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Mechanism of mutation by thymine starvation in Escherichia coli: clues from mutagenic specificity.

To probe the mechanisms of mutagenesis induced by thymine starvation, we examined the mutational specificity of this treatment in strains of Escherichia coli that are wild type (Ung+) or deficient in uracil-DNA-glycosylase (Ung-). An analysis of Ung+ his-4 (ochre) revertants revealed that the majority of induced DNA base substitution events were A:T----G:C transitions. However, characterization of lacI nonsense mutations induced by thymine starvation demonstrated that G:C----A:T transitions and all four possible transversions also occurred. In addition, thymineless episodes led to reversion of the trpE9777 frameshift allele. Although the defect in uracil-DNA-glycosylase did not appear to affect the frequency of total mutations induced in lacI by thymine deprivation, the frequency of nonsense mutations was reduced by 30%, and the spectrum of nonsense mutations was altered. Furthermore, the reversion of trpE9777 was decreased by 90% in the Ung- strain. These findings demonstrate that in E. coli, thymine starvation can induce frameshift mutations and all types of base substitutions. The analysis of mutational specificity indicates that more than a single mechanism is involved in the induction of mutation by thymine depletion. We suggest that deoxyribonucleoside triphosphate pool imbalances, the removal of uracil incorporated into DNA during thymine starvation, and the induction of recA-dependent DNA repair functions all may play a role in thymineless mutagenesis.

DNA Glycosylases↗

Transcriptional regulation of Bacillus subtilis glucose starvation-inducible genes: control of gsiA by the ComP-ComA signal transduction system.

The Bacillus subtilis glucose starvation-inducible transcription units, gsiA and gsiB, were characterized by DNA sequencing, transcriptional mapping, mutational analysis, and expression in response to changes in environmental conditions. The gsiA operon was shown to consist of two genes, gsiAA and gsiAB, predicted to encode 44.9- and 4.8-kDa polypeptides, respectively. The gsiB locus contains a single cistron which encodes a protein of unusual structure; most of its amino acids are arranged in five highly conserved, tandemly repeated units of 20 amino acids. The 5' ends of gsiA and gsiB mRNAs were located by primer extension analysis; their locations suggest that both are transcribed by RNA polymerase containing sigma A. Expression of both gsiA and gsiB was induced by starvation for glucose or phosphate or by addition of decoyinine, but only gsiA was induced by exhaustion of nutrient broth or by amino acid starvation. Regulation of gsiA expression was shown to be dependent upon the two-component signal transduction system ComP-ComA, which also controls expression of genetic competence genes. Mutations in mecA bypassed the dependency of gsiA expression on ComA. Disruption of gsiA relieved glucose repression of sporulation but did not otherwise interfere with sporulation, development of competence, motility, or glucose starvation survival. We propose that gsiA and gsiB are members of an adaptive pathway of genes whose products are involved in responses to nutrient deprivation other than sporulation.

Amino Acid Sequence↗

Stringent control during carbon starvation of marine Vibrio sp. strain S14: molecular cloning, nucleotide sequence, and deletion of the relA gene.

In order to evaluate the role of the stringent response in starvation adaptations of the marine Vibrio sp. strain S14, we have cloned the relA gene and generated relaxed mutants of this organism. The Vibrio relA gene was selected from a chromosomal DNA library by complementation of an Escherichia coli delta relA strain. The nucleotide sequence contains a 743-codon open reading frame that encodes a polypeptide that is identical in length and highly homologous to the E. coli RelA protein. The amino acid sequences are 64% identical, and they share some completely conserved regions. A delta relA::kan allele was generated by replacing 53% of the open reading frame with a kanamycin resistance gene. The Vibrio relA mutants displayed a relaxed control of RNA synthesis and failed to accumulate ppGpp during amino acid limitation. During carbon and energy starvation, a relA-dependent burst of ppGpp synthesis concomitant with carbon source depletion and growth arrest was observed. Also, in the absence of the relA gene, there was an accumulation of ppGpp during carbon starvation, but this was slower and smaller than that which occurred in the stringent strains, and it was preceded by a marked decrease in the [ATP]/[ADP] ratio. In both the wild-type and the relaxed strains, carbon source depletion caused an immediate decrease in the size of the GTP pool and a block of net RNA accumulation. The relA mutation did not affect long-term survival or the development of resistance against heat, ethanol, and oxidative stress during carbon starvation of Vibrio sp. strain S14.

