Physiology of the inhibition by glucose of the induced synthesis of the beta-galactosideenzyme system of Escherichia coli

Inducer exclusion, by itself, cannot account for the glucose-mediated lac repression of Escherichia coli

The lac operon of Escherichia coli is repressed several 100-fold in the presence of glucose. This repression has been attributed to cAMP receptor protein-mediated inhibition of lac transcription and EIIA^Glc-mediated inhibition of lactose transport (inducer exclusion). The growing evidence against the first mechanism has led to the postulate that the repression is driven by inducer exclusion. Although inducer exclusion reduces the permease activity only 2-fold in fully induced cells, it could be more potent in partially induced cells. Here, we show that even in partially induced cells, inducer exclusion reduces the permease activity no more than 6-fold. Moreover, the repression is so small because these experiments are performed in the presence of chloramphenicol. Indeed, when glucose is added to a culture growing on glycerol and TMG, but no chloramphenicol, lac expression is repressed 900-fold. This repression is primarily due to reversal of the positive feedback loop, i.e., the decline of the intracellular TMG level leads to a lower permease level, which reduces the intracellular TMG level even further. The repression in the absence of chloramphenicol is therefore primarily due to positive feedback, which does not exist during measurements of inducer exclusion.

Phenotypic instability in fungi

Fungi are prone to phenotypic instability, that is, the vegetative phase of these organisms, be they yeasts or molds, undergoes frequent switching between two or more behaviors, often with different morphologies, but also sometime having different physiologies without any obvious morphological outcome. In the context of industrial utilization of fungi, this can have a negative impact on the maintenance of strains and/or on their productivity. Instabilities have been shown to result from various mechanisms, either genetic or epigenetic. This chapter will review different types of instabilities and discuss some lesser-known ones, mostly in filamentous fungi, while it will direct readers to additional literature in the case of well-known phenomena such as the amyloid prions or fungal senescence. It will present in depth the "white/opaque" switch of Candida albicans and the "crippled growth" degeneration of the model fungus Podospora anserina. These are two of the most thoroughly studied epigenetic phenotypic switches. I will also discuss the "sectors" presented by many filamentous ascomycetes, for which a prion-based model exists but is not demonstrated. Finally, I will also describe intriguing examples of phenotypic instability for which an explanation has yet to be provided.

Understanding carbon catabolite repression in Escherichia coli using quantitative models

Carbon catabolite repression (CCR) controls the order in which different carbon sources are metabolized. Although this system is one of the paradigms of the regulation of gene expression in bacteria, the underlying mechanisms remain controversial. CCR involves the coordination of different subsystems of the cell that are responsible for the uptake of carbon sources, their breakdown for the production of energy and precursors, and the conversion of the latter to biomass. The complexity of this integrated system, with regulatory mechanisms cutting across metabolism, gene expression, and signaling, and that are subject to global physical and physiological constraints, has motivated important modeling efforts over the past four decades, especially in the enterobacterium Escherichia coli. Different hypotheses concerning the dynamic functioning of the system have been explored by a variety of modeling approaches. We review these studies and summarize their contributions to the quantitative understanding of CCR, focusing on diauxic growth in E. coli. Moreover, we propose a highly simplified representation of diauxic growth that makes it possible to bring out the salient features of the models proposed in the literature and confront and compare the explanations they provide.

Hysteresis can grant fitness in stochastically varying environment

Although the existence of multiple stable phenotypes of living organisms enables random switching between phenotypes as well as non-random history dependent switching called hysteresis, only random switching has been considered in prior experimental and theoretical models of adaptation to variable environments. This work considers the possibility that hysteresis may also evolve together with random phenotype switching to maximize population growth. In addition to allowing the possibility that switching rates between different phenotypes may depend not only on a continuous environmental input variable, but also on the phenotype itself, the present work considers an opportunity cost of the switching events. This opportunity cost arises as a result of a lag phase experimentally observed after phenotype switching and stochastic behavior of the environmental input. It is shown that stochastic environmental variation results in maximal asymptotic growth rate when organisms display hysteresis for sufficiently slowly varying environmental input. At the same time, sinusoidal input does not cause evolution of memory suggesting that the connection between the lag phase, stochastic environmental variation and evolution of hysteresis is a result of a stochastic resonance type phenomenon.

