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PubMed1997

Transcriptional activation of the bkd operon of Pseudomonas putida by BkdR.

Reinvestigation of the transcriptional start site of the bkd operon of Pseudomonas putida revealed that the transcriptional start site was located 86 nucleotides upstream of the translational start. There was a sigma 70 binding site 10 bp upstream of the transcriptional start site. The dissociation constants for BkdR, the transcriptional activator of the bkd operon, were 3.1 x 10(-7) M in the absence of L-valine and 8.9 x 10(-8) M in the presence of L-valine. Binding of BkdR to substrate DNA in the absence of L-valine imposed a bend angle of 92 degrees in the DNA. In the presence of L-valine, the angle was 76 degrees. BkdR did not bind to either of the two fragments of substrate DNA resulting from digestion with AgeI. Because AgeI attacks between three potential BkdR binding sites, this suggests that binding of BkdR is cooperative. P. putida JS110 and JS112, mutant strains which do not express any of the components of branched-chain keto acid dehydrogenase, were found to contain missense mutations in bkdR resulting in R40Q and T22I changes in the putative helix-turn-helix of BkdR. Addition of glucose to the medium repressed expression of lacZ from a chromosomal bkdR-lacZ fusion, suggesting that catabolite repression of the bkd operon was the result of reduced expression of bkdR. These data are used to present a model for the role of BkdR in transcriptional control of the bkd operon.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗
PubMed2003

CcpA-independent regulation of expression of the Mg2+ -citrate transporter gene citM by arginine metabolism in Bacillus subtilis.

Transcriptional regulation of the Mg(2+)-citrate transporter, CitM, the main citrate uptake system of Bacillus subtilis, was studied during growth in rich medium. Citrate in the growth medium was required for induction under all growth conditions. In Luria-Bertani medium containing citrate, citM expression was completely repressed during the exponential growth phase, marginally expressed in the transition phase, and highly expressed in the stationary growth phase. The repression was relieved when the cells were grown in spent Luria-Bertani medium. The addition of a mixture of 18 amino acids restored repression. L-Arginine in the mixture appeared to be solely responsible for the repression, and ornithine appeared to be an equally potent repressor of citM expression. Studies of mutant strains deficient in RocR and SigL, proteins required for the expression of the enzymes of the arginase pathway, confirmed that uptake into the cell and, most likely, conversion of arginine to ornithine were required for repression. Arginine-mediated repression was independent of a functional CcpA, the global regulator protein in carbon catabolite repression (CCR). Nevertheless, CCR-mediated repression was the major mechanism controlling the expression during exponential growth, while the newly described, CcpA-independent arginine-mediated repression was specifically apparent during the transition phase of growth.

Arginine↗
PubMed1965

Lifetime of bacterial messenger ribonucleic acid.

Moses, V. (University of California, Berkeley), and M. Calvin. Lifetime of bacterial messenger ribonucleic acid. J. Bacteriol. 90:1205-1217. 1965.-When cells from a stationary culture of Escherichia coli were placed in fresh medium containing inducer for beta-galactosidase, growth, as represented by increase in turbidity and by total protein synthesis, started within 30 sec. By contrast, beta-galactosidase synthesis was greatly delayed compared with induction during exponential growth. Two other inducible enzymes (d-serine deaminase and l-tryptophanase) and one repressible enzyme (alkaline phosphatase) showed similar lags. The lags were not due to catabolite repression. They could not be reduced by pretreatment of the culture with inducer, or by supplementing the fresh medium with amino acids or nucleotides. The lag was also demonstrated by an i(-) mutant constitutive for beta-galactosidase synthesis. An inhibitor of ribonucleic acid (RNA) synthesis, 6-azauracil, preferentially inhibited beta-galactosidase synthesis compared with growth in both inducible and constitutive strains. Puromycin, an inhibitor of protein synthesis, acted as an inhibitor at additional sites during the induction of beta-galactosidase synthesis. No inhibition of the reactions proceeding during the first 20 sec of induction was observed, but puromycin seemed to prevent the accumulation of messenger RNA during the period between 20 sec and the first appearance of enzyme activity after 3 min. It is suggested that these observations, together with many reports in the literature that inducible enzyme synthesis is more sensitive than total growth to some inhibitors and adverse growth conditions, can be explained by supposing that messenger RNA for normally inducible enzymes is biologically more labile than that for some normally constitutive proteins. The possible implications of this hypothesis for the achievement of cell differentiation by genetic regulation of enzyme synthesis are briefly discussed.