Adaptation, Physiological↗

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

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

Base Sequence↗

Starvation- and Stationary-phase-induced resistance to the antimicrobial peptide polymyxin B in Salmonella typhimurium is RpoS (sigma(S)) independent and occurs through both phoP-dependent and -independent pathways.

A common stress encountered by Salmonella serovars involves exposure to membrane-permeabilizing antimicrobial peptides and proteins such as defensins, cationic antibacterial proteins, and polymyxins. We wanted to determine if starvation induces cross-resistance to the membrane-permeabilizing antimicrobial peptide polymyxin B (PmB). We report here that starved and stationary-phase (Luria-Bertani [LB] medium) cells exhibited ca. 200- to 1,500-fold-higher (cross-)resistance to a 60-min PmB challenge than log-phase cells. Genetic analysis indicates that this PmB resistance involves both phoP-dependent and -independent pathways. Furthermore, both pathways were sigma(S) independent, indicating that they are different from other known sigma(S) -dependent cross-resistance mechanisms. Additionally, both pathways were important for PmB resistance early during C starvation and for cells in stationary phase in LB medium. However, only the phoP-independent pathway was important for P-starvation-induced PmB resistance and the sustained PmB resistance seen in 24-h-C-starved (and N-starved) or stationary-phase cells in LB medium. The results indicate the presence of an rpoS- and phoP-independent pathway important to starvation- and stationary-phase-induced resistance to membrane-permeabilizing antimicrobial agents.

Anti-Bacterial Agents↗

Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis.

SigmaB-dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the development of glucose-starvation-induced cross-resistance to oxidative challenge. However, the proteins directly involved in this nonspecific resistance to oxidative stress have to be identified. We found that one prominent Gsp displayed strong sequence similarity to the previously characterized oxidative-stress-inducible MrgA protein of B. subtilis and to the starvation-induced Dps/PexB protein of Escherichia coli. We therefore designated this prominent Gsp Dps. While MrgA belongs to the peroxide-stress-inducible proteins needed for the H2O2-inducible adaptive response to oxidative stress, Dps belongs to the proteins induced by heat, salt, or ethanol stress and after starvation for glucose but not by a sublethal oxidative challenge. Primer extension experiments identified two overlapping promoters upstream of the coding region of dps, one being sigmaB dependent (PB) and the other being sigmaB independent (P1). Both promoters contribute to the basal level of dps during growth. After stress or during entry into the stationary phase, transcription from PB strongly increased whereas transcription from P1 decreased. Mutant strains lacking Dps completely failed to develop glucose-starvation-induced resistance to oxidative stress. These results confirm our suggestion that sigmaB-dependent general stress proteins of B. subtilis are absolutely required for the development of nonspecific resistance to oxidative stress.

Amino Acid Sequence↗

A two-component regulator of universal stress protein expression and adaptation to oxygen starvation in Mycobacterium smegmatis.

