Regulation of pyruvate metabolism in Lactococcus lactis depends on the imbalance between catabolism and anabolism

Two strains of Lactococcus lactis ssp. cremoris, MG 1820 and MG 1363, which differed by the presence or absence of the lactose plasmid, respectively, were cultivated in batch-mode fermentation on lactose as carbon substrate. A correlation between the rate of sugar consumption, the growth rate, and the type of metabolism was observed. The MG 1820 strain grew rapidly on lactose and homolactic fermentation occurred. The major regulating factor was the NADH/NAD(+) ratio proportional to the catabolic flux, which inhibited glyceraldehyde-3-phosphate dehydrogenase activity. This control led to an increase in metabolite concentration upstream of this enzyme, glyceraldehyde-3-phosphate and dihydroxyacetone-phosphate, and inhibition of pyruvate formate lyase activity, while lactate dehydrogenase was strongly activated by the high coenzyme ratio. The contrary was observed during growth of the MG 1363 strain. Further investigation during growth of L. lactis ssp. lactis NCDO 2118 on galactose as carbon substrate and on various culture media enabling the growth rate to proceed at various rates demonstrated that the relative flux between catabolism and anabolism was the critical regulating parameter rather than the rate of glycolysis itself. In a minimal medium, where anabolism was strongly limited, the rate of sugar consumption was reduced to a low value to avoid carbon and energy waste. Despite this low sugar consumption rate, the catabolic flux was in excess relative to the anabolic capability and the NADH/NAD+ ratio was high, typical of a situation of nonlimiting catabolism leading to a homolactic metabolism.     

Anabolism versus catabolism of [5-3H]uridine and its relationship to ribonucleic acid labelling in mouse liver after partial hepatectomy

The balance between anabolism and catabolism of [5-(3)H]uridine was studied in the mouse after partial hepatectomy. Labelling of RNA and UDP-glucose was determined and evaluated in relation to changes in the specific radioactivity of UTP. The amounts of labelled catabolic products of uridine were increased several-fold in liver and blood after partial hepatectomy. The specific radioactivity of RNA decreased to about 60% of the control value at 6h and was in the same range as that of control liver at 24h after operation. Decreased labelling of RNA and UDP-glucose was attributable to decreased specific radioactivity of UTP. No changes in the size of the UTP pool or in the balance between uridine anabolism and catabolism were found that could explain the decreased specific radioactivity of UTP. Rather, the alterations in the labelling of this metabolite induced by the partial hepatectomy may be related to decreased phosphorylating capacity in the liver cells and/or dilution of the labelled precursor in an expanded uridine pool. The enhanced amounts of uridine catabolic products in liver and blood were probably a consequence of accumulation and altered incorporation of the metabolites from the blood into the liver cells. Despite the increased amounts of labelled catabolic products and the decreased labelling of RNA, the results reported here actually suggest decreased uridine catabolism and slightly increased RNA synthesis in mouse liver after partial hepatectomy. The results stress the importance of proper controls in determination of nucleic acid synthesis and in metabolic studies by use of labelled precursors.     

A balanced model for biofilms developed at different growth and detachment forces

In a steady state biofilm culture, dissolved organic carbon (DOC) distribution between catabolism and anabolism can be described by a ratio of the DOC channeled into carbon dioxide (S_CO2) to the DOC converted into biomass (S_g). Based on a balanced oxidative reaction of DOC, a S_CO2/S_g-dependent observed growth yield (Y_obs) model was developed for biofilm culture and was verified with literature data. Growth and detachment forces are two decisive factors in biofilm process. The detachment force (D_f) normalized with respect to the growth force (G_f) was introduced to describe the interaction between the biofilm growth and detachment processes. Biofilm metabolism and structure were closely related to the D_