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Catabolite Repression (catabolite + repression)
Kinds of Catabolite Repression Selected AbstractsCatabolite repression in Escherichia coli, a comparison of modelling approachesFEBS JOURNAL, Issue 2 2009Andreas Kremling The phosphotransferase system in Escherichia coli is a transport and sensory system and, in this function, is one of the key players of catabolite repression. Mathematical modelling of signal transduction and gene expression of the enzymes involved in the transport of carbohydrates is a promising approach in biotechnology, as it offers the possibility to achieve higher production rates of desired components. In this article, the relevance of methods and approaches concerning mathematical modelling in systems biology is discussed by assessing and comparing two comprehensive mathematical models that describe catabolite repression. The focus is thereby on modular modelling with the relevant input in the central modules, the impact of quantitative model validation, the identification of control structures and the comparison of model predictions with respect to the available experimental data. [source] Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dotsFEMS MICROBIOLOGY REVIEWS, Issue 3 2002Terrance G. Cooper Abstract Major advances have recently occurred in our understanding of GATA factor-mediated, nitrogen catabolite repression (NCR)-sensitive gene expression in Saccharomyces cerevisiae. Under nitrogen-rich conditions, the GATA family transcriptional activators, Gln3 and Gat1, form complexes with Ure2, and are localized to the cytoplasm, which decreases NCR-sensitive expression. Under nitrogen-limiting conditions, Gln3 and Gat1 are dephosphorylated, move from the cytoplasm to the nucleus, in wild-type but not rna1 and srp1 mutants, and increase expression of NCR-sensitive genes. ,Induction' of NCR-sensitive gene expression and dephosphorylation of Gln3 (and Ure2 in some laboratories) when cells are treated with rapamycin implicates the Tor1/2 signal transduction pathway in this regulation. Mks1 is posited to be a negative regulator of Ure2, positive regulator of retrograde gene expression and to be itself negatively regulated by Tap42. In addition to Tap42, phosphatases Sit4 and Pph3 are also argued by some to participate in the regulatory pathway. Although a treasure trove of information has recently become available, much remains unknown (and sometimes controversial) with respect to the precise biochemical functions and regulatory pathway connections of Tap42, Sit4, Pph3, Mks1 and Ure2, and how precisely Gln3 and Gat1 are prevented from entering the nucleus. The purpose of this review is to provide background information needed by students and investigators outside of the field to follow and evaluate the rapidly evolving literature in this exciting field. [source] Transcriptional responses of Saccharomyces cerevisiae to preferred and nonpreferred nitrogen sources in glucose-limited chemostat culturesFEMS YEAST RESEARCH, Issue 4 2007Viktor M. Boer Abstract Aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae grown with six different nitrogen sources were subjected to transcriptome analysis. The use of chemostats enabled an analysis of nitrogen-source-dependent transcriptional regulation at a fixed specific growth rate. A selection of preferred (ammonium and asparagine) and nonpreferred (leucine, phenylalanine, methionine and proline) nitrogen sources was investigated. For each nitrogen source, distinct sets of genes were induced or repressed relative to the other five nitrogen sources. In total, 131 such ,signature transcripts' were identified in this study. In addition to signature transcripts, genes were identified that showed a transcriptional coresponse to two or more of the six nitrogen sources. For example, 33 genes were transcriptionally upregulated in leucine-grown, phenylalanine-grown and methionine-grown cultures; this was partly attributed to the involvement of common enzymes in the dissimilation of these amino acids. In addition to specific transcriptional responses elicited by individual nitrogen sources, their impact on global regulatory mechanisms such as nitrogen catabolite repression (NCR) were monitored. NCR-sensitive gene expression in the chemostat cultures showed that ammonium and asparagine were ,rich' nitrogen sources. By this criterion, leucine, proline and methionine were ,poor' nitrogen sources, and phenylalanine showed an ,intermediate' NCR response. [source] Identification of direct and indirect targets of the Gln3 and Gat1 activators by transcriptional profiling in response to nitrogen availability in the short and long termFEMS YEAST RESEARCH, Issue 5 2006Bart Scherens Abstract Nitrogen catabolite repression (NCR) consists in the specific inhibition of transcriptional activation of genes encoding the permeases and catabolic enzymes needed to degrade poor nitrogen sources. Under nitrogen limitation or rapamycin treatment, NCR genes are activated by Gln3 or Gat1, or by both factors. To compare the sets of genes responding to rapamycin or to nitrogen limitation, we used DNA microarrays to establishing the expression profiles of a wild type strain, and of a double gln3,,gat1, strain, grown on glutamine, after addition of rapamycin, on proline, or after a shift from glutamine to proline. Analysis of microarray data revealed 392 genes whose expression was dependent on the nitrogen source quality. 