Chemical Phenomena↗
PubMed1995

The plasma membrane of Saccharomyces cerevisiae: structure, function, and biogenesis.

The composition of phospholipids, sphingolipids, and sterols in the plasma membrane has a strong influence on the activity of the proteins associated or embedded in the lipid bilayer. Since most lipid-synthesizing enzymes in Saccharomyces cerevisiae are located in intracellular organelles, an extensive flux of lipids from these organelles to the plasma membrane is required. Although the pathway of protein traffic to the plasma membrane is similar to that of most of the lipids, the bulk flow of lipids is separate from vesicle-mediated protein transport. Recent advances in the analysis of membrane budding and membrane fusion indicate that the mechanisms of protein transport from the endoplasmic reticulum to the Golgi and from the Golgi to plasma membrane are similar. The majority of plasma membrane proteins transport solutes across the membrane. A number of ATP-dependent export systems have been detected that couple the hydrolysis of ATP to transport of molecules out of the cell. The hydrolysis of ATP by the plasma membrane H(+)-ATPase generates a proton motive force which is used to drive secondary transport processes. In S. cerevisiae, many substrates are transported by more than one system. Transport of monosaccharide is catalyzed by uniport systems, while transport of disaccharides, amino acids, and nucleosides is mediated by proton symport systems. Transport activity can be regulated at the level of transcription, e.g., induction and (catabolite) repression, but transport proteins can also be affected posttranslationally by a process termed catabolite inactivation. Catabolite inactivation is triggered by the addition of fermentable sugars, intracellular acidification, stress conditions, and/or nitrogen starvation. Phosphorylation and/or ubiquitination of the transport proteins has been proposed as an initial step in the controlled inactivation and degradation of the target enzyme. The use of artificial membranes, like secretory vesicles and plasma membranes fused with proteoliposomes, as model systems for studies on the mechanism and regulation of transport is evaluated.

Amino Acid Sequence↗
PubMed1975

The synthesis of beta-galactosidase by constitutive and other regulatory mutants of Escherichia coli in chemostat culture.

The synthesis of beta-galactosidase by an E. coli constitutive mutant was examined in a chemostat using glucose-, glycerol-, succinate- or N-limited growth media. Except for glucose-grown bacteria, the steady-state intracellular level of beta-galactosidase was maximal at dilution rates between 0-2 and 0-3 h-1. At higher dilution rates enzyme synthesis was reduced by catabolite repression, which could be relieved by the addition of cyclic AMP. With a catabolite-resistant mutant (UV5c), no decrease in enzyme level at high dilution rates were observed. All mutants examined were constitutive and gave decreased enzyme levels at low dilution rates, with the exception of lac-/F'lac UV5c mutants where the enzyme levels rose at low dilution rates. Hyper-producing mutants were isolated but were unstable. A constitutive mutant growing on glycerol-limited media was considered the most suitable for large-scale production of beta-galactosidase in a chemostat.

Bacteriological Techniques↗
PubMed2002

The genes gmdA, encoding an amidase, and bzuA, encoding a cytochrome P450, are required for benzamide utilization in Aspergillus nidulans.

Two unlinked loci, gmdA and bzuA, have previously been identified as being required for the utilization of benzamide as the sole nitrogen source by Aspergillus nidulans. We have cloned each of these genes via direct complementation. The gmdA gene encodes a predicted product belonging to the amidase signature sequence family that displays similarity to AmdS from A. nidulans. However, identity is significantly higher to the amdS gene from Aspergillus niger. The bzuA gene encodes a protein belonging to the cytochrome P450 superfamily and is orthologous to the benzoate para-hydroxylase-encoding gene bphA of A. niger. The bzuA1 mutation prevents the use of benzoate as a carbon source and intracellular accumulation of benzoate results in growth inhibition on benzamide. Northern blot analysis has shown that gmdA expression is subject solely to AreA-dependent nitrogen metabolite repression while bzuA is strongly benzoate inducible and subject to CreA-mediated carbon catabolite repression and a probable inactivation of benzoate induction by glucose. Fluorescence microscopy of a fusion of the N-terminal end of BzuA to green fluorescent protein revealed that this protein localizes to the endoplasmic reticulum.