Catabolite repression control of napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12

Escherichia coli, a facultative aerobe, expresses two distinct respiratory nitrate reductases. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments, whereas the membrane-bound NarGHI enzyme functions during growth in nitrate-rich environments. Maximal expression of the napFDAGHBC operon encoding periplasmic nitrate reductase results from synergistic transcription activation by the Fnr and phospho-NarP proteins, acting in response to anaerobiosis and nitrate or nitrite, respectively. Here, we report that, during anaerobic growth with no added nitrate, less-preferred carbon sources stimulated napF operon expression by as much as fourfold relative to glucose. Deletion analysis identified a cyclic AMP receptor protein (Crp) binding site upstream of the NarP and Fnr sites as being required for this stimulation. The napD and nrfA operon control regions from Shewanella spp. also have apparent Crp and Fnr sites, and expression from the Shewanella oneidensis nrfA control region cloned in E. coli was subject to catabolite repression. In contrast, the carbon source had relatively little effect on expression of the narGHJI operon encoding membrane-bound nitrate reductase under any growth condition tested. Carbon source oxidation state had no influence on synthesis of either nitrate reductase. The results suggest that the Fnr and Crp proteins may act synergistically to enhance NapABC synthesis during growth with poor carbon sources to help obtain energy from low levels of nitrate.

Comparative analysis of some models of gene regulation in mixed-substrate microbial growth

Mixed-substrate microbial growth is of fundamental interest in microbiology and bioengineering. Several mathematical models have been developed to account for the genetic regulation of such systems, especially those resulting in diauxic growth. In this work, we compare the dynamics of three such models (Narang, 1998a. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species. Biotechnol. Bioeng. 59, 116-121; Thattai and Shraiman, 2003. Metabolic switching in the sugar phosphotransferase system of Escherichia coli. Biophys. J. 85(2), 744-754; Brandt et al., 2004. Modelling microbial adaptation to changing availability of substrates. Water Res. 38, 1004-1013). We show that these models are dynamically similar--the initial motion of the inducible enzymes in all the models is described by the Lotka-Volterra equations for competing species. In particular, the prediction of diauxic growth corresponds to "extinction" of one of the enzymes during the first few hours of growth. The dynamic similarity occurs because in all the models, the inducible enzymes possess properties characteristic of competing species: they are required for their own synthesis, and they inhibit each other. Despite this dynamic similarity, the models vary with respect to the range of dynamics captured. The Brandt et al. model always predicts the diauxic growth pattern, whereas the remaining two models exhibit both diauxic and non-diauxic growth patterns. The models also differ with respect to the mechanisms that generate the mutual inhibition between the enzymes. In the Narang model, mutual inhibition occurs because the enzymes for each substrate enhance the dilution of the enzymes for the other substrate. The Brandt et al. model superimposes upon this dilution effect an additional mechanism of mutual inhibition. In the Thattai and Shraiman model, the mutual inhibition is entirely due to competition for the phosphoryl groups. For quantitative agreement with the data, all models must be modified to account for specific mechanisms of mutual inhibition, such as inducer exclusion.

Transcriptional regulation and characterization of a novel beta-fructofuranosidase-encoding gene from Bifidobacterium breve UCC2003

