Effects of inhibition and repression on the utilization of substrates by heterogeneous bacterial communities

This investigation attempts to evaluate to what extent enzyme inhibition and repression by metabolites, indigenous to the cell, are significant phenomena in natural microbial communities. Three case histories of the kinetics of substrate utilization and growth in multisubstrate media by heterogeneous bacterial populations are presented: (i) concurrent substrate utilization and growth on both substrates simultaneously (glucose plus benzoate); (ii) sequential substrate elimination accompanied by diauxic growth as a result of inhibition of enzyme activity (glucose plus galactose); (iii) sequential substrate utilization accompanied by diauxic growth caused by repression of enzyme formation (glucose plus l-phenylalanine, benzoate plus l-phenylalanine). It is shown that enzyme inhibition was observed in two-substrate media as well as in multisubstrate media and was maintained at low substrate concentrations (few milligrams per liter). A special attempt has been made to maintain the diversity of the experimental microbial population during the adaptation and enrichment period. All substrates were determined with sensitive analytical methods specific for the individual substrates. The results obtained confirm that catabolite repression and the resulting sequential substrate utilization are observed in heterogeneous bacterial populations.     

Cell growth and extracellular enzyme synthesis in fermentations

The synthesis of extracellular enzymes by microorganisms frequently occurs under genetic control. A simple two-parameter model is developed describing the degree of repression or induction in fermentation media. The case of substrate utilization by an extracellular enzyme was analyzed for a vegetable oil-lipase-yeast system. It is shown that fatty acids released by the lipase may accumulate in the early stage of growth and exert an influence on the limiting after which relatively little repression or induction takes place. Expressions are also derived for growth and extracellular enzyme synthesis in single-and multistage continuous cultures. When the cells grow on a directly available soluble substrate, the specific enzyme synthesis is maximal at low dilution rates in the case of repression and at high dilution rates in the case of induction. If the substrate is not directly available, a single continuous stirred tank reactor stage may not be sufficient for efficient substrate utilization; for fermentation processes where an insoluble has to be broken down before the cells can assimilate it, a plug flow type fermentor rather than a mixed chemostat may prove more satisfactory.     

Mathematical modeling for mixed culture growth of two bacterial populations with opposite substrate preferences

An unstructured mathematical model is proposed for mixed culture growth of two different bacterial species that exhibit "opposite" substrate preferences in response to the "same" environmental conditions. The model incorporates enzymatic control mechanisms such as induction, repression, and inhibition in the microorganisms as manifested in their preferential utilization of substrates and microbial interactions such as amensalism and competition. The model predicts cell mass, substrate concentrations, dissolved oxygen tension, as well as key enzyme levels. The predictions of the model are compared with experimental data for pure culture growth and for mixed culture growth on two substrates, glucose and citrate, in a batch reactor.     

Enhanced cellulase production using Solka Floc in a fed-batch fermentation

Summary Use of a fed-batch mode of cultivation of T. reesei has permitted high concentrations of substrate to be consumed. This has resulted in the production of high titre cellulase preparations around 30 FPU/ml at high volumetric productivities (177 IU/L.hr).Perhaps the most obvious area for major improvement in the process of cellulose utilization is the production of cellulase enzyme for hydrolysis of wood and agricultural residues. It has been estimated that some 50% of the cost of producing glucose from cellulosic material is attributable to enzyme production alone (Perez, et al., 1980). Improvements in the area would therefore have a dramatic impact, and are of paramount importance if economical hydrolysis processes are to be realized. The first major thrust in the area has been the development of improved mutant strains of T. reesei, free from catabolite repression and capable of constitutive cellulase production (Montenecourt and Eveleigh, 1977; Gallo, 1982).While this effort continues to develop further high yielding mutants, improvement must also come from developments in fermentation techniques. A major advance is the use of fed-batch cultivation, which provides a means of avoiding the agitation and aeration difficulties, as well as repression effects encountered with high substrate concentration batch fermentation. This report briefly compares batch and fed-batch operation over a range of substrate concentrations.     