We identified a response regulator in Mycobacterium smegmatis which plays an important role in adaptation to oxygen-starved stationary phase. The regulator exhibits strong sequence similarity to DevR/Rv3133c of M. tuberculosis. The structural gene is present on a multigene locus, which also encodes a sensor kinase. A devR mutant of M. smegmatis was adept at surviving growth arrest initiated by either carbon or nitrogen starvation. However, its culturability decreased several orders of magnitude below that of the wild type under oxygen-starved stationary-phase conditions. Two-dimensional gel analysis revealed that a number of oxygen starvation-inducible proteins were not expressed in the devR mutant. Three of these proteins are universal stress proteins, one of which is encoded directly upstream of devR. Another protein closely resembles a proposed nitroreductase, while a fifth protein corresponds to the alpha-crystallin (HspX) orthologue of M. smegmatis. None of the three universal stress proteins or nitroreductase, and a considerably lower amount of HspX was detected in carbon-starved wild-type cultures. A fusion of the hspX promoter to gfp demonstrated that DevR directs gene expression when M. smegmatis enters stationary phase brought about, in particular, by oxygen starvation. To our knowledge, this is the first time a role for a two-component response regulator in the control of universal stress protein expression has been shown. Notably, the devR mutant was 10(4)-fold more sensitive than wild type to heat stress. We conclude that DevR is a stationary-phase regulator required for adaptation to oxygen starvation and resistance to heat stress in M. smegmatis.

Adaptation, Physiological↗

Effects of tryptophan starvation on levels of the trp RNA-binding attenuation protein (TRAP) and anti-TRAP regulatory protein and their influence on trp operon expression in Bacillus subtilis.

The anti-TRAP protein (AT), encoded by the rtpA gene of Bacillus subtilis, can bind to and inhibit the tryptophan-activated trp RNA-binding attenuation protein (TRAP). AT binding can prevent TRAP from promoting transcription termination in the leader region of the trp operon, thereby increasing trp operon expression. We show here that AT levels continue to increase as tryptophan starvation becomes more severe, whereas the TRAP level remains relatively constant and independent of tryptophan starvation. Assuming that the functional form of AT is a trimer, we estimate that the ratios of AT trimers per TRAP molecule are 0.39 when the cells are grown under mild tryptophan starvation conditions, 0.83 under more severe starvation conditions, and approximately 2.0 when AT is expressed maximally. As the AT level is increased, a corresponding increase is observed in the anthranilate synthase level. When AT is expressed maximally, the anthranilate synthase level is about 70% of the level observed in a strain lacking TRAP. In a nutritional shift experiment where excess phenylalanine and tyrosine could potentially starve cells of tryptophan, both the AT level and anthranilate synthase activity were observed to increase. Expression of the trp operon is clearly influenced by the level of AT.

Anthranilate Synthase↗

Influence of phosphate starvation on cultures of Pseudomonas aeruginosa.

Hou, Cynthia I. (University of British Columbia, Vancouver, B.C., Canada), Audrey F. Gronlund, and J. J. R. Campbell. Influence of phosphate starvation on cultures of Pseudomonas aeruginosa. J. Bacteriol. 92:851-855. 1966.-The changes occurring in Pseudomonas aeruginosa during phosphate starvation in a phosphate-deficient medium were assessed by measuring alterations in optical density, viable-cell count, chemical composition, and ribosome patterns. After a 24-hr period of starvation, optical density, protein, and deoxyribonucleic acid per milliliter of culture increased, whereas ribonucleic acid decreased. Extensive ribosomal degradation was apparent from sucrose density gradient centrifugation patterns. The induction of an alkaline phosphomonoesterase during phosphate starvation was observed. A linear response of phosphate-starved cells to low levels of phosphate supplied exogenously was evident from optical-density measurements, and a threshold requirement for phosphate analogous to the "energy of maintenance" was not detected.

Alkaline Phosphatase↗

Magnesium starvation of Aerobacter aerogenes. I. Changes in nucleic acid composition.