91 genes were activated in a GATA factor-dependent manner in all growth conditions, suggesting a direct role of Gln3 and Gat1 in their expression. Other genes were only transiently up-regulated (stress-responsive genes) or down-regulated (genes encoding ribosomal proteins and translational factors) upon nitrogen limitation, and this regulation was delayed in a gln3,,gat1, strain. Repression of amino acid and nucleotide biosynthetic genes after a nitrogen shift did not depend on Gcn4. Several transporter genes were repressed as a consequence of enhanced levels of NCR-responsive permeases present at the plasma membrane. [source] Mechanism of catabolite repression in the bgl operon of Escherichia coli: involvement of the anti-terminator BglG, CRP-cAMP and EIIAGlc in mediating glucose effect downstream of transcription initiationGENES TO CELLS, Issue 4 2000Abhilasha Gulati Background Expression of the bgl operon of Escherichia coli, involved in the regulated uptake and utilization of aromatic ,-glucosides, is extremely sensitive to the presence of glucose in the growth medium. We have analysed the mechanism by which glucose exerts its inhibitory effect on bgl expression. Results Our studies show that initiation of transcription from the bgl promoter is only marginally sensitive to glucose. Instead, glucose exerts a more significant inhibition on the elongation of transcription beyond the rho-independent terminator present within the leader sequence. Transcriptional analyses using plasmids that carry mutations in bglG or within the terminator, suggest that the target for glucose-mediated repression is the anti-terminator protein, BglG. Introduction of multiple copies of bglG or the presence of mutations that inhibit its phosphorylation by Enzyme IIBgl (BglF), result in loss of glucose repression. Studies using crp, cya and crr strains show that both CRP-cAMP and the Enzyme IIAGlc (EIIAGlc) are involved in the regulation. Although transcription initiation is normal in a crp, cya double mutant, no detectable transcription is seen downstream of the terminator, which is restored by a mutation within the terminator. Transcription past the terminator is also partly restored by the addition of exogenous cAMP to glucose-grown cultures of a crp+ strain. Glucose repression is lost in the crr mutant strain. Conclusions The results summarized above indicate that glucose repression in the bgl operon is mediated at the level of transcription anti-termination, and glucose affects the activity of BglG by altering its phosphorylation by BglF. The CRP-cAMP complex is also involved in this regulation. The results using the crr mutant suggest a negative role for EIIAGlc in the catabolite repression of the bgl genes. [source] The role of GAP1 gene in the nitrogen metabolism of Saccharomyces cerevisiae during wine fermentationJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009R. Chiva Abstract Aim:, The aim of this study was to analyse the relevance of the general amino acid permease gene (GAP1) of the wine yeast Saccharomyces cerevisiae on nitrogen metabolism and fermentation performance. Methods and Results:, We constructed a gap1 mutant in a wine strain. We compared fermentation rate, biomass production and nitrogen consumption between the gap1 mutant and its parental strain during fermentations with different nitrogen concentrations. The fermentation capacity of the gap1 mutant strain was impaired in the nitrogen-limited and -excessive conditions. The nitrogen consumption rate between the wild strain and the mutant was different for some amino acids, especially those affected by nitrogen catabolite repression (NCR). The deletion of GAP1 gene also modified the gene expression of other permeases. Conclusions:, The Gap1 permease seems to be important during wine fermentations with low and high nitrogen content, not only because of its amino acid transporter role but also because of its function as an amino acid sensor. Significance and Impact of the Study:, A possible biotechnological advantage of a gap1 mutant is its scarce consumption of arginine, whose metabolism has been related to the production of the carcinogenic ethyl carbamate. [source] Flocculation onset in Saccharomyces cerevisiae: the role of nutrientsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2005S. Sampermans Abstract Aims:, To examine the role of the nutrients on the onset of flocculation in an ale-brewing strain, Saccharomyces cerevisiae NCYC 1195. Methods and Results:, Flocculation was evaluated using the method of Soares, E.V. and Vroman, A. [Journal of Applied Microbiology (2003) 95, 325]. For cells grown in chemically defined medium (yeast nitrogen base with glucose) or in rich medium (containing yeast extract, peptone and fermentable sugars: fructose or maltose), the onset of flocculation occurred after the end of exponential respiro-fermentative phase of growth being coincident with the attainment of the lower level of carbon source in the culture medium. Cells, in exponential respiro-fermentative phase of growth, transferred to a glucose-containing medium without nitrogen source, developed a flocculent phenotype, while these carbon source starved cells, in the presence of all other nutrients that support growth, did not flocculate. In addition, cells in exponential phase of growth, under catabolite repression, when transferred to a medium containing 0·2% (w/v) of fermentable sugar (fructose or maltose) or 2% (v/v) ethanol, showed a rapid triggering of flocculation, while when incubated in 2% (v/v) glycerol did not develop a flocculent phenotype. Conclusions:, The onset of flocculation occurs when a low sugar and/or nitrogen concentration is reached in culture media. The triggering of flocculation is an energetic dependent process influenced by the carbon source metabolism. The presence of external nitrogen source is not necessary for developing a flocculent phenotype. Significance and Impact of the Study:, This work contributes to the elucidation of the role of nutrients on the onset of flocculation in NewFlo phenotype yeast strains. This information might be useful to the brewing industry, in the control of yeast flocculation, as the time when the onset of flocculation occurs can determine the fermentation performance and the beer quality. [source] Improvement of Yarrowia lipolytica lipase production by fed-batch fermentationJOURNAL OF BASIC MICROBIOLOGY, Issue 2 2009Patrick Fickers Abstract Two different types of fed-batch fermentation were investigated to improve production yields of the Lip2 extracellular lipase in Y. lipolytica mutant-strain LgX64.81 grown in a 20l bioreactor. Compare to batch cultures, culture feeding with the complete medium led to a 2-fold increased lipase production (2016 ± 76 U ml,1) whereas addition of a combination of glucose and olive oil led to a 3-fold increase. The high level of lipase production obtained on glucose media with Y. lipolytica LgX64.81 could be related to its phenotype i.e. a lower sensibility to glucose catabolite repression due to a modification in the level of HXK1 expression. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Production of delta-endotoxin by Bacillus thuringiensis subsp kurstaki and overcoming of catabolite repression by using highly concentrated gruel and fish meal media in 2- and 20-dm3 fermentersJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 8 2002Nabil Zouari Abstract Delta-endotoxin production by a strain of Bacillus thuringiensis subsp kurstaki exhibiting larvicidal toxicity towards lepidoptera was investigated in 2- and 20-dm3 fermenters, using gruel- and fish meal-based media. The results show clearly that in such complex media, aeration plays an important role in bioinsecticide production. Optimal aeration led to improvement of delta-endotoxin concentrations with decreases of final spore count and proteolytic activity. Moreover, in order to use high gruel concentrations, a fermenter configuration with an efficient aeration system should be used. In a 20-dm3 Biolafite fermenter, 59,g,dm,3 or 75,g,dm,3 gruel was used to produce bioinsecticides with a significant reduction of carbon catabolite repression of delta-endotoxin synthesis. This result is very interesting in order to produce high final delta-endotoxin concentrations in the culture broth. It was also concluded, by considering the key role of oxidative pathways in delta-endotoxin synthesis, that oxygen supply must be adequate for bioinsecticide production at high substrate concentrations. Moreover, the role of sodium chloride in improving delta-endotoxin production is dependent not only on protease synthesis and its effect on crystal stability, but also on the aeration level of the production medium. © 2002 Society of Chemical Industry [source] Improvement of a fed-batch process for high level xylanase production by a Bacillus strainJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 5 2001Gerhard Schneider Abstract In this paper, the improvement of a fed-batch fermentation from the point of view of an industrial xylanase production process is described. The Bacillus strain chosen for this study is able to produce high