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PubMed2004

Influence of catabolite repression and inducer exclusion on the bistable behavior of the lac operon.

A mathematical model of the lac operon which includes all of the known regulatory mechanisms, including external-glucose-dependent catabolite repression and inducer exclusion, as well as the time delays inherent to transcription and translation, is presented. With this model we investigate the influence of external glucose, by means of catabolite repression and the regulation of lactose uptake, on the bistable behavior of this system.

Catalysis↗

PubMed1981

Impaired induction and self-catabolite repression of extracellular pectate lyase in Erwinia chrysanthemi mutants deficient in oligogalacturonide lyase.

The pectate lyase (PL; EC 4.2.2.2) secreted by the plant pathogen Erwinia chrysanthemi is induced and catabolite repressed by different concentrations of its own product, digalacturonic acid 4,5-unsaturated at the nonreducing end [u(GalUA)(2)]. Both activities of u(GalUA)(2) depend on its cleavage by oligogalacturonide lyase (OGL; EC 4.2.2.6). This intracellular enzyme converts u(GalUA)(2) to the deoxyketuronic acid 4-deoxy-L-threo-5-hexosulose uronic acid, which is then isomerized to 3-deoxy-D-glycero-2,5-hexodiulosonic acid. An OGL-deficient mutant unable to grow on u(GalUA)(2) was poorly induced by u(GalUA)(2) or by D-galacturonan but produced wild-type levels of PL when supplied with 3-deoxy-D-glycero-2,5-hexodiulosonic acid. PL synthesis in the mutant could also be stimulated by 4,5-unsaturated trigalacturonic acid, from which deoxyketuronic acid is released by another intracellular enzyme. An OGL-deficient mutant that grew slowly on u(GalUA)(2) in comparison with the wild-type parent was hyperinduced by u(GalUA)(2) unless catabolite repression was relieved by cyclic AMP or imposed by logarithmic growth on glycerol. PL synthesis is also stimulated by saturated digalacturonic acid, which is released from D-galacturonan by another extracellular enzyme, exo-poly-alpha-D-galacturonosidase (EC 3.2.1.82). Because these dimers stimulate PL synthesis at concentrations (wt/vol) 1/1000th of the concentration required by D-galacturonan, and because an OGL-deficient mutant uninducible by dimers was also uninducible by D-galacturonan, we postulate that PL induction by pectic polymers entails extracellular formation of dimers and subsequent intracellular conversion to deoxyketuronic acids, the apparent inducers of PL.

Journal Article↗

PubMed2006

In vitro reconstitution of catabolite repression in Escherichia coli.

A widely accepted model for catabolite repression posits that phospho-IIAGlc of the bacterial phosphotransferase system activates adenylyl cyclase (AC) activity. For many years, attempts to observe such regulatory properties of AC in vitro have been unsuccessful. To further study the regulation, AC was produced fused to the transmembrane segments of the serine chemoreceptor Tsr. Cells harboring Tsr-AC and normal AC, expressed from the cya promoter on a low copy number vector, exhibit similar behavior with respect to elevation of cAMP levels resulting from deletion of crp, expressing the catabolite regulatory protein. Membrane-bound Tsr-AC exhibits activity comparable with the native form of AC. Tsr-AC binds IIAGlc specifically, regardless of its phosphorylation state, but not the two general phosphotransferase system proteins, enzyme I and HPr; IIAGlc binding is localized to the C-terminal region of AC. Binding to membranes of either dephospho- or phospho-IIAGlc has no effect on AC activity. However, in the presence of an Escherichia coli extract, P-IIAGlc, but not IIAGlc, stimulates AC activity. Based on these findings of a direct interaction of IIAGlc with AC, but activity regulation only in the presence of E. coli extract, a revised model for AC activity regulation is proposed.

Adenylyl Cyclase Inhibitors↗

PubMed2005

Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression.