An operon involved in fructooligosaccharide breakdown was identified in the genome of Bifidobacterium breve UCC2003. This 2.6-kb transcriptional unit was comprised of three genes that encoded a putative permease, a conserved hypothetical protein, and a beta-fructofuranosidase. Active transcription of the operon was observed when B. breve UCC2003 was grown on sucrose or Actilight, while transcription appeared to be repressed when the organism was grown on glucose, fructose, a combination of glucose and sucrose, or a combination of fructose and sucrose. The beta-fructofuranosidase encoded by this operon was purified and biochemically characterized. The optimum pH and temperature for catalytic activity were determined to be pH 6.0 and 37 degrees C, respectively, and there was a dependence on bivalent cations, particularly manganese. The Km and Vmax values for sucrose hydrolysis were determined to be 25 +/- 2 mM and 24 +/- 3 micromol min(-1) mg(-1), respectively. Interestingly, the enzyme was shown to specifically catalyze cleavage of the beta(2-1) glycosidic bond between glucose and its neighboring fructose moiety in sucrose and other fructooligosaccharides with a relatively low degree of polymerization, and there was no detectable activity towards the beta(2-1) glycosidic bond between two fructose moieties within the same substrate. To our knowledge, such an enzymatic activity has not previously been described in bifidobacteria or other gram-positive bacteria.

Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior

A biological introduction serves to remind us that differentiation is an epigenetic process, that multistationarity can account for epigenetic differences, including those involved in cell differentiation, and that positive feedback circuits are a necessary condition for multistationarity and, by inference, for differentiation. The core of the paper is comprised of a formal description of feedback circuits and unions of disjoint circuits. We introduce the concepts of full-circuit (a circuit or union of disjoint circuits which involves all the variables of the system), and of ambiguous circuit (a circuit whose sign depends on the location in phase space). We describe the partition of phase space (a) according to the signs of the ambiguous circuits, and (b) according to the signs of the eigenvalues or their real part. We introduce a normalization of the system versus one of the circuits; in two variables, this permits an entirely general description in terms of a common diagram in the "circuit space." The paper ends with general statements concerning the requirements for multistationarity, stable periodicity, and deterministic chaos. (c) 2001 American Institute of Physics.

The effect of exogenous energy sources on the synthesis of beta-galactosidase in resting-cell suspensions of Escherichia coli

Using methyl-1-thio-β-D-galactoside as the inducer, the biosynthesis of β-galactosidase was observed in Escherichia coli B with only endogenous sources of nitrogen and energy available. The addition of glucose, ribose, xylose, or glycerol as exogenous energy sources to nitrogen-deficient media blocked enzyme formation. Preinduction of the resting cells failed to overcome inhibition by the added energy sources. With limited quantities of glucose, ribose, xylose, or glycerol, synthesis of β-galactosidase resumed abruptly and continued at the rate normal for cells in nitrogen-deficient media. Comparison of enzyme activities with oxygen uptake data revealed a reduction in the rate of oxygen uptake at the time enzyme synthesis resumed in media originally containing small amounts of energy sources. This change corresponded to only a fraction of the oxygen required for complete oxidation of one of the exogenous substrates. It is suggested that inhibition by these particular exogenous substrates involves metabolism to a common repressor or interference with an energy-transfer system.

Tryptophanase-tryptophan synthetase systems in Escherichia coli. II. Effect of glucose

Freundlich, Martin (University of Minnesota, Minneapolis) and Herman C. Lichstein. Tryptophanase-tryptophan synthetase systems in Escherichia coli. II. Effect of glucose. J. Bacteriol. 84:988-995. 1962.-The effect of glucose and other compounds on the formation of tryptophanase and tryptophan synthetase in Escherichia coli was examined. Although most of these compounds were potent inhibitors of the synthesis of tryptophanase, they invariably increased the formation of tryptophan synthetase. The severity of tryptophanase inhibition depended upon the degree of utilization of the compound by the growing bacterial cells. It was found that high levels of tryptophan overcame by 40% the repression caused by glucose. The stimulatory effect of glucose on tryptophan synthetase formation in E. coli 9723E could be duplicated by indole-3-propionic acid. A study of the amino acid pool of E. coli 9723E revealed no free tryptophan in cells harvested from the basal medium containing glucose. In contrast, cells grown in the absence of glucose possessed a measurable amount of this amino acid. The possible mechanisms of the effect of glucose and related compounds on tryptophanase and tryptophan synthetase formation, as well as the relationship of these effects to the metabolic control of tryptophan metabolism, are discussed.