Regulation of Homocysteine Biosynthesis in Salmonella typhimurium

The regulation of the homocysteine branch of the methionine biosynthetic pathway in Salmonella typhimurium has been reexamined with the aid of a new assay for the first enzyme. The activity of this enzyme is subject to synergistic feedback inhibition by methionine plus S-adenosylmethionine. The synthesis of all three enzymes of the pathway is regulated by noncoordinate repression. The enzymes are derepressed in metJ and metK regulatory mutants, suggesting the existence of regulatory elements common to all three. Experiments with a methionine/vitamin B(12) auxotroph (metE) grown in a chemostat on methionine or vitamin B(12) suggested that the first enzyme is more sensitive to repression by methionine derived from exogenous than from endogenous sources. metB and metC mutants grown on methionine in the chemostat did not show hypersensitivity to repression by exogenous methionine. Therefore, it appears that the metE chemostat findings are peculiar to the phenotype of this mutant; such evidence suggests a possible role for a functional methyltetrahydrofolate-homocysteine transmethylase in regulating the synthesis of the first enzyme. Thus there appear to be regulatory elements which are common to the repression of all three enzymes, as well as some that are unique to the first enzyme. The nature of the corepressor is not known, but it may be a derivative of S-adenosylmethionine. metJ and metK mutants of Salmonella have a normal capacity for S-adenosylmethionine synthesis but may be blocked in synthesis or utilization of a corepressor derived from it.     

Theory of the kinetics of reactions catalyzed by enzymes attached to membranes

A theoretical treatment has been worked out for the kinetics of solid-supported enzyme systems, with diffusive and electrostatic effects taken into account. A utilization factor, defined as the ratio of the actual reaction rate to the rate of substrate consumption in the outer solution, is defined, and equations to evaluate the utilization factor are given for five kinetic conditions: (a) Michaelis-Menten behavior, (b) substrate inhibition, (c) product inhibition (competitive), (d) product inhibition (noncompetitive), and (e) product inhibition (anticompetitive). When the solid-supported enzymes obey a Michaelis-Menten relationship, an equation for the apparent Michaelis constant is given and a criterion for insignificant diffusion effects is shown. A substrate-inhibited enzyme reaction may display multiple steady-state behavior, and a criterion for uniqueness is presented. In the case of product-inhibited enzyme reactions, the utilization factor is always less than that which corresponds to a Michaelis-Menten relationship. Equations to evaluate the apparent Michaelis and inhibition constants are given.     

A model of photoinhibition related to mRNA instability in ethylene production by a recombinant cyanobacterium

Photoinhibition mechanism is studied for ethylene production by a recombinant cyanobacterium. The kinetic pattern of the production is similar to that of substrate inhibition in enzyme reactions, whereas the photoinhibition is believed not to be substrate-related, but to originate from the enzyme for ethylene formation. In a proposed model, the inhibition is attributed to the process of enzyme synthesis, where light-dependent mRNA decomposition affects enzyme concentration. A mathematical formula derived accordingly for light dependence of ethylene production rate gives the same form as a well-known equation of substrate inhibition. The model also predicts ethylene production under dark condition, which has been observed experimentally.     

alpha-D-Mannosidase of Saccharomyces cerevisiae. Characterization and modulation of activity.

A unique and interesting alpha-D-mannosidase (alpha-D-mannoside mannohydrolase EC 3.2.1.24) activity has been isolated from Saccharomyces cerevisiae. The enzyme was localized in a crude particulate fraction of the cell extract and was not solubilized by treatment with detergents or high ionic strength NaCl. The enzyme had a pH optimum of 6.3, Km 50 micron with p-nitrophenyl-alpha-D-mannopyranoside, and was competitively inhibited by D-mannose (Ki 20 mM). The enzyme is not affected by ethylenediaminetetraacetic acid, a number of different cations, or sulfhydryl reagents. It was inhibited by p-chloromercuriphenyl sulfonic acid and this inhibition is prevented by the addition of substrate. The cellular concentration of alpha-D-mannosidase is inversely proportional to growth rate, suggesting that the enzyme is under catabolite repression. The level of enzyme was found to increase approx. 8-fold during sporulation. This is apparently due to de novo synthesis, since inhibition of protein synthesis by cycloheximide prevents the increase in enzyme activity.     

Effect of ammonium and ferricyanide on nitrate utilization by Chlorella vulgaris

It has been shown previously that added ammonium salts cause a cessation of nitrate utilization in some Chlorella species. It has also been shown that Chlorella vulgaris can form an inactivated nitrate reductase which is an HCN complex. In the present study, a comparison has been made of the rate of nitrate utilization and the rate of nitrate reductase inactivation in Chlorella vulgaris in response to the addition of ammonium salts and light-dark changes. The rate of formation of HCN-inactivated enzyme is too slow to account for the prompt inhibition of nitrate utilization caused by adding ammonium. In contrast, when nitrate utilization is inhibited by addition of ferricyanide to intact cells, the HCN-inactivated enzyme is promptly formed in vivo, and might account for the inhibition of nitrate utilization, though inhibition of nitrate uptake can not be excluded.     

