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PubMed2000

Inhibitory effects of carbohydrates on cholesterol esterase biosynthesis in Streptomyces lavendulae H646-SY2.

The inhibitory effects of various carbohydrates on cholesterol esterase (CHE) biosynthesis were investigated in a CHE-producing Streptomyces lavendulae H646-SY2. A marked decrease in CHE production and preferential utilization of glucose were observed when glucose was added to a medium containing palmitic acid as the sole carbon source and an inducer of CHE production. This catabolite repression was also caused by other carbohydrates such as sucrose, glycerol, galactose and arabinose. Sucrose, however, did not inhibit the utilization of palmitic acid by the strain, suggesting that the mechanism of the catabolite repression by sucrose is different from that by glucose.

Journal Article↗
PubMed2000

Environmental regulation of glycosidase and peptidase production by Streptococcus gordonii FSS2.

The synthesis of cell-associated and secreted proteins by Streptococcus gordonii FSS2, an infective endocarditis (IE) isolate, was influenced by both environmental pH and carbon source. Controlling the pH at 7.5 in stirred batch cultures showed that cell-associated and secreted protein concentrations were increased during late exponential and stationary phase by 68% and 125%, respectively, compared with similar cultures without pH control. The expression of five glycosidase and eight peptidase activities were examined using fluorogen-labelled synthetic substrates. Enzyme activities were significantly down-regulated during exponential growth, increasing during stationary phase (P<0.01) whether the culture pH was controlled at pH 7.5 or allowed to fall naturally to pH 4.4. Culture-supernatant activities were significantly increased (P<0.05) when the pH was maintained at 6.0 or 7.5, indicating modulation of enzyme activity by pH. Growth under nitrogen-limitation/glucose-excess conditions resulted in a significant repression of cell-associated glycosidase activities (P<0.01), whilst in the supernatant, activities were generally reduced. The expression of peptidase activities in the culture supernatant did not significantly change. The results suggest a possible role for catabolite repression by glucose in regulating enzyme expression. When S. gordonii FSS2 was cultured with 50% (v/v) added heat-inactivated foetal bovine serum, several cell-associated enzyme activities increased initially but were then reduced as the culture time was extended to 116 h. Culture-supernatant enzyme activities (N-acetyl-beta-D-glucosaminidase, N-acetyl-beta-D-galactosaminidase, thrombin, Hageman factor, collagenase and chymotrypsin), however, were significantly increased (P<0.01) over the same time period. The findings indicated that most of the important glycosidases synthesized by S. gordonii FSS2 were down-regulated by acid growth conditions and may also be subject to catabolite repression by glucose but conversely may be up-regulated by growth in serum. These results may have implications for streptococcal growth in an IE vegetation and in the mouth between meals or during sleep.

Adaptation, Physiological↗
PubMed1987

Regulation of beta-glucosidase in Bacteroides ruminicola by a different mechanism: growth rate-dependent derepression.

Bacteroides ruminicola B(1)4, a predominant ruminal and cecal bacterium, was grown in batch and continuous cultures, and beta-glucosidase activity was measured by following the hydrolysis of p-nitrophenyl-beta-glucopyranoside. Specific activity was high when the bacterium was grown in batch cultures containing cellobiose, mannose, or lactose (greater than 286 U/g of protein). Activity was reduced approximately 90% when the organism was grown on glucose, sucrose, fructose, maltose, or arabinose. The specific activity of cells fermenting glucose was initially low but increased as glucose was depleted. When glucose was added to cultures growing on cellobiose, beta-glucosidase synthesis ceased immediately. Catabolite repression by glucose was not accompanied by diauxic growth and was not relieved by cyclic AMP. Since glucose-grown cultures eventually exhibited high beta-glucosidase activity, cellobiose was not needed as an inducer. Catabolite repression explained beta-glucosidase activity of batch cultures and high-dilution-rate chemostats where glucose accumulated, but it could not account for activity at slow dilution rates. Maximal beta-glucosidase activity was observed at a dilution rate of approximately 0.35 h-1, and cellobiose-limited chemostats showed a 15-fold decrease in activity as the dilution rate declined. An eightfold decline was observed in glucose-limited chemostats. Since inducer availability was not a confounding factor in glucose-limited chemostats, the growth rate-dependent derepression could not be explained by other mechanisms.