quantities of a xylanase that is suitable to be used as bleach boost agent in chlorine-free bleaching sequences of paper pulp. It was found that xylo-oligosaccharides (hydrolysis products from xylan by xylanase action) were indispensable for induction of the enzyme synthesis, but that their presence in quantities of only 0.1,g,dm,3 xylose equivalents led to catabolite repression. A substrate-limited fed-batch process, that is the most adapted, was furthermore improved with regard to nutrient requirement of the microorganism, especially the nitrogen source. A process with constant supply of a culture medium containing xylan, peptone and mineral nitrogen was able to produce 20,240,nkat,cm,3 with a productivity of 910,nkat,cm,3,h,1, which places the process among the best ever reported. © 2001 Society of Chemical Industry [source] Inorganic phosphate has a crucial effect on Cry3Aa , -endotoxin productionLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2005A. Kurt Abstract Aims:, The study aimed at increasing Cry3Aa , -endotoxin production by a local isolate of Bacillus thuringiensis (B.t. strain Mm2). To this end, different nutritional conditions were tested for their effects on Cry3Aa yields. Methods and Results:,Bacillus thuringiensis Mm2 was grown by shaking at 30°C in different media. Samples were taken from the cultures at intervals and used for protein extraction. SDS-PAGE was performed for toxin analysis. Inclusion of inorganic phosphate (Pi) into the Difco's sporulation medium at an increased level of 200 mmol l,1 caused a fivefold increase (from 3 to 15·6 ,g ml,1) in toxin production. Omission of FeSO4 from the medium decreased this yield by half. Resuspension experiments suggested catabolite repression of toxin biosynthesis by glucose. The inclusion of high Pi invariably increased toxin synthesis, even in the absence of sugars. Conclusions:, Inorganic phosphate had the most striking effect on toxin biosynthesis. Iron effect was found to be unique to our isolate whereas Pi effect seemed to be common to the biosynthesis of Cry3Aa-type toxins. Stimulation of toxin synthesis by Pi did not seem to represent a relief from glucose repression. Significance and Impact of the Study:,Bacillus thuringiensis is the most versatile biopesticide for use in pest management. Regarding cost-effectiveness of related fermentations, high Pi supplement drastically increases Coleoptera-specific toxin synthesis. [source] Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteriaMOLECULAR MICROBIOLOGY, Issue 4 2000Dmitry A. Rodionov The comparative approach is a powerful tool for the analysis of gene regulation in bacterial genomes. It can be applied to the analysis of regulons that have been studied experimentally as well as that of regulons for which no known regulatory sites are available. It is assumed that the set of co-regulated genes and the regulatory signal itself are conserved in related genomes. Here, we use genomic comparisons to study the regulation of transport and utilization systems for sugar acids in gamma purple bacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae, Yersinia pestis, Erwinia chrysanthemi, Haemophilus influenzae and Vibrio cholerae. The variability of the operon structure and the location of the operator sites for the main transcription factors are demonstrated. The common metabolic map is combined with known and predicted regulatory interactions. It includes all known and predicted members of the GntR, UxuR/ExuR, KdgR, UidR and IdnR regulons. Moreover, most members of these regulons seem to be under catabolite repression mediated by CRP. The candidate UxuR/ExuR signal is proposed, the KdgR consensus is extended, and new operators for all transcription factors are identified in all studied genomes. Two new members of the KdgR regulon, a hypothetical ATP-dependent transport system OgtABCD and YjgK protein with unknown function, are detected. The former is likely to be the transport system for the products of pectin degradation, oligogalacturonides. [source] Carbon metabolism and product inhibition determine the epoxidation efficiency of solvent-tolerant Pseudomonas sp. strain VLB120,CBIOTECHNOLOGY & BIOENGINEERING, Issue 6 2007Jin-Byung Park Abstract Utilization of solvent tolerant bacteria as biocatalysts has been suggested to enable or improve bioprocesses for the production of toxic compounds. Here, we studied the relevance of solvent (product) tolerance and inhibition, carbon metabolism, and the stability of biocatalytic activity in such a bioprocess. Styrene degrading Pseudomonas sp. strain VLB120 is shown to be solvent tolerant and was engineered to produce enantiopure (S)-styrene oxide from styrene. Whereas glucose as sole source for carbon and energy allowed efficient styrene epoxidation at rates up to 97 µmol/min/(g cell dry weight), citrate was found to repress epoxidation by the