Amidohydrolases↗
PubMed1997

Coregulation of beta-galactoside uptake and hydrolysis by the hyperthermophilic bacterium Thermotoga neapolitana

Regulation of the beta-galactoside transport system in response to growth substrates in the extremely thermophilic anaerobic bacterium Thermotoga neapolitana was studied with the nonmetabolizable analog methyl-beta-D-thiogalactopyranoside (TMG) as the transport substrate. T. neapolitana cells grown on galactose or lactose accumulated TMG against a concentration gradient in an intracellular free sugar pool that was exchangeable with external galactose or lactose and showed induced levels of beta-galactosidase. Cells grown on glucose, maltose, or galactose plus glucose showed no capacity to accumulate TMG, though these cells carried out active transport of the nonmetabolizable glucose analog 2-deoxy-D-glucose. Glucose neither inhibited TMG uptake nor caused efflux of preaccumulated TMG; rather, glucose promoted TMG uptake by supplying metabolic energy. These data show that beta-D-galactosides are taken up by T. neapolitana via an active transport system that can be induced by galactose or lactose and repressed by glucose but which is not inhibited by glucose. Thus, the phenomenon of catabolite repression is present in T. neapolitana with respect to systems catalyzing both the transport and hydrolysis of beta-D-galactosides, but inducer exclusion and inducer expulsion, mechanisms that regulate permease activity, are not present. Regulation is manifest at the level of synthesis of the beta-galactoside transport system but not in the activity of the system.

Journal Article↗
PubMed1987

Regulation of cobalamin biosynthetic operons in Salmonella typhimurium.

Transcription of cobalamin (cob) biosynthetic genes in Salmonella typhimurium is repressed by cobalamin and by molecular oxygen. These genes seem to be subject to catabolite repression, and they are maximally expressed under conditions of anaerobic respiration of glycerol-fumarate. A 215-fold increase in the expression of cob genes occurs when S. typhimurium shifts from aerobic growth on glucose to anaerobic respiration of glycerol-fumarate under strictly anoxic growth conditions. Exogenous cyclic AMP substantially stimulates the transcription of cob-lac fusions during aerobic growth. However, cyclic AMP is not absolutely required for the expression of the pathway, nor does it mediate the aerobic control. Cobalamin biosynthesis is not seen under aerobic growth conditions, even when transcription is stimulated by the addition of cyclic AMP. Hence, additional control mechanisms triggered by the presence of molecular oxygen must operate independently from transcription effects on the cob operons.

Anaerobiosis↗
PubMed1992

Global regulation of mitochondrial biogenesis in Saccharomyces cerevisiae: ABF1 and CPF1 play opposite roles in regulating expression of the QCR8 gene, which encodes subunit VIII of the mitochondrial ubiquinol-cytochrome c oxidoreductase.

The multifunctional DNA-binding proteins ABF1 and CPF1 bind in a mutually exclusive manner to the promoter region of the QCR8 gene, which encodes 11-kDa subunit VIII of the Saccharomyces cerevisiae mitochondrial ubiquinol-cytochrome c oxidoreductase (QCR). We investigated the roles that the two factors play in transcriptional regulation of this gene. To this end, the overlapping binding sites for ABF1 and CPF1 were mutated and placed in the chromosomal context of the QCR8 promoter. The effects on transcription of the QCR8 gene were analyzed both under steady-state conditions and during nutritional shifts. We found that ABF1 is required for repressed and derepressed transcription levels and for efficient induction of transcription upon escape from catabolite repression, independently of DNA replication. CPF1 acts as a negative regulator, modulating the overall induction response. Alleviation of repression through CPF1 requires passage through the S phase. Implications of these findings for the roles played by ABF1 and CPF1 in global regulation of mitochondrial biogenesis are discussed.