Oxidative metabolism in Pediococcus pentosaceus. II. Factors controlling the formation of oxidative activities

Dobrogosz, Walter J. (The Pennsylvania State University, University Park) and Robert W. Stone. Oxidative metabolism in Pediococcus pentosaceus. II. Factors controlling the formation of oxidative activities. J. Bacteriol. 84:724-729. 1962.-Studies were conducted on some factors which regulate the formation of oxidative activities in Pediococcus pentosaceus, a homofermentative lactic acid organism. Oxidative abilities were defined as the capacities to oxidize glucose and glycerol, and to exhibit catalase activity. Factors such as the type of growth substrate, the growth substrate concentration, pH, and oxygen tension were considered. The results suggested that the development of oxidative activities in this organism is under adaptive control and subject to repression by the well-known "glucose effect," as well as by anaerobiosis. In addition to the necessity for the formation of aerobic systems for the metabolism of glycerol, which can be utilized only under aerobic conditions, data are presented which suggest that aerobic reactions may play a physiologically important role toward the induction of growth on other substrates such as d-xylose and lactose.

Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria

Numerous gram-negative and gram-positive bacteria take up carbohydrates through the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS). This system transports and phosphorylates carbohydrates at the expense of PEP and is the subject of this review. The PTS consists of two general proteins, enzyme I and HPr, and a number of carbohydrate-specific enzymes, the enzymes II. PTS proteins are phosphoproteins in which the phospho group is attached to either a histidine residue or, in a number of cases, a cysteine residue. After phosphorylation of enzyme I by PEP, the phospho group is transferred to HPr. The enzymes II are required for the transport of the carbohydrates across the membrane and the transfer of the phospho group from phospho-HPr to the carbohydrates. Biochemical, structural, and molecular genetic studies have shown that the various enzymes II have the same basic structure. Each enzyme II consists of domains for specific functions, e.g., binding of the carbohydrate or phosphorylation. Each enzyme II complex can consist of one to four different polypeptides. The enzymes II can be placed into at least four classes on the basis of sequence similarity. The genetics of the PTS is complex, and the expression of PTS proteins is intricately regulated because of the central roles of these proteins in nutrient acquisition. In addition to classical induction-repression mechanisms involving repressor and activator proteins, other types of regulation, such as antitermination, have been observed in some PTSs. Apart from their role in carbohydrate transport, PTS proteins are involved in chemotaxis toward PTS carbohydrates. Furthermore, the IIAGlc protein, part of the glucose-specific PTS, is a central regulatory protein which in its nonphosphorylated form can bind to and inhibit several non-PTS uptake systems and thus prevent entry of inducers. In its phosphorylated form, P-IIAGlc is involved in the activation of adenylate cyclase and thus in the regulation of gene expression. By sensing the presence of PTS carbohydrates in the medium and adjusting the phosphorylation state of IIAGlc, cells can adapt quickly to changing conditions in the environment. In gram-positive bacteria, it has been demonstrated that HPr can be phosphorylated by ATP on a serine residue and this modification may perform a regulatory function.

Effects of aerobic and anaerobic shock on catabolite repression in cyclic AMP suppressor mutants of Escherichia coli

Cultures of Escherichia coli K-12 grown on glucose or gluconate under aerobic conditions exhibited catabolite repression of beta-galactosidase synthesis. Depression occurred when these cultures were subjected to anaerobic shock. These states of repression and depression were found to be associated with low and high differential rates of cyclic AMP synthesis, respectively. This observation is consistent with the view that cyclic AMP plays a central role in the catabolite repression phenomenon. We report here, however, that identical stages of repression and derepression occur in mutant strains possessing cya crp(Csm) genotypes and therefore unable to synthesize cyclic AMP. These results suggest that cyclic AMP is not the sole regulator involved in catabolite repression.

Regulation of Klebsiella pneumoniae hut operons by oxygen

We investigated the regulation of genes concerned with nitrogen metabolism by oxygen in the facultative anaerobe Klebsiella pneumoniae. We found oxygen to be required for the expression of the hut operons; the effect of O2 on the glutamine synthetase and urease was less pronounced than on the hut operons. Glutamine synthetase was transiently repressed during the transition from an aerobic to an anaerobic environment. Regulation of hut by O2 suppressed the effect of nitrogen limitation on the expression of these genes.