Production of cell wall-degrading enzymes by Aspergillus nidulans: a model system for fungal pathogenesis of plants.

The cell wall-degrading enzymes polygalacturonase and pectate lyase have been suggested to be crucial for penetration and colonization of plant tissues by some fungal pathogens. We have found that Aspergillus nidulans (= Emericella nidulans), a saprophytic Ascomycete, produces levels of these enzymes equal to those produced by soft-rotting Erwinia species. Induction of polygacturonase and pectate lyase in A. nidulans requires substrate and is completely repressed by glucose. Surprisingly, inoculation of excised plant tissues with A. nidulans conidia leads to formation of necrotic, water-soaked lesions within which the organism sporulates. Thus, A. nidulans has phytopathogenic potential. The release of glucose and other sugars from wounded tissues may repress pectolytic enzyme production and limit disease development. Therefore, we tested creA204, a mutation that relieves glucose repression of some A. nidulans carbon utilization enzymes, for its effect on production of pectolytic enzymes. creA204 failed to relieve catabolite repression of polygalacturonase or pectate lyase and had no effect on disease severity.     

Interaction Between the First Enzyme for Histidine Biosynthesis and Histidyl Transfer Ribonucleic Acid

Previous studies suggested that phosphoribosyltransferase, which catalyzes the first step of the pathway for histidine biosynthesis in Salmonella typhimurium and which is sensitive to inhibition by histidine, plays a role in repression of the histidine operon. Recently, we showed that the enzyme has a high affinity for histidyl transfer ribonucleic acid (His-tRNA), which is known to participate in the repression process. In the present study, we have investigated further the interaction between the enzyme and His-tRNA. We found that His-tRNA binds at a site on phosphoribosyltransferase distinct from the catalytic site and the histidine-sensitive site; that the substrates of the enzyme inhibit the binding of His-tRNA, whereas histidine does not do so; that, once a complex has been formed between phosphoribosyltransferase and His-tRNA, the substrates of the enzyme decrease the stability of the complex, whereas histidine is without effect; and that purified phosphoribosyltransferase which has a defect in its inhibition by histidine (produced by mutation) displays an altered ability to bind His-tRNA, a finding which may be a reflection of the fact that mutants producing such a defective enzyme display an alteration of the repression process.     

Cybernetic modeling of the cephalosporin C fermentation process by Cephalosporium acremonium

A cybernetic mathematical model has been developed to describe the production of cephalosporin C. In developing the model, diauxic behavior of substrate consumption, morphological differentiation of cells, and catabolite repression of cephalosporin C production by the preferred substrate, glucose, were considered. The proposed model was tested on the experimental data from the literature and could adequately describe the morphological differentiation of cells, the sequential utilization of carbon sources and the production of cephalosporin C. It could be a useful tool to optimize the production of cephalosporin C by Cephalosporium acremonium in batch, fed-batch or continuous operations.     

Substrate inhibition mode of omega-transaminase from Vibrio fluvialis JS17 is dependent on the chirality of substrate

Substrate inhibition is a common phenomenon in enzyme chemistry, which is observed only with a fast-reacting substrate enantiomer. We report here for the first time substrate inhibition of an enantioselective enzyme by both substrate enantiomers. The enantioselective substrate inhibition, i.e., different mode of inhibition by each substrate enantiomer, of (S)-specific omega-transaminase was found with various chiral amines. A kinetic model based on ping-pong bi-bi mechanism has been developed and kinetic parameters were measured. The kinetic model reveals that the inhibition by (R)-amine results from formation of Michaelis complex with enzyme-pyridoxal 5'-phosphate, whereas the inhibition by (S)-amine results from the formation of the complex with enzyme-pyridoxamine 5'-phosphate. Substrate inhibition constants (K(SI)) of each (S)-enantiomer of four chiral amines showed a linear correlation with those of cognate (R)-amines. Such a correlation was also found between the K(SI) values and Michaelis constants of (S)-amines. These correlations indicate that recognition mechanisms and active site structures of both enzyme-pyridoxal 5'-phosphate, enzyme-pyridoxamine 5'-phosphate are similar. Taken together with the results, high propensity for non-productive substrate binding strongly suggests that binding pockets of the omega-transaminase is loosely defined, which accounts for the enantioselective substrate inhibition.     