Base Sequence↗
PubMed1986

Structure-function analysis of three cAMP-independent forms of the cAMP receptor protein.

cAMP receptor protein (CRP)-dependent operon expression in Escherichia coli requires the CRP X cAMP complex form of wild-type CRP. One class of crp mutants (crp*) activates CRP-dependent promoters in strains (cya) incapable of endogenous cAMP synthesis. Of fundamental interest is the difference in regulatory properties exhibited by crp* mutant strains, some of which exhibit glucose-mediated repression of beta-galactosidase synthesis, some of which do not. To gain a better understanding of the mechanisms of cAMP-independent promoter activation and repression we have: determined through cloning and DNA sequence analysis the primary structure of three CRP* forms of CRP; purified the mutant proteins; characterized the effect of these mutations on CRP secondary structure; and studied CRP*-activated lac promoter regulation in a purified in vitro transcription system. The results of this study provide strong evidence that mutations in crp alter the conformation of CRP and result in cAMP-independent activation of CRP-dependent promoters in vitro. In addition, a CRP allele-specific inhibition of CRP* activity by spermidine was observed in vitro that parallels crp* strain-specific sensitivity to glucose-mediated repression of CRP-dependent enzyme synthesis in vivo. This observation provides evidence that catabolite repression in cells lacking cAMP may be mediated through a mechanism that inhibits CRP* activity.

Bacterial Proteins↗
PubMedDate not supplied

[Amino acid regulation of L-asparaginase formation in Bacillus mesentericus].

The role of amino acids in regulation of L-asparaginase formation was studied in Bacillus mesentericus 43A. Asparagic acid and, to a less extent, asparagine repress biosynthesis of the enzyme. Glutamic acid, glutamine, and other 15 studied amino acids, added separately at a concentration of 10 or 20 mM to the growing culture, have no effect on the activity of the enzyme. Addition of a combination of all 18 amino acids, each at a concentration of 4 mM, to the culture represses the activity by 64%; addition of an acid hydrolysate of lactoalbumin (10 g/litre) represses the activity of the enzyme by 80%. A mixture of amino acids without asparagic acid and asparagine also displays a strong repressing action. Amino acids formed from asparagic acid--lysine, methionine, and isoleucine--do not repress biosynthesis of the enzyme, neither together nor separately. Ammonium nitrogen also does not participate in regulation of asparaginase formation. The cumulative repressing action of amino acids is supposed to be manifested via the mechanism of catabolite repression.

Amino Acids↗
PubMed1982

Mutations releasing mitochondrial biogenesis from glucose repression in Saccharomyces cerevisiae.

Mutants which exhibit a constitutive glucose-insensitive expression of respiratory activity were selected by use of a triphenyltetrazolium staining technique. These mutants lack carbon catabolite repression, as was demonstrated by measuring cytochromes, the activity of succinate cytochrome c reduction, total cellular respiration, mitochondrial protein, and DNA synthesis. High growth rates of mutant cells in glucose medium and normal fermentative CO2 production exclude the possibility that this carbon catabolite insensitivity of mitochondrial functions is merely due to a decreased utilization of glucose. Accordingly, the activities of the two cytoplasmic enzymes measured, maltase and malate synthase, were glucose repressible to the same extent in the mutants as in the wild type. The mutations are dominant and showed nuclear inheritance. The results are discussed in terms of carbon catabolite-regulated expression of genes involved in the biogenesis of mitochondria.

DNA, Mitochondrial↗
PubMed1991

Glucose control of staphylococcal enterotoxin A synthesis and location is mediated by cyclic AMP.

The regulation of staphylococcal enterotoxin A (SEA) synthesis in a defined medium was studied using continuous culture techniques. SEA production was repressed by glucose and repression could be overcome by addition of exogenous cyclic AMP. As well as this classical catabolite repression control, addition of glucose to de-repressed steady-state cultures resulted in rapid disappearance of toxin from the medium (also mediated by loss of cyclic AMP). When the toxin dissappeared from the medium, it was taken up again by the bacteria without apparent modification.

Culture Media↗
PubMed1995

Regulation of expression of the valine (branched-chain amino acid) dehydrogenase-encoding gene from Streptomyces coelicolor.