Glucose effect in tgl mutant of Escherichia col K12 defective in methyl-alpha-D-glucoside transport

1. The dependence of the rate of accumulation of methyl-alpha-D-glucoside on its extracellular concentration was studied in the tgl mutant of Escherichia coli K12, isolated earlier. It has been shown that the kinetics of methyl-alpha-D-glucoside transport differ sharply from those in wild-type bacteria. 2. The beta-galactosidase synthesis in tgl strain is much less sensitive both to permanent and transient glucose catabolite repression. The level of cyclic AMP in mutant cells under the conditions of glucose catabolite repression is several times higher than in the parent strain. 3. The tgl mutation does not affect the manifestation of catabolite inhibition and inducer exclusion with glucose. 4. The data obtained are discussed in the light of a hypothesis concerning the existence of two sites, binding and pecific enzyme II of the phosphoenolpyruvate-dependent phosphotransferase system. The tgl mutation alters the first site, and the second one is damaged by the pgt mutation. 5. It is suggested that the products of the tgl and gpt genes are necessary for the manifestation of the phenomena of glucose permanent and transient repression. The effects of catabolite inhibition and inducer exclusion are realized irrespective of the existence or absence of the tgl product.

Degradation of blood group antigens in human colon ecosystems. I. In vitro production of ABH blood group-degrading enzymes by enteric bacteria

Human feces contain enzymes produced by enteric bacteria that degrade the A, B, and H blood group antigens of gut mucin glycoproteins. We have studied their production in fecal cultures to determine if such cultures can be a source for enzyme purification and to explore how blood group antigen-degrading enzymes are adapted in individual human colon ecosystems. They were present in fecal cultures from each of 27 healthy subjects, including ABH nonsecretors. Heat-sensitive obligate anaerobes are their major source. From 39 to 85% of the total enzyme activity produced by growing cultures was extracellular. Commercial hog gastric mucin and salivary glycoproteins, including Lea saliva which lacks A, B, and H antigens, enhance production of A-, B-, and H-degrading activity in anaerobic fecal cultures irrespective of the glycoprotein's blood group specificity. There is evidence that the host's ABO blood type and secretor status affects the specificity of blood group-degrading enzymes produced by his fecal bacteria in vitro. Thus, fecal inocula from B secretors incubated with hog gastric mucin (A and H specificity) or with Lea saliva produced greater levels of B-degrading than A- or H-degrading activity, and inocula from A secretors in similar media produced greater levels of A-degrading than B- or H-degrading activity. Blood group-degrading enzymes produced in fecal cultures are glycosidases and not proteases. The B-degrading enzyme cleaves the B antigenic determinant alpha-D-galactose from the oligosaccharide side chains of mucin glycoproteins with B specificity. Anaerobic fecal cultures containing blood group substances are a feasible source for purifying blood group antigen-degrading enzymes. Prior adaptation to blood group antigens in the gut mucins of type A and type B secretors affects the specificity of the enzymes produced in vitro.

Catabolite repression in Escherichia coli K12 mutants defective in glucose transport

The phenomenon of glucose catabolite repression was studied in Escherichia coli mutants unable to transport this carbohydrate. The pts I,H mutant P34 was much less sensitive to permanent and transient repressive effect of glucose on beta-galactosidase synthesis than parental type. The 1103 mutant with lack of enzyme 1 of the phosphoenolpyruvate-dependent phosphotransferase system (ptsI) behaves as well as P34 mutant after addition of glucose to casamino acids mineral medium. But in minimal medium with succinate as the sole source of carbon cells of the 1103 mutant (in accordance with the data of Perlman and Pastan, 1969) show hightened sensibility to transient glucose repression. The effect of hypersensibility disappears when the lacI mutation rendering the beta-galactosidase synthesis to costitutivity is introduced in 1103 mutant. It is shown that the hightened sensibility of beta-galactosidase synthesis to glucose transient repression in 1103 mutant is not an effect of the pts mutation and most probably is due to "inducer exclusion" of the lac operon. It is also shown that if one introduces the P34 mutation in strain devoided of one of the enzymes II for glucose (gptA) (and due to this resistant to glucose catabolite repression) then the level of resistance in double mutant does not increase in spite of considerable supression of 14C glucose accumulation. It is discussed the role of separate components of Escherichia coli K12 glucose transport system in realization of the phenomenon of catabolite repression.