Reaction path of phosphofructo-1-kinase is altered by mutagenesis and alternative substrates

Escherichia coli phosphofructokinase (PFK) has been proposed to have a random, nonrapid equilibrium mechanism that produces nonallosteric ATP inhibition as a result of substrate antagonism. The consequences of such a mechanism have been investigated by employing alternative substrates and mutants of the enzyme that produce a variety of nonallosteric kinetic patterns demonstrating substrate inhibition and sigmoid velocity curves. Mutations of a methionine residue in the sugar phosphate binding site produced apparent cooperativity in the interaction of fructose 6-phosphate. Cooperativity could also be seen with native enzyme using a poorly binding substrate, fructose 1-phosphate. With an alternative nucleotide, 1-carboxymethyl-ATP, coupled with a mutation that introduced a negative charge in the nucleotide binding site, one could observe substrate inhibition by fructose 6-phosphate and apparent cooperativity in the interaction with nucleotide. Furthermore, the use of a phosphoryl donor, gamma-thiol-ATP, which greatly reduced the catalytic rate, apparently facilitated the equilibration of all binding reactions and eliminated ATP inhibition. These unusual kinetic patterns could be interpreted within the random, steady-state model as reflecting changes in the rates of particular binding and catalytic events.     

Characterization of cinnamyl alcohol dehydrogenase of Helicobacter pylori. An aldehyde dismutating enzyme

Cinnamyl alcohol dehydrogenases (CAD; 1.1.1.195) catalyse the reversible conversion of p-hydroxycinnamaldehydes to their corresponding alcohols, leading to the biosynthesis of lignin in plants. Outside of plants their role is less defined. The gene for cinnamyl alcohol dehydrogenase from Helicobacter pylori (HpCAD) was cloned in Escherichia coli and the recombinant enzyme characterized for substrate specificity. The enzyme is a monomer of 42.5 kDa found predominantly in the cytosol of the bacterium. It is specific for NADP(H) as cofactor and has a broad substrate specificity for alcohol and aldehyde substrates. Its substrate specificity is similar to the well-characterized plant enzymes. High substrate inhibition was observed and a mechanism of competitive inhibition proposed. The enzyme was found to be capable of catalysing the dismutation of benzaldehyde to benzyl alcohol and benzoic acid. This dismutation reaction has not been shown previously for this class of alcohol dehydrogenase and provides the bacterium with a means of reducing aldehyde concentration within the cell.     

Inhibition of co-operative enzymes by substrate-analogues: Possible implications for the physiological significance of negative co-operativity illustrated by phenylalanine metabolism in higher plants

The “Hill” equation for co-operative binding-systems has been extended to describe the effect of substrate-analogue on the binding of substrate to an oligomeric protein. It is demonstrated that the more negatively co-operative the binding-system, the more sensitive is the binding of substrate to inhibition by increases in the relative concentration of substrate-analogue. It is proposed that the physiological significance of negative co-operativity for enzymes may be complementary to the physiological significance of positive co-operativity. The effect of negative co-operativity is to make substrate binding more sensitive to inhibition by relative increases in the concentration of substrate-analogue (e.g. for many enzymes product of the reaction) at the expense of decreased sensitivity of substrate binding to relative changes in substrate concentration compared to a system with equivalent, independent substrate binding sites. In contrast, the effect of positive co-operativity is to make the enzyme more sensitive to relative changes in substrate concentration at the expense of decreased sensitivity to inhibition by relative increases in product concentration, compared to an enzyme without co-operative binding.     

Extensive studies of the heme coordination structure of indoleamine 2,3-dioxygenase and of tryptophan binding with magnetic and natural circular dichroism and electron paramagnetic resonance spectroscopy