Expression from the Escherichia coli nrf operon promoter is activated by the anaerobically triggered transcription factor, FNR, and by the nitrate/nitrite ion-controlled response regulators, NarL or NarP, but is repressed by the IHF and Fis proteins. Here, we present in vitro studies on the nrf promoter, using permanganate footprinting to measure open complex formation, and DNase I footprinting to monitor binding of the different regulators and the interactions between them. Our results show that open complex formation is completely dependent on FNR and is enhanced by NarL, but is repressed by IHF or Fis. NarL counteracts repression by IHF but is unable to alter repression by Fis. These results suggest mechanisms by which nrf promoter activity is modulated by the different factors. Expression from the nrf promoter is known to be repressed in rich media, especially in the presence of glucose, but the molecular basis of this is not understood. Here, we show that this catabolite repression is relieved by mutations that weaken the DNA site for Fis, improve the DNA site for FNR or improve the promoter -10 or -35 elements. Hence, Fis protein is a major factor responsible for catabolite repression at the nrf promoter, and Fis can override activation by FNR and NarL or NarP.

Base Sequence↗

PubMed1990

The relationship of growth rate and catabolite repression with WHI2 expression and cell size in Saccharomyces cerevisiae.

Mixtures of D-glucosamine and glucose were used to slow the growth of wild-type and whi2 mutant strains of Saccharomyces cerevisiae without affecting the level of catabolite repression. The following observations were made. Firstly, mutant cells were found to be partially resistant to the inhibitory effect of glucosamine. Secondly, slow growth induced by glucosamine resulted in cells becoming larger, in direct contrast to the effect of slowing growth by glucose limitation in a chemostat or by carbon source substitution. It is concluded that the level of repression/derepression, rather than absolute growth rate, is responsible for controlling cell size. Thirdly, when WHI2 transcript levels were measured it was found that expression was correlated with growth rate rather than the level of repression. These results are interpreted in terms of a model which envisages that the WHI2 product acts as a negative regulator of catabolite repression. A test of this model is reported: it is shown that mutant cells respired more actively in the presence of glucose and grew more rapidly on glycerol, whereas overexpression of WHI2 from multicopy plasmids prevented growth on glycerol and depressed respiration.

Cell Cycle↗

PubMed1994

Analysis of a cis-active sequence mediating catabolite repression in gram-positive bacteria.

One form of catabolite repression (CR) in the Gram-positive genus, Bacillus, is mediated by a cis-acting element (CRE). We use here a consensus sequence to identify such elements in sequenced genes of Gram-positive bacteria. These are analysed with respect to position and type of gene in which they occur. CRE sequences near the promoter region are mainly identified in genes encoding carbon catabolic enzymes, which are thus likely to be subject to CR by a global mechanism. Functional aspects of CREs are evaluated.

Amino Acid Sequence↗

PubMed1970

Adenosine 3':5'-cyclic monophosphate and catabolite repression in Escherichia coli.

1. Both permanent and transient catabolite repression of beta-galactosidase synthesis in Escherichia coli are abolished by 5mm-3':5'-cyclic-AMP when elicited by glucose, but not when caused by a mixture of glucose, glucose 6-phosphate, gluconate and casein hydrolysate (casamino acids). 2. Glucose uptake is slightly increased by 3':5'-cyclic-AMP. 3. No significant effects of the nucleotide were found on the synthesis of protein and RNA, either in exponential growth on one substrate, or during a growth shift from glycerol to glycerol plus glucose. 4. Marked changes in the soluble-protein profiles of cells growing in glycerol and glucose were caused by the presence of 3':5'-cyclic-AMP. 5. Measurements of (14)CO(2) release from specifically-labelled glucose showed that 3':5'-cyclic-AMP greatly stimulated glycolytic activity while having a minor depressing effect on the metabolic flow through the pentose phosphate cycle. 6. The concentrations of several metabolic intermediates, particularly fructose 1,6-diphosphate, were greatly affected by the presence of 3':5'-cyclic-AMP. 7. Several metabolites partially relieved glucose repression of beta-galactosidase synthesis in EDTA-treated cells; three out of five of these metabolites reversed the effect more effectively than did 3':5'-cyclic-AMP. 8. The evidence for and against a direct role for 3':5'-cyclic-AMP is discussed. It is concluded that the evidence for indirect action is at least as strong as that for direct action.