Regulation of staphylococcal enterotoxin B: effect of anaerobic shock

The metabolism of glucose during enterotoxin B synthesis in Staphylococcus aureus S-6 was examined under anaerobic conditions in the presence and absence of nitrate. The repression of enterotoxin synthesis which occurs during the oxidative metabolism of glucose was relieved after a shift to anaerobic conditions; glucose was then converted primarily to lactic acid and was metabolized more rapidly, presumably to obtain the equivalent amount of energy available aerobically. A greater proportion of oxidized end products and evidently more energy per glucose molecule was produced in the presence of oxygen. Thus, available energy as judged by a change in the type and proportion of end products appears to be related to the degree of toxin repression. As expected, the addition of nitrate during anaerobic glucose metabolism prevented derepression of toxin synthesis.

Correlation of M protein production with those factors found to influence growth and substrate utilization of Streptococcus pyogenes

In the absence of proteinase formation, factors reported to influence the growth or fermentation by streptococci have been evaluated to determine their quantitative effect upon the production of M protein during the growth of Streptococcus pyogenes. Buffers, amino acids, peptides, gross organic additions, and carbohydrate substrates were tested under a variety of cultural conditions. The M protein content was remarkably constant throughout the late logarithmic period of growth, i.e., when the cell population doubled, the M protein doubled. However, several factors affected the M protein content per milligram of cells (dry weight). When types 1, 12, and 22 were grown aerobically in a semidefined medium, the M protein content of the cell population essentially doubled; in Todd-Hewitt broth, this aerobic effect on M protein synthesis was not observed. When cells grown on Todd-Hewitt broth were transferred to medium containing 0.1% starch and no added glucose, the M protein content per milligram of cells (dry weight) increased as much as fourfold. When growth was initiated in glucose, the rate of M protein formation was at a maximum in the early logarithmic phase of growth and was comparatively greater than the rate of cellular multiplication. When the amount of substrate fermented was greater than 0.2%, increased M protein was not observed. An evaluation of the effects of medium or conditions of growth showed the units of M per milligram of cells (dry weight) were not influenced by a shift in the stoichiometry of either the anaerobic or aerobic fermentation, substrate used, or adenosine triphosphate utilized for growth. These results show that M protein synthesis is subject to limited glucose repression or substrate catabolite repression.

Cyclic adenosine monophosphate in bacteria

Both cyclic AMP and a specific inducer acting in concert are required for the synthesis of many inducible enzymes in E. coli. Little enzyme is made in the absence of either. In contrast to the specific inducers which stimulate the synthesis only of the proteins required for their metabolism, cyclic AMP controls the synthesis of many proteins. Glucose and certain other carbohydrates decrease the differential rate of synthesis of inducible enzymes by lowering cyclic AMP concentrations. In the lac operon, cyclic AMP acts at the promoter site to facilitate initiation of transcription. This action requires another protein, the cyclic AMP receptor protein. The nucleotide stimulates tryptophanase synthesis at a translational level. The action of cyclic AMP in E. coli may serve as a model to understand its action on transcriptional and translational processes in eukaryotes.

Control Mechanisms Operative in a Natural Microbial Population Selected for Its Ability to Degrade L-Lysine. II. Effects of Fructose and Ribose in Batch Systems

A natural microbial population was acclimated to L-lysine as the sole carbon source when ammonia nitrogen was provided in the medium. Fructose exerted a slight retarding effect upon the metabolic removal of lysine. The response was due to catabolite repression of the inducible enzyme system responsible for lysine degradation. Inhibition of activity of preformed enzymes played no part in the response. Ribose caused a slight increase in the rate of synthesis of lysine-degrading enzymes.