation is reversed. Suppression is much reduced by the presence of the relA⁺ allele or an allele of rpsL which restricts ribosomal ambiguity. In one case, the suppressed product has been identified by radioimmune assay and gel electrophoresis, and is a full-length lacZ protomer. Mechanisms are discussed whereby aberrations of translation at codons calling for an aminoacyl-tRNA species in short supply might lead to readthrough of a nearby nonsense codon.     

Interactions between carbon dioxide and oxygen in the photosynthesis of three species of marine red macroalgae

Summary

Red algae have the highest known selectivity factor (S_rel) for CO₂ over O₂ of ribulose bisphosphate carboxylase-oxygenase (RUBISCO). This allows the prediction that a red alga relying on diffusive supply of CO₂ to RUBISCO from air-equilibrated solution should have less O₂ inhibition of photosynthesis than would an otherwise similar non-red alga with a lower S_rel of RUBISCO. Furthermore, RUBISCO shows an increased S_rel values at low temperatures. The prediction that O ₂inhibition of photosynthesis should be small for marine red algae relying on diffusive CO₂ entry growing in the North Sea with an annual temperature range of 4–16°C was tested in O₂ electrode experiments at 12°C. Phycodrys rubens and Plocamium cartilagineum, which rely on diffusive CO₂ entry showed, as predicted, only a small inhibition at lower inorganic C concentrations. Palmaria palmata, which has a CO₂ concentrating mechanism, had the expected negligible O ₂ inhibition of photosynthesis at any inorganic C concentration except (non-significantly) for saturating inorganic C.     

Differential effect of amino acid starvation on polysome decay in escherichia coli

In arelA⁺ strain ofE. coli starved separately for each of four required amino acids, the intracellular concentration of polysomes decreases as a function of time in all cases: very rapidly in the absence of arginine or leucine, slowly in the absence of threonine or histidine. In a starved isogenicrelA strain, the polysome level is either totally stable or else drops slowly. The decrease in the level, when it occurs, does not significantly affect the polysome size distribution. Models for polysome metabolism in amino acid starved cells are discussed.     

Instability of protease production in a rel+/rel−-pair of Bacillus licheniformis and associated morphological and physiological characteristics

A naturally occurring relaxed/protease-producing (A-type) versus stringent/not protease-producing (B-type) pair of an industrial Bacillus licheniformis has been characterized; either of the two types can convert into the other. Both types can sporulate, grow anaerobically, grow at 56°C and reduce nitrate; morphologically, they can easily be distinguished by cell- and colony-shape. They differ in the ability to use 12 substrates, as determined in API-tests. The two types are remarkably different in their content of extrachromosomal elements (A-type: 2; B-type: 4); furthermore, they differ in their rel-status (A-type: relaxed; B-type: stringent). We propose that the differences in the ability of the two types to use different substrates probably are due to integration/extrusion of the extrachromosomal elements in and out of the chromosome, distorting or restoring a number of genes, together with induction of certain catabolic genes that are under control of the rel-system.