Adenine Nucleotides↗

PubMed2001

Evidence for a dimerisation state of the Bacillus subtilis catabolite repression HPr-like protein, Crh.

The Bacillus subtilis catabolite repression HPr (Crh) exhibits 45% sequence identity when compared to histidine-containing protein (HPr), a phosphocarrier protein of the phosphoenolpyruvate:carbohydrate phosphotransferase system. We report here that Crh preparations contain a mixture of monomers and homodimers, whereas HPr is known to be monomeric in solution. The dissociation rate of dimers is very slow (t1/2 of about 10 hours), and the percentage of dimers in Crh preparations increases with rising temperature or protein concentration. However, at temperatures above 25 degrees C and a protein concentration of 10 mg/ml, Crh dimers slowly aggregate. Typically, NMR spectra recorded at 25 degrees C showed the coexistence of both forms of Crh, while in Crh solutions kept at 35 degrees C, almost exclusively Crh monomers could be detected. Circular dichroism analysis revealed that the monomeric and dimeric forms of Crh are well folded and exhibit the same overall structure. The physiological significance of the slow Crh monomer/dimer equilibrium remains enigmatic.

Bacillus subtilis↗

PubMed1991

Release of glucose-mediated catabolite repression due to a defect in the membrane fraction of phosphoenolpyruvate: mannose phosphotransferase system in Pediococcus halophilus.

A spontaneous mutant 9R-4 resistant to 2-deoxyglucose (2DG) was derived from a wild-type strain Pediococcus halophilus I-13. Phosphoenolpyruvate (PEP)-dependent glucose-6-phosphate formation by the permeabilized 9R-4 cells was less than 5% of that observed with the parent I-13. In vitro complementation of PEP-dependent 2DG-6-phosphate formation was assayed with combination of the cytoplasmic and membrane fractions prepared from the I-13 and the mutants (9R-4, and X-160 isolated from nature), which were defective in PEP:mannose phosphotransferase system (man:PTS). The defects in man:PTS of both the strain 9R-4 and X-160 were restricted to the membrane fraction (e.g. EIIman), not to the cytoplasmic one. Kinetic studies on the glucose transport with intact cells and iodoacetate-treated cells also supported the presence of two distinct transport systems in this bacterium as follows: (i) The wild-type I-13 possessed a high-affinity man:PTS (Km = 11 microM) and a low-affinity proton motive force driven glucose permease (GP) (Km = 170 microM). (ii) Both 9R-4 and X-160 had only the low-affinity system (Km = 181 microM for 9R-4, 278 microM for X-160). In conclusion, a 2DG-induced selective defect in the membrane component (EIIman) of the man:PTS could partially release glucose-mediated catabolite repression but not fructose-mediated catabolite repression in soy pediococci.

Biological Transport↗

PubMed1972

Regulation of secondary metabolite biosynthesis: catabolite repression of phenoxazinone synthase and actinomycin formation by glucose.

Synthesis of the secondary metabolite, actinomycin, and the enzyme, phenoxazinone synthase, involved in the biosynthesis of the antibiotic, were shown to be under severe catabolite repression by glucose. Of a variety of hexoses and carbon compounds examined, glucose, and to a lesser extent, mannose, proved to be the most repressive for enzyme synthesis. The repression by glucose was most evident before production of the antibiotic. In a chemically defined medium suitable for actinomycin production, synthesis of phenoxazinone synthase began at the time the glucose (0.1%) supply was depleted. Soon after, antibiotic synthesis was initiated. Galactose, the major carbon source for growth and antibiotic synthesis, was not utilized until the glucose was consumed. Generally, carbon compounds which supported a rapid rate of growth were most effective in producing catabolite repression.