Aerobacter aerogenes incubated in a medium containing all factors necessary for exponential growth except Mg(++) continued to synthesize nucleic acids and proteins for more than 70 hr, provided the major carbon source was in excess at all times. After 24 hr of Mg(++) starvation, deoxyribonucleic acid content in the culture had increased 10-fold. In contrast, the viable-cell count increased only about threefold during the first few hours and then remained approximately constant for the subsequent 70 hr. After specified intervals of Mg(++) starvation, extracts of the bacteria, or ribonucleic acid (RNA) purified from them, was centrifuged through gradients of sucrose to separate transfer RNA from ribosomal components. After correcting for losses, we obtained the following results. (i) There was a progressive rise in the content of transfer RNA competent to accept amino acids and during starvation it remained completely stable. (ii) In contrast, the contents of normally sedimenting ribosomal RNA and ribosomal subunits (30 and 50S) remained approximately constant for more than 24 hr. This did not result from stability of ribosomes made prior to starvation together with an inhibition of synthesis of new particles. Rather, ribosomes were continually breaking down and being replaced by an equivalent number of new ones. (iii) The breakdown of ribosomes appeared to be sequentially ordered; polysomes yielded 70S monomers, which then gave 30 and 50S particles, and these disintegrated to smaller units and finally to acid-soluble products. (iv) Furthermore, the particles derived from breakdown do not appear to exchange with subparticles on the path of assembly. Thus, ribosome decay was age-dependent and ribosomal RNA molecules had a minimal life expectancy of 90 min; however, some survived much longer.

Bacterial Proteins↗

Initiation of deoxyribonucleic acid synthesis after thymine starvation of Bacillus subtilis.

Evidence for premature initiation of deoxyribonucleic acid (DNA) replication after thymine starvation of Bacillus subtilis W23T(-) is presented, based on (i) increase in the number of ade(+) relative to met(+) transformants yielded by the DNA isolated from cultures after starvation (the ade(-) marker being near the origin of replication, whereas met(-) is close to the terminus), and (ii) increase in both the initial rate and final level of tritiated thymine incorporation in the presence of chloramphenicol after release from starvation. The marker ratio data agree quantitatively with the hypothesis that the initiation is induced only on one arm of each chromosome which was replicating prior to starvation.

Bacillus subtilis↗

Heat shock transcription factor activates yeast metallothionein gene expression in response to heat and glucose starvation via distinct signalling pathways.

Metallothioneins constitute a class of low-molecular-weight, cysteine-rich metal-binding stress proteins which are biosynthetically regulated at the level of gene transcription in response to metals, hormones, cytokines, and other physiological and environmental stresses. In this report, we demonstrate that the Saccharomyces cerevisiae metallothionein gene, designated CUP1, is transcriptionally activated in response to heat shock and glucose starvation through the action of heat shock transcription factor (HSF) and a heat shock element located within the CUP1 promoter upstream regulatory region. CUP1 gene activation in response to both stresses occurs rapidly; however, heat shock activates CUP1 gene expression transiently, whereas glucose starvation activates CUP1 gene expression in a sustained manner for at least 2.5 h. Although a carboxyl-terminal HSF transcriptional activation domain is critical for the activation of CUP1 transcription in response to both heat shock stress and glucose starvation, this region is dispensable for transient heat shock activation of at least two genes encoding members of the S. cerevisiae hsp70 family. Furthermore, inactivation of the chromosomal SNF1 gene, encoding a serine-threonine protein kinase, or the SNF4 gene, encoding a SNF1 cofactor, abolishes CUP1 transcriptional activation in response to glucose starvation without altering heat shock-induced transcription. These studies demonstrate that the S. cerevisiae HSF responds to multiple, distinct stimuli to activate yeast metallothionein gene transcription and that these stimuli elicit responses through nonidentical, genetically separable signalling pathways.

AMP-Activated Protein Kinases↗

Serum starvation and growth factor receptor expression in vascular smooth muscle cells.

BACKGROUND: Smooth muscle cell (SMC) proliferation in atherosclerosis is regulated through the interaction of growth factors like platelet-derived growth factor-BB (PDGF-BB) and insulin-like growth factor-1 (IGF-1) and their receptors (R). We hypothesized that serum starvation of SMCs may affect PDGFbeta-R and IGF-1-R expression and, consequently, the effect of their cognate ligands on SMC survival/proliferation. METHODS AND RESULTS: Serum starvation significantly increases PDGFbeta-R but not IGF-1-R mRNA and protein expression in SMCs. PDGF-BB stimulates cell survival but not proliferation in serum-starved SMCs of the synthetic phenotype, whereas SMCs of the contractile phenotype respond to PDGF-BB by a significant increase in proliferation. Immunohistochemical analysis of coronary atherosclerotic lesions reveals PDGFbeta-R expression in SMCs in the lamina fibromuscularis, but not in the media and in healthy parts of the arterial wall. No such differential expression was observed for IGF-1-R. CONCLUSIONS: Differential regulation of PDGFbeta-R and IGF-1-R expression by serum starvation might represent a mechanism for the control of SMC survival/proliferation in atherogenesis and restenosis. The distribution of PDGFbeta-Rs and IGF-1-Rs in atherosclerotic lesions may indicate an effect of serum starvation on SMCs in the arterial wall.