In order to probe the active site of the heme protein indoleamine 2,3-dioxygenase, magnetic and natural circular dichroism (MCD and CD) and electron paramagnetic resonance (EPR) studies of the substrate (L-tryptophan)-free and substrate-bound enzyme with and without various exogenous ligands have been carried out. The MCD spectra of the ferric and ferrous derivatives are similar to those of the analogous myoglobin and horseradish peroxidase species. This provides strong support for histidine imidazole as the fifth ligand to the heme iron of indoleamine 2,3-dioxygenase. The substrate-free native ferric enzyme exhibits predominantly high-spin EPR signals (g perpendicular = 6, g parallel = 2) along with weak low-spin signals (g perpendicular = 2.86, 2.28, 1.60); similar EPR, spin-state and MCD features are found for the benzimidazole adduct of ferric myoglobin. This suggests that the substrate-free ferric enzyme has a sterically hindered histidine imidazole nitrogen donor sixth ligand. Upon substrate binding, noticeable MCD and EPR spectral changes are detected that are indicative of an increased low spin content (from 30 to over 70% at ambient temperature). Concomitantly, new low spin EPR signals (g = 2.53, 2.18, 1.86) and MCD features characteristic of hydroxide complexes of histidine-ligated heme proteins appear. For almost all of the other ferric and ferrous derivatives, only small substrate effects are observed with MCD spectroscopy, while substantial substrate effects are seen with CD spectroscopy. Thus, changes in the heme coordination structure of the ferric enzyme and in the protein conformation at the active site of the ferric and ferrous enzyme are induced by substrate binding. The observed substrate effects on the ferric enzyme may correlate with the previously observed kinetic substrate inhibition of indoleamine 2,3-dioxygenase activity, while such effects on the ferrous enzyme suggest the possibility that the substrate is activated during turnover.     

Studies on Induction and Repression in Activated Sludge Systems

Both repression and induction of substrate utilization have been the subject of many basic research investigations employing pure cultures. In this investigation these effects were studied using heterogeneous microbial populations prevalent in such biological treatment processes as activated sludge systems.Diauxic substrate removal by activated sludge was observed in a multicomponent medium consisting of glucose and sorbitol. The sludge was acclimated solely to sorbitol; however, the presence of glucose blocked sorbitol removal until glucose was completely utilized. Both diphasic and triphasic oxygen utilization was shown for activated sludges metabolizing multicomponent synthetic wastes consisting of glucose, melibiose, and lactose. It appears from these studies that melibiose utilization was suppressed by the presence of glucose and, although melibiose induced acclimation to lactose, the presence of melibose suppressed lactose utilization. Studies were also conducted using glycogen and starch systems in which it was found that acclimation to either compound conferred immediate acclimation to the other. It was also found that loss of acclimation to lactose was a passive phenomenon and its kinetics could be predicted on the basis of simple diluting out of the enzyme(s) responsible for such acclimation.     

Nitrate regulation of alpha-aminoadipate reductase formation and lysine inhibition of its activity in Penicillium chrysogenum and Acremonium chrysogenum

alpha-Aminoadipate reductase (alpha-AAR) is a key enzyme in the branched pathway for lysine and beta-lactam biosynthesis of filamentous fungi since it competes with alpha-aminoadipyl-cysteinyl-valine synthetase for their common substrate L-alpha-aminoadipic acid. The alpha-AAR activity in two penicillin-producing Penicillium chrysogenum strains and two cephalosporin-producing Acremonium chrysogenum strains has been studied. The alpha-AAR activity peaked during the growth-phase preceding the onset of antibiotic production, which coincides with a decrease in alpha-AAR activity, and was lower in high penicillin- or cephalosporin-producing strains. The alpha-AAR required NADPH for enzyme activity and could not use NADH as electron donor for reduction of the alpha-aminoadipate substrate. The alpha-AAR protein of P. chrysogenum was detected by Western blotting using anti-alpha-AAR antibodies. The mechanism of lysine feedback regulation in these two filamentous fungi involves inhibition of the alpha-AAR activity but not repression of its synthesis by lysine. This is different from the situation in yeasts where lysine feedback inhibits and represses alpha-AAR. Nitrate has a strong negative effect on alpha-AAR formation as shown by immunoblotting studies of alpha-AAR. The nitrate effect was reversed by lysine.     

Kinetics of the enzymatic hydrolysis of cellulose: 2. A mathematical model for the process in a plug-flow column reactor

The kinetics of enzymatic cellulose hydrolysis in a plug-flow column reactor catalysed by cellulases [see 1,4-(1,3;1,4)-β-d-glucan 4-glucanohydrolase, EC 3.2.1.4] from Trichoderma longibrachiatum adsorbed on cellulose surface have been studied. The maximum substrate conversion achieved was 90–94%. The possibility of enzyme recovery for a reactor of this type is discussed. A mathematical model for enzymatic cellulose hydrolysis in a plug-flow column reactor has been developed. The model allows for the component composition of the cellulase complex, adsorption of cellulases on the substrate surface, inhibition by reaction products, changes in cellulose reactivity and the inactivation of enzymes in the course of hydrolysis. The model affords a reliable prediction of the kinetics of d-glucose and cellobiose formation from cellulose in a column reactor as well as the degree of substrate conversion and reactor productivity with various amounts of adsorbed enzymes and at various flow rates.