Bacterial Proteins↗

PubMed2001

Cloning, expression, and carbon catabolite repression of the bamM gene encoding beta-amylase of Bacillus megaterium DSM319.

The bamM gene from Bacillus megaterium DSM319 encoding an extracellular beta-amylase was isolated and completely sequenced. Chromosomal inactivation by deletion mutagenesis resulted in total loss of amylolytic activity, indicative of a single starch-degrading enzyme. Functional characterization of the expressed protein revealed a maltogenic enzyme exhibiting optimal activities at pH 7.5 and 50 degrees C. Amylase expression is subject to catabolite repression by glucose. A putative cis-acting catabolite-responsive element (CRE) was identified; it is located within the bamM coding region, matching the position of the predicted signal peptide processing site. Base substitutions introduced by site-directed mutagenesis within the bamM-CRE--retaining unchanged the amino acid sequence--provoked a remarkable relief from carbon catabolite repression (CCR), thereby proving functionality of the CRE for CCR.

Amino Acid Sequence↗

PubMed1975

Catabolite repression of Pseudomonas aeruginosa amidase: the effect of carbon source on amidase synthesis.

Synthesis of the Pseudomonas aeruginosa aliphatic amidase was repressed severely by succinate and malate and less severely by glucose, acetate or lactate. Amidase synthesis in inducible and constitutive strains was stimulated by cyclic AMP, which also gave partial relief to catabolite repression produced by the addition of lactate to cultures growing in pyruvate medium. Mutants which were resistant to catabolite repression were isolated from succinate+lactamide medium.

Acetamides↗

PubMed1986

Catabolite repressive effects of 5-thio-D-glucose on Saccharomyces cerevisiae.

The effect of the glucose analogue 5-thio-D-glucose (5TG) on the yeast Saccharomyces cerevisiae was studied. Derepression of mitochondrial respiratory chain cytochromes, alcohol dehydrogenase (isoenzyme II), NADH dehydrogenase and maltase was inhibited by 0.5-2 mM-5TG. Growth rate was only slightly affected. Ethanol was efficiently produced with 2 mM-5TG in medium initially containing 0.25% glucose. Mutants resistant to the growth inhibitory effects of 5TG on glycerol medium showed resistance to the catabolite repressing effects of glucose. Other mutants, known to be catabolite repression resistant, showed resistance to 5TG. The analogue seems to inhibit derepression of glucose repressible enzymes with greater potency than glucose itself.

Cytochromes↗

PubMed2001

Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses.

Previous studies have shown that the CcpA protein of Bacillus subtilis is a major transcription factor mediating catabolite repression. We report here whole-transcriptome analyses that characterize CcpA-dependent, glucose-dependent gene expression and correlate the results with full-genome computer analyses of DNA binding (CRE) sites for CcpA. The data obtained using traditional approaches show good agreement with those obtained using the transcriptome approach. About 10% of all genes in B. subtilis are regulated > 3x by glucose, with repressed genes outnumbering activated genes three to one. Eighty per cent of these genes depend on CcpA for regulation. Classical approaches have provided only evidence for CcpA-mediated, glucose-dependent activation or repression. We show here that CcpA also mediates glucose-independent activation or repression, and that glucose may alter either the direction or the intensity of either effect. Computer analyses revealed the presence of CRE sites in most operons subject to CcpA-mediated glucose repression, but not in those subject to glucose activation, suggesting that either secondary transcription factors regulate the latter genes or activation by CcpA involves a dissimilar binding site. Operons encoding the constituents of ABC-type transporters that are subject to CcpA-mediated glucose regulation show two distinct patterns: either all genes in the operon are regulated in parallel (the minor class) or the gene encoding the extracytoplasmic solute-binding receptor is preferentially regulated (the major class). Genes subject to CcpA-independent catabolite repression are primarily concerned with sporulation. Several transcription factors were identified that are themselves regulated by CcpA at the transcriptional level. Representative data with functionally characterized genes are presented to illustrate the novel findings. The comprehensive transcriptome data are available on our website: www.biology.uesd.edu/~MSAIER/regulation/ and also on http://www.blackwell-science.com/ products/journals/suppmat/MMI/MMI2328/MMI2328sm.htm

ATP-Binding Cassette Transporters↗

PubMed1995

AbrB modulates expression and catabolite repression of a Bacillus subtilis ribose transport operon.