Animals↗
PubMed1997

Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene.

A regulatory gene, reg1, was identified in Streptomyces lividans. It encodes a 345-amino-acid protein (Reg1) which contains a helix-turn-helix DNA-binding motif in the N-terminal region. Reg1 exhibits similarity with the LacI/GalR family members over the entire sequence. It displays 95% identity with MalR (the repressor of malE in S. coelicolor), 65% identity with ORF-Sl (a putative regulatory gene of alpha-amylase of S. limosus), and 31% identity with CcpA (the carbon catabolite repressor in Bacillus subtilis). In S. lividans, the chromosomal disruption of reg1 affected the expression of several genes. The production of alpha-amylases of S. lividans and that of the alpha-amylase of S. limosus in S. lividans were enhanced in the reg1 mutant strains and relieved of carbon catabolite repression. As a result, the transcription level of the alpha-amylase of S. limosus was noticeably increased in the reg1 mutant strain. Moreover, the induction of chitinase production in S. lividans was relieved of carbon catabolite repression by glucose in the reg1 mutant strain, while the induction by chitin was lost. Therefore, reg1 can be regarded as a pleiotropic regulatory gene in S. lividans.

Amino Acid Sequence↗
PubMed2004

Translational control by internal ribosome entry site in Saccharomyces cerevisiae.

To confirm the active involvement of the internal ribosome entry site (IRES)-dependent translation in living eukaryotes, Saccharomyces cerevisiae and HAP4 IRES were used for in vitro and in vivo experiments. Since HAP4 protein might be required for activating mRNAs transcription in yeast cells when they are released from catabolite repression, the translational efficiency of HAP4 mRNA is presumed to increase under such a condition. The in vitro experiment showed clearly that the translational mechanism was shifted from the cap-dependent to the completely IRES-dependent translation when the yeast cells were derepressed from catabolite repression. From in vivo experiment, it was confirmed that the IRES-dependent translational efficiency was in a low level at the beginning of the stationary growth phase, and was enhanced at the glucose-exhausted phase. These results indicate that yeast cells on the catabolite derepressed condition could get a large amount of HAP4 protein for the completely IRES-dependent translation, while the IRES-dependent translational efficiency is increased. It has been proven that IRES functions directing the initiation of translation in living yeast cells.

Gene Expression Regulation, Fungal↗
PubMed2006

Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol.

Here, we describe how the recently published Aspergillus nidulans genome sequence [Galagan, J.E., Calvo, S.E., Cuomo, C., Li-Jun, M., Wortman, J.R., et al., 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438 (7071), 1105-1115] was used to design a high-density oligo array with probes for 3,278 selected genes using the Febit Geniom One array system. For this purpose, the program OligoWiz II was used to design 24,125 probes to cover the 3,278 selected genes. Subsequently, the Febit system was used to investigate carbon catabolite repression by comparing the gene expression of a creA deleted mutant strain with a reference strain grown either with glucose or ethanol as the sole carbon source. In order to identify co-regulated genes and genes influenced by either the carbon source or CreA, the most significantly regulated genes (p<or=0.01) were grouped in eight clusters based on their expression profile. Analysis of the clusters allowed identification of numerous genes that are presumably not regulated by CreA, or alternatively are either directly or indirectly regulated by CreA. Surprisingly, we found evidence that more than 25% of the genes (54 out of the 200 significantly regulated) that are repressed by glucose are not completely de-repressed during growth on ethanol, as deletion of the creA resulted in increased expression of the genes in question even during growth on ethanol. Thus, the expression profiles obtained in the eight clusters indicate that the carbon catabolite repression is not a simple on/off switch but a more complex system not only dependent on the presence or absence of CreA but also on the carbon source.

Aspergillus nidulans↗
PubMed1997

Effect of glucose concentration on swimming motility in enterobacteria.

Since the observation that glucose prevents the synthesis of flagella in Escherichia coli was first reported in 1967, many studies have addressed the underlying mechanism. Currently, it is thought that an increase in glucose concentration decreases the intracellular CRP/cAMP concentration. This leads to an inhibitory effect on the expression of the flhD operon, the master operon for flagella synthesis. In our study on defining factors influencing the cell differentiation of Serratia marcescens, glucose catabolite repression of hag expression and swimming/swarming motility was not observed. Further experiments using a simple swimming motility assay extended this observation to other members of Enterobacteriaceae. Although the underlying mechanism is still uncharacterised, our results suggest that glucose catabolite repression of swimming motility may not be a common phenomenon in Enterobacteriaceae.

DNA-Binding Proteins↗
PubMed1998

Physiology of carbohydrate to solvent conversion by clostridia.

The solvent-forming clostridia have attracted interest because of their ability to convert a range of carbohydrates to end-products such as acetone, butanol and ethanol. Polymeric substrates such as cellulose, hemicellulose and starch are degraded by extracellular enzymes. The majority of cellulolytic clostridia, typified by Clostridium thermocellum, produce a multi-enzyme cellulase complex in which the organization of components is critical for activity against the crystalline substrate. A variety of enzymes involved in degradation of hemicellulose and starch have been identified in different strains. The products of degradation, and other soluble substrates, are accumulated via membrane-bound transport systems which are generally poorly characterized. It is clear, however, that the phosphoenolpyruvate-dependent phosphotransferase system (PTS) plays a major role in solute uptake in several species. Accumulated substrates are converted by intracellular enzymes to end-products characteristic of the organism, with production of ATP to support growth. The metabolic pathways have been described, but understanding of mechanisms of regulation of metabolism is incomplete. Synthesis of extracellular enzymes and membrane-bound transport systems is commonly subject to catabolite repression in the presence of a readily metabolized source of carbon and energy. While many genes encoding cellulases, xylanases and amylases have been cloned and sequenced, little is known of control of their expression. Although the mechanism of catabolite repression in clostridia is not understood, some recent findings implicate a role for the PTS as in other low G-C Gram-positive bacteria. Emphasis has been placed on describing the mechanisms underlying the switch of C. acetobutylicum fermentations from acidogenic to solventogenic metabolism at the end of the growth phase. Factors involved include a lowered pH and accumulation of undissociated butyric acid, intracellular concentration of ATP and reduced pyridine nucleotides, nutrient limitation, and the interplay between pathways of carbon and electron flow. Genes encoding enzymes of solvent pathways have been cloned and sequenced, and their expression correlated with the pattern of end-product formation in fermentations. There is evidence that the initiation of solvent formation may be subject to control mechanisms similar to other stationary-phase phenomena, including sporulation. The application of recently developed techniques for genetic manipulation of the bacterium is improving understanding of the regulatory circuits, but a complete molecular description of the control of solvent formation remains elusive. Experimental manipulation of the pathways of electron flow in other species has been shown to influence the range and yield of fermentation end-products. Acid-forming clostridia can, under appropriate conditions, be induced to form atypical solvents as products. While the mechanisms of regulation of gene expression are not at all understood, the capacity to adapt in this way further illustrates the metabolic flexibility of clostridial strains.

Acetone↗
PubMed1981

Transcription regulation of colicin Ib synthesis.

Bacteriophage Mud (Casadaban and Cohen 1979) was used to bring the transcription of the gene for beta galactosidase (lacZ) under the control of the promoter of the structural gene for colicin Ib (cia(Ib)) on a derivative of the Col plasmid Col-Ib.P9. Transcription of this fusion operon was stimulated by agents which damaged cellular DNA (mitomycin C, bleomycin and colicin E2). Increased transcription of the cia-lacZ operon could be detected within 13 min of the addition of these agents. In a strain bearing the tif-1 (recA441) mutation, constitutive expression of the SOS DNA repair system at 42 degree C also increased transcription of the cia-lacZ operon. Transcription of the cia-lacZ operon was also stimulated by inhibition of DNA gyrase activity with nalidixic acid but not with novobiocin. Transitory inhibition of protein synthesis with chloramphenicol or by proline starvation of a proline auxotroph did not stimulate cia-lacZ transcription. Transcription of the cia-lacZ operon was substantially reduced in the presence of a recA mutation, but was largely unaffected by a mutation in recB affecting the RecBC DNase or by catabolite repression. Control experiments in which the production of colicin Ib was measured confirmed that the experiments with the fusion operon gave an accurate indication as to the activity of the wild type cia gene except for the effect of catabolite repression, where we observed up to 99% reduction in colicin Ib production in strains carrying mutant crp or cya alleles. The overall results confirm previous suggestions that there was considerable similarity between the regulatory systems controlling production of colicins and the repressor-dependent regulation of lambdoid prophage induction.