Becaplermin↗

Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes.

Autophagy, fundamentally a lysosomal degradation pathway, functions in cells during normal growth and certain pathological conditions, including starvation, to maintain homeostasis. Autophagosomes are formed through a mechanism that is not well understood, despite the identification of many genes required for autophagy. We have studied the mammalian homologue of Atg9p, a multi-spanning transmembrane protein essential in yeast for autophagy, to gain a better understanding of the function of this ubiquitious protein. We show that both the N- and C-termini of mammalian Atg9 (mAtg9) are cytosolic, and predict that mAtg9 spans the membrane six times. We find that mAtg9 is located in the trans-Golgi network and late endosomes and colocalizes with TGN46, the cation-independent mannose-6-phosphate receptor, Rab7 and Rab9. Amino acid starvation or rapamycin treatment, which upregulates autophagy, causes a redistribution of mAtg9 from the TGN to peripheral, endosomal membranes, which are positive for the autophagosomal marker GFP-LC3. siRNA-mediated depletion of the putative mammalian homologue of Atg1p, ULK1, inhibits this starvation-induced redistribution. The redistribution of mAtg9 also requires PI 3-kinase activity, and is reversed after restoration of amino acids. We speculate that starvation-induced autophagy, which requires mAtg9, may rely on an alteration of the steady-state trafficking of mAtg9, in a Atg1-dependent manner.

Animals↗

Comparative study on the metabolic responses of subterranean and surface-dwelling amphipods to long-term starvation and subsequent refeeding

The effects of long-term starvation and subsequent refeeding on intermediary and energy metabolism were investigated in two subterranean aquatic crustaceans, Niphargus rhenorhodanensis and Niphargus virei, and in a morphologically similar surface-dwelling species, Gammarus fossarum. The metabolic response to prolonged food deprivation was monophasic in G. fossarum, showing an immediate, linear and large decline in all of the energy reserves. In contrast, both subterranean organisms displayed successive periods of glucidic, proteo-glucidic then lipidic-dominant catabolism during food deprivation. In both subterranean species, lipids (51 % of the energy consumed during a 180-day starvation period) and proteins (44 %) were the most metabolized substrates in terms of total energy, whereas glycogen (5 %) contributed little energy. G. fossarum displayed a different energetic strategy: proteins comprised 56 % of the energy losses during a 28-day starvation period, total lipids some 39 % and glycogen reserves only 5 %. We propose an energy strategy for food-limited subterranean crustaceans involving the possession of (1) higher amounts of stored arginine phosphate, triglycerides and glycogen and (2) lower utilization rates of stored metabolites than G. fossarum and numerous other surface-dwelling crustaceans, making the fueling of food deprivation possible for a longer time. In addition, these species had a faster and more efficient assimilation of available nutrients during recovery from food deprivation, enabling preparation for a new nutritional stress. These specific adaptive responses might be considered, for N. virei and N. rhenorhodanensis, as an efficient energy-saving strategy for an environment where extended starvation periods alternate with sporadic feeding events, therefore improving their competitive advantages.

Journal Article↗

Reduction of disulfide bridges in the lumenal domain of ATF6 in response to glucose starvation.