A Bacillus subtilis ribose transport operon (rbs) was shown to be subject to AbrB-mediated control through direct AbrB-DNA binding interactions in the vicinity of the promoter. Overproduction of AbrB was shown to relieve catabolite repression of rbs during growth in the presence of poorer carbon sources such as arabinose but had much less effect when cells were grown in the presence of glucose, a rapidly metabolizable carbon source. A ccpA mutation relieved catabolite repression of rbs under all conditions tested. One of the AbrB-binding sites on the rbs promoter contains the putative site of action for the B. subtilis catabolite repressor protein CcpA, suggesting that competition for binding to this site could be at least partly responsible for modulating rbs expression during carbon-limited growth.

Bacillus subtilis↗

PubMed2001

The cyo operon of Pseudomonas putida is involved in carbon catabolite repression of phenol degradation.

A bicistronic reporter consisting of the promoterless genes aacC1 (conferring gentamycin resistance) and lacZ fused to the catabolic promoter of the phenol degradation genes was used to identify and analyse mutants of Pseudomonas putida with altered carbon catabolite repression (CR) of phenol degradation. Out of approximately 2500 mini-Tn5 mutants analysed so far, 12 mutants that were resistant to gentamycin during growth on succinate were identified. In eight of these mutants mini-Tn5 was inserted into one of the genes of the cyo operon. The cyo operon encodes the cytochrome o ubiquinol oxidase, the terminal oxidase of the cyanide-sensitive branch of the respiratory chain. In these mutants the activity of the PphlA promoter was significantly increased during growth on succinate and reached 15-20% of that found during growth with the non-repressing carbon source pyruvate. During growth on glucose the reduction of CR was less obvious, during growth on lactate CR was unchanged. The possible significance of the cyo operon for the generation of signal(s) for carbon catabolite repression is discussed.

Bacterial Proteins↗

PubMed1984

Influence of carbon catabolite repression on the G1 arrest of Saccharomyces cerevisiae MATa cells by alpha factor.

Cells of the yeast Saccharomyces cerevisiae of the a mating type were arrested at the G1 phase of the cell division cycle after treatment with alpha factor in a culture medium containing a high concentration (2%, w/v, or higher) of a catabolite-repressing sugar. In media containing either a lower concentration of sugar or a non-fermentable carbon source, the extent of G1 arrest induced by the pheromone was reduced or became undetectable. Under catabolite-derepressing conditions alpha factor was inactivated by a cells at a higher rate than that found in repressing media. These results indicate the existence of a close correlation between the action of alpha factor on a cells and conditions of catabolite repression or derepression. A joint mechanism of action of alpha factor and catabolite-repressing carbon sources on a cells is postulated.

Enzyme Repression↗

PubMed1998

Cloning, expression, and catabolite repression of a gene encoding beta-galactosidase of Bacillus megaterium ATCC 14581.

A gene encoding beta-galactosidase, designated mbgA, was isolated from Bacillus megaterium ATCC 14581. Chromosomal beta-galactosidase production could be dramatically induced by lactose but not by isopropyl-beta-D-thiogalactopyranoside (IPTG) and was subject to catabolite repression by glucose. Disruption of mbgA in the B. megaterium chromosome resulted in loss of lactose-inducible beta-galactosidase production. A 27-bp inverted repeat was found to overlap the mbgA promoter sequence. Two partially overlapping catabolite-responsive elements (CREs) were identified within the inverted repeat. Base substitutions within CRE-I and/or CRE-II caused partial relief from catabolite repression. The results suggest that the 27-bp inverted repeat may serve as a target for a catabolite repressor(s).

Bacillus megaterium↗