Expression of the Streptomyces coelicolor (Sc) valine (branched-chain amino acid) dehydrogenase-encoding gene (vdh) is regulated by valine, glucose and NH+4 at the transcriptional level. The results of assays for the level of accumulated vdh mRNA in the Sc J802 strain by primer extension experiments and for the level of catechol dioxygenase (XylE) activity in Sc J802 (vdh::xylE) transformants show that transcription of the vdh gene is induced approx. 2.5-fold by valine, as compared to asparagine as the sole nitrogen source in the presence of glucose as carbon source. Valine induction is repressed by glucose, as compared to glycerol as the carbon source, and by NH+4. Glucose catabolite repression is relieved in Sc M480, a glucose kinase (glkA) deletion mutant. This suggests that glucose repression of vdh and carbohydrate metabolism are due to the same mechanism in Sc, which involves glucose kinase.

Amino Acid Oxidoreductases↗
PubMedDate not supplied

[Regulation of alpha-amylase biosynthesis in Bacillus diastaticus mutants with various levels of enzyme synthesis].

The regulation of alpha-amylase biosynthesis was studied in Bacillus diastaticus mutants with different levels of the enzyme synthesis (by two orders of magnitude). The enzyme biosynthesis was shown to be regulated by induction and catabolite repression. Maltose, starch and methyl-alpha,D-glucoside (which cannot be metabolised) induced the synthesis while glucose and fructose acted as catabolite repressors.

Bacillus↗
PubMed1987

Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast.

Expression of the yeast arginase gene (CAR1) responds to both induction and nitrogen catabolite repression. Regulation is mediated through sequences that both positively and negatively modulate CAR1 transcription. A short sequence, 5'-TAGCCGCCGAGGG-3', possessing characteristics of a repressor binding site, plays a central role in the induction process. A fragment containing this upstream repression sequence (URS1) repressed gene expression when placed either 5' or 3' to the upstream activation sequences of the heterologous gene CYC1. Action of the URS and its cognate repressor was overcome by CAR1 induction when the URS was situated cis to the CAR1 flanking sequences. This was not observed, however, when it was situated downstream of a heterologous CYC1 upstream activation sequence indicating that URS function is specifically neutralized by cis-acting elements associated with CAR1 induction. Searches of sequences in various gene banks revealed that URS1-like sequences occur ubiquitously in genetic regulatory regions including those of bacteriophage lambda, yeast, mammalian, and viral genes. In a significant number of cases the sequence is contained in a region associated with negative control of yeast gene regulation. These data suggest the URS identified in this work is a generic repressor target site that apparently has been conserved during the evolution of transcriptional regulatory systems.

Arginase↗
PubMed1972

Induction of galactokinase in Saccharomyces cerevisiae: kinetics of induction and glucose effects.

The induced synthesis of galactokinase and the repressing effects of glucose on this synthesis have been investigated in whole yeast cells rendered permeable by treatment with dimethyl sulfoxide. It was found that the induction response of uninduced cells to galactose is clearly dependent on the nature of the carbon source upon which the culture was grown prior to exposure to galactose. Glucose-grown cells exhibited a long lag before induction, whereas lactate-grown cells exhibited induced synthesis within 8 min. A concentration of 0.5% galactose was found to be optimal for induction. The addition of glucose to yeast cultures growing on galactose resulted in a severe transient repression of synthesis which was followed by a resumed rate of synthesis characteristic of a weaker permanent catabolite repression. Neither 2-deoxygalactose nor fucose acted as gratuitous inducers of the pathway, nor did they serve as a substrates for galactokinase.

Carbon Isotopes↗
PubMed1989

A second global regulator gene (arcB) mediating repression of enzymes in aerobic pathways of Escherichia coli.

In Escherichia coli anaerobic growth lowers the basal or induced levels of numerous enzymes associated with aerobic metabolism. Mutations in arcA (dye) at min 0 relieve this pleiotropic anaerobic repression and render the cell sensitive to the redox dye toluidine blue. In this study we identified a second pleiotropic control gene, arcB, at min 69.5. Mutations, including a deletion, in this gene also relieved the anaerobic repression and caused sensitivity to toluidine blue. Mutations in arcA or arcB did not significantly change the catabolite repression of the target phi(sdh-lacZ) operon, in which lacZ is fused to a structural gene for succinate dehydrogenase, nor did the mutations strikingly influence the pattern of excretion products during glucose fermentation. The presence of arcA+ in a multicopy plasmid restored anaerobic repression in arcB mutants, as indicated by the expression of phi(sdh-lacZ). The arcB product might be a sensor protein for the redox or energy state of the arc regulatory system.

Aerobiosis↗