Mammalian transcription factor ATF6 is constitutively synthesized as a type II transmembrane protein embedded in the endoplasmic reticulum (ER). Upon ER stress ATF6 is transported to the Golgi apparatus where it is cleaved to release its cytoplasmic domain. This is then translocated into the nucleus where it activates transcription of ER-localized molecular chaperones and folding enzymes to maintain the homeostasis of the ER. We recently found that, owing to the presence of intra- and intermolecular disulfide bridges, ATF6 occurs in unstressed ER in monomer, dimer and oligomer forms. Disulfide-bonded ATF6 is reduced on treatment of cells with various chemical ER stress inducers, and only the reduced monomer ATF6 reaches the Golgi apparatus. In this study, we evoked ER stress under more physiological conditions, namely, glucose starvation, and analyzed its consequence for ATF6 activation. Glucose starvation activated ATF6 and induced the ER chaperone BiP, albeit weakly. ATF6 was thus dissociated from BiP, transported to the Golgi apparatus, and cleaved. Glucose starvation enhanced the synthesis of ATF6 approximately two-fold, probably via transcriptional induction. Importantly, reduction of disulfide bridges and transport of reduced monomer occurred in response to glucose starvation. We conclude that ER stress-induced reduction of ATF6 represents a general feature of the ATF6 activation process.

Activating Transcription Factor 6↗

Effects of the olfactory environment and nutrition on the ability of male Mediterranean fruit flies to endure starvation.

The Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), is targeted for control using the sterile insect technique (SIT). For this technique to succeed, released males must be able to compete with wild males for copulations. Male success is mediated by survival in the field often in adverse conditions. Manipulation of the postteneral environment experienced by sterile males before release has been shown to affect male sexual success and survival. The objectives of this study were to determine how various diets, combined with exposure to volatiles containing alpha-copaene, affect the ability of male Mediterranean fruit flies (from a wild and two unisexual strains) to withstand starvation. Accordingly, we maintained males on one of eight regimes combing a diet of either sugar, sugar and protein, a protein pulse or apricot, with or without the aroma of the sexual stimulant alpha-copaene. The apricot diet was associated with the lowest ability to resist starvation. The sugar-only diet was associated with the highest ability to resist starvation by sterile males. Exposure to alpha-copaene, in combination with the apricot diet, had a significant negative effect on the ability of males (from all strains) to resist starvation relative to other regimes examined. We conclude that the holding regimes that elicit the best sexual performance from males paradoxically also hasten their demise, probably by initiating an irreversible metabolic cascade. The search for the optimal prerelease regime continues.

Animal Nutritional Physiological Phenomena↗

Synthesis and secretion of phosphatases by endophytic isolates of Colletotrichum musae grown under conditions of nutritional starvation.

Even though fungal phosphatases are widely used to study ambient-regulated gene expression, little is known about these enzymes in the agriculturally important genus Colletotrichum. We have therefore identified several phosphatase activities in endophytic isolates of Colletotrichum musae grown under conditions of nutritional sufficiency or starvation for sources of phosphorus (P), nitrogen (N), carbon (C), and sulphur (S). These enzyme forms could be distinguished by substrate specificity, optimum pH, activation and inhibition by some substances, response to nutritional starvation, and pattern of migration in native gel electrophoresis. At least four individual phosphatase activities were identified under the growth conditions employed. A pH 5.0 acid phosphatase and an Mg(2+)-dependent pH 7.5 phosphodiesterase were expressed under all growth conditions at constant rates. Under conditions of P-starvation, derepression of a major pH 6.0-acid phosphatase was observed in cell-free extracts and the culture medium. A synthesis of alkaline phosphatase activities followed a more distinct pattern. Under conditions of nutritional sufficiency of P- or N-starvation, only a single intracellular enzyme form (optimum pH 10) was observed, which was resolved as a single electrophoretic activity band. However, in media lacking C or S sources additional alkaline phosphatase forms were derepressed with a concomitant increase in the overall enzyme activity level measured at pH 10. To our knowledge, this report represents the most detailed study of phosphatases in Colletotrichum and the first partial characterization of the phosphatase system in an endophytic fungus.

Journal Article↗