engineered Pseudomonas sp. strain VLB120,C emphasizing that carbon source selection and control is critical. In comparison to recombinant Escherichia coli, the VLB120,C-strain tolerated higher toxic product levels but showed less stable activities during fed-batch cultivation in a two-liquid phase system. Epoxidation activities of the VLB120,C-strain decreased at product concentrations above 130 mM in the organic phase. During continuous two-liquid phase cultivations at organic-phase product concentrations of up to 85 mM, the VLB120,C-strain showed stable activities and, as compared to recombinant E. coli, a more efficient glucose metabolism resulting in a 22% higher volumetric productivity. Kinetic analyses indicated that activities were limited by the styrene concentration and not by other factors such as NADH availability or catabolite repression. In conclusion, the stability of activity of the solvent tolerant VLB120,C-strain can be considered critical at elevated toxic product levels, whereas the efficient carbon and energy metabolism of this Pseudomonas strain augurs well for productive continuous processing. Biotechnol. Bioeng. 2007;98: 1219,1229. © 2007 Wiley Periodicals, Inc. [source] Effect of Vitreoscilla hemoglobin on production of a chemotherapeutic enzyme, L -asparaginase, by Pseudomonas aeruginosaBIOTECHNOLOGY JOURNAL, Issue 2 2006Hikmet Geckil Abstract The production of L -asparaginase, an enzyme widely used in cancer chemotherapy, is mainly regulated by carbon catabolite repression and oxygen. This study was carried out to understand how different carbon sources and Vitreoscilla hemoglobin (VHb) affect the production of this enzyme in Pseudomonas aeruginosa and its VHb-expressing recombinant strain (PaJC). Both strains grown with various carbon sources showed a distinct profile of the enzyme activity. Compared to no carbohydrate supplemented medium, glucose caused a slight repression of L -asparaginase in P. aeruginosa, while it stimulated it in the PaJC strain. Glucose, regarded as one of the inhibitory sugars for the production L -asparaginase by other bacteria, was determined to be the favorite carbon source compared to lactose, glycerol and mannitol. Furthermore, contrary to common knowledge of oxygen repression of L -asparaginase in other bacteria, oxygen uptake provided by VHb was determined to even stimulate the L -asparaginase synthesis by P. aeruginosa. This study, for the first time, shows that in P. aeruginosa utilizing a recombinant oxygen uptake system, VHb, L -asparaginase synthesis is stimulated by glucose and other carbohydrate sources compared to the host strain. It is concluded that carbon catabolite and oxygen repression of L -asparaginase in fermentative bacteria is not the case for a respiratory non-fermentative bacterium like P. aeruginosa. [source] Effect of Different Carbon Sources on the Production of Succinic Acid Using Metabolically Engineered Escherichia coliBIOTECHNOLOGY PROGRESS, Issue 2 2007Christian Andersson Succinic acid (SA) is an important platform molecule in the synthesis of a number of commodity and specialty chemicals. In the present work, dual-phase batch fermentations with the E. coli strain AFP184 were performed using a medium suited for large-scale industrial production of SA. The ability of the strain to ferment different sugars was investigated. The sugars studied were sucrose, glucose, fructose, xylose, and equal mixtures of glucose and fructose and glucose and xylose at a total initial sugar concentration of 100 g L,1. AFP184 was able to utilize all sugars and sugar combinations except sucrose for biomass generation and succinate production. For sucrose as a substrate no succinic acid was produced and none of the sucrose was metabolized. The succinic acid yield from glucose (0.83 g succinic acid per gram glucose consumed anaerobically) was higher than the yield from fructose (0.66 g g,1). When using xylose as a carbon source, a yield of 0.50 g g,1 was obtained. In the mixed-sugar fermentations no catabolite repression was detected. Mixtures of glucose and xylose resulted in higher yields (0.60 g g,1) than use of xylose alone. Fermenting glucose mixed with fructose gave a lower yield (0.58 g g,1) than fructose used as the sole carbon source. The reason is an increased pyruvate production. The pyruvate concentration decreased later in the fermentation. Final succinic acid concentrations were in the range of 25,40 g L,1. Acetic and pyruvic acid were the only other products detected and accumulated to concentrations of 2.7,6.7 and 0,2.7 g L,1. Production of succinic acid decreased when organic acid concentrations reached approximately 30 g L,1. This study demonstrates that E. coli strain AFP184 is able to produce succinic acid in a low cost medium from a variety of sugars with only small amounts of byproducts formed. [source] | ||||||||||||||||||||||