Bacteriophage mu↗
PubMed1977

Tyramine oxidase and regulation of arylsulfatase synthesis in Klebsiella aerogenes.

The participation of tyramine oxidase in the regulation of arylsulfatase synthesis in Klebsiella aerogenes was studied. Arylsulfatase was synthesized when this organism was grown with methionine or taurine as the sulfur source (nonrepressing conditions) and was repressed by inorganic sulfate or cysteine; this repression was relieved by tyramine and related compounds (derepressing conditions). Under nonrepressing conditions, arylsulfatase synthesis was not regulated by tyramine oxidase synthesis. However, derepression of arylsulfatase and induction of tyramine oxidase synthesis by tyramine were both antagonized by glucose and other carbohydrate compounds. The derepressed synthesis of arylsulfatase, like that of tyramine oxidase, was released from catabolite repression by use of tyramine as the sole source of nitrogen. A mutant strain that exhibits constitutive synthesis of glutamine synthetase and high levels of histidase when grown in glucose-ammonium medium was subject to the catabolite repression of both tyramine oxidase and arylsulfatase syntheses. Mutants in which repression of arylsulfatase could not be relieved by tyramine could not utilize tyramine as the sole source of nitrogen and were defective in the gene for tyramine oxidase.

Amino Acid Oxidoreductases↗
PubMed1985

Purification and regulation of glutamine synthetase in a collagenolytic Vibrio alginolyticus strain.

Glutamine synthetase (EC 6.3.1.2) has been purified from a collagenolytic Vibrio alginolyticus strain. The apparent molecular weight of the glutamine synthetase subunit was approximately 62,000. This indicates a particle weight for the undissociated enzyme of 744,000, assuming the enzyme is the typical dodecamer. The glutamine synthetase enzyme had a sedimentation coefficient of 25.9 S and seems to be regulated by adenylylation and deadenylylation. The pH profiles assayed by the gamma-glutamyltransferase method were similar for NH4-shocked and unshocked cell extracts and isoactivity point was not obtained from these curves. The optimum pH for purified and crude cell extracts was 7.9. Cell-free glutamine synthetase was inhibited by some amino acids and AMP. The transferase activity of glutamine synthetase from mid-exponential phase cells varied greatly depending on the sources of nitrogen or carbon in the growth medium. Glutamine synthetase level was regulated by nitrogen catabolite repression by (NH4)2SO4 and glutamine, but cells grown in the presence of proline, leucine, isoleucine, tryptophan, histidine, glutamic acid, glycine and arginine had enhanced levels of transferase activity. Glutamine synthetase was not subject to glucose, sucrose, fructose, glycerol or maltose catabolite repression and these sugars had the opposite effect and markedly enhanced glutamine synthetase activity.

Ammonium Sulfate↗
PubMed1975

Regulatory factors affecting alpha-amylase production in bacillus licheniformis.

Possible factors regulating alpha-mylase synthesis in wild-type Bacillus licheniformis and in mutants producing elevated levels of the enzyme were studied in terms of catabolite repression, apparent temperature-sensitive repression, induction, and culture age. The synthesis of alpha-amylase in the parent strain occurred long after the culture reached the stationary phase of growth as a result of de novo protein synthesis, occurred only at high temperature around 50 C and not below 45 C, appeared to be induced in the presence of oligosaccharides with some linkage of alpha-1,4-, beta-1,4, beta-1,6-glucosyl glucose, or alpha-1,6-galactosyl glucose, and was repressed by the addition of exogenous glucose or low-molecular-weight metabolites. The addition of cyclic adenosine 3',5'-monophosphate stimulated alpha-amylase accumulation in growing cultures of the parent strain, but neither shortened the long lap period prior to the start of alpha-amylase synthesis nor mitigated the repressive effect of glucose. Mutant strains derived from the parent strain showed variation in the pattern of alpha-amylase synthesis, and some of them such as F-12s and F-14 produced alpha-amylase constitutively and without sensitivity to catabolite repression or transient repression from the moment of cell growth. These results are discussed in relation to possible regulatory mechanisms that might account for the observed characteristics of alpha-amylase synthesis in this facultative thermophilic microorganism.

Aerobiosis↗
PubMed1999

Alterations in protein expression caused by the hha mutation in Escherichia coli: influence of growth medium osmolarity.

The Hha protein belongs to a new family of regulators involved in the environmental regulation of virulence factors. The aim of this work was to study the effect of the hha mutation on the overall protein pattern of Escherichia coli cells by two-dimensional polyacrylamide gel electrophoresis. The growth medium osmolarity clearly influenced the effect of the hha mutation. The number of proteins whose expression was altered in hha cells, compared with wild-type cells, was three times larger at a high osmolarity than at a low osmolarity. Among the proteins whose expression was modified by the hha allele, both OmpA and protein IIAGlc of the phosphotransferase system could be identified. As this latter enzyme participates in the regulation of the synthesis of cyclic AMP and hence influences the catabolite repression system, we tested whether the expression of the lacZ gene was also modified in hha mutants. This was the case, suggesting that at least some of the pleiotropic effects of the hha mutation could be caused by its effect on the catabolite repression system.

Alleles↗
PubMed1974

Outer membrane proteins of Escherichia coli. IV. Differences in outer membrane proteins due to strain and cultural differences.

When the 42,000-dalton major outer membrane protein of Escherichia coli O111 is examined on alkaline polyacrylamide gels containing sodium dodecyl sulfate, it is resolved into three distinct bands designated as proteins 1, 2, and 3. Band 3 consists of two distinct polypeptides, proteins 3a and 3b. E. coli K-12 does not make any protein 2, but makes proteins similar to 1, 3a, and 3b as indicated by comparison of cyanogen bromide peptide patterns. Several Shigella species and most other strains of E. coli resemble E. coli K-12 in that they lack protein 2, whereas Salmonella typhimurium is more similar to E. coli O111. In addition to these species and strain differences, cultural differences resulted in differences in the outer membrane protein profiles. Under conditions of catabolite repression, the level of protein 2 in E. coli O111 decreased while the level of protein 1 increased. An enterotoxin-producing strain similar to E. coli O111 produced no protein 1 and an elevated level of protein 2 under conditions of low catabolite repression. The levels of proteins 1 and 3 are also different in different phases of the growth curve, with protein 1 being the major species in the exponential-phase cells and protein 3 being the major species in stationary-phase cells. A multiply phage-resistant mutant of E. coli K-12 with no obvious cell wall defects produced no protein 1 or 2, but made increased amounts of protein 3. Thus, the major outer membrane proteins of E. coli and related species may vary considerably without affecting outer membrane integrity.

Bacterial Proteins↗
PubMed1986

Induction of L-arabinose isomerase in gamma-irradiated Escherichia coli.

Gamma irradiation of Escherichia coli B/r caused a dose-dependent inhibition of the capacity of the cells to synthesize L-arabinose isomerase in response to the inducer. At higher doses (18 krad and above), postirradiation incubation led to further inhibition of the capacity to synthesize L-arabinose isomerase, whereas cells receiving lower doses recovered from the damage to the enzyme synthesizing system following incubation. Cyclic AMP partially reversed the inhibitory effect on L-arabinose isomerase induction produced immediately after irradiation by all gamma-ray doses (up to 30 krad), but the enhanced inhibitory effect caused by induction in cells irradiated at higher doses could not be reversed by the nucleotide. It is suggested that although catabolite repression is partly responsible for causing the inhibition of the enzyme synthesizing capacity of the cells observed immediately after gamma irradiation, the enhanced inhibition caused by incubating cells irradiated at higher doses is not due to interference with the control mechanism regulated by catabolite repression.

Aldose-Ketose Isomerases↗
PubMed2001

Phosphorylation regulates the interaction between Gln3p and the nuclear import factor Srp1p.

Gln3p is a GATA-type transcription activator of nitrogen catabolite repressible (NCR) genes. Gln3p was recently found to be hyperphosphorylated in a TOR-dependent manner and resides in the cytoplasm in high quality nitrogen. In contrast, during nitrogen starvation or rapamycin treatment, Gln3p becomes rapidly dephosphorylated and accumulates in the nucleus, thereby activating nitrogen catabolite repression genes. However, a detailed mechanistic understanding is lacking for the regulation of Gln3p nucleocytoplasmic distribution. In this study, we applied a functional genomics approach to identify the nuclear transport factors for Gln3p. We found that yeast karyopherin alpha/Srp1p and Crm1p are required for the nuclear import and export of Gln3p, respectively. Similarly, the Ran GTPase pathway is also involved in the nuclear translocation of Gln3p. Finally, we show that Srp1p preferentially interacts with the hypophosphorylated versus the hyperphosphorylated Gln3p. These findings define a possible mechanism for regulated nucleocytoplasmic transport of Gln3p by phosphorylation in vivo.

Amino Acid Transport Systems↗
PubMed2000

The HPr kinase from Bacillus subtilis is a homo-oligomeric enzyme which exhibits strong positive cooperativity for nucleotide and fructose 1,6-bisphosphate binding.

Carbon catabolite repression allows bacteria to rapidly alter the expression of catabolic genes in response to the availability of metabolizable carbon sources. In Bacillus subtilis, this phenomenon is controlled by the HPr kinase (HprK) that catalyzes ATP-dependent phosphorylation of either HPr (histidine containing protein) or Crh (catabolite repression HPr) on residue Ser-46. We report here that B. subtilis HprK forms homo-oligomers constituted most likely of eight subunits. Related to this complex structure, the enzyme displays strong positive cooperativity for the binding of its allosteric activator, fructose 1,6-bisphosphate, as evidenced by either kinetics of its phosphorylation activity or the intrinsic fluorescence properties of its unique tryptophan residue, Trp-235. It is further shown that activation of HPr phosphorylation by fructose 1,6-bisphosphate essentially occurs at low ATP and enzyme concentrations. A positive cooperativity was also detected for the binding of natural nucleotides or their 2'(3')-N-methylanthraniloyl derivatives, in either phosphorylation or fluorescence experiments. Most interestingly, quenching of the HprK tryptophan fluorescence by using either iodide or acrylamide revealed a heterogeneity of tryptophan residues within the population of oligomers, suggesting that the enzyme exists in two different conformations. This result suggests a concerted-symmetry model for the catalytic mechanism of positive cooperativity displayed by HprK.

Adenosine Diphosphate↗
PubMed1979

Characterization of an inducible porter required for L-proline catabolism by Escherichia coli K12.

L-Proline can serve as sole source of carbon and nitrogen for the growth of Escherichia coli K12 and other Enterobacteria. L-Proline uptake and L-proline oxidase are subject both to catabolite repression and to specific induction by L-proline or glycyl-L-proline, although their regulation is not strictly coordinate. A strain defective for L-proline uptake due to a lesion at the locus putP does not show elevated uptake activity either on relief of catabolite repression or when grown on glycyl-L-proline as nitrogen source. The apparent Km for L-proline uptake decreases up to 14-fold as uptake Vm increases when cells are induced for both L-proline uptake and L-proline oxidase; cells with increased uptake activity, alone, do not show an altered Km. Although L-proline is metabolized during the uptake measurements, uptake is always active. The observed variations in uptake Km are unlikely to result from the escape of radioactive L-proline metabolites or from reversal of the transport reaction during the uptake measurements. We conclude that the L-proline porter encoded in putP is responsible for 80 to 90% of the constitutive and for the inducible L-proline uptake activity of wild-type bacteria. Although this porter is amplified in cells induced for L-proline catabolism, the observed values for uptake Vm may not be taken as a direct indicator of porter concentration.

Biological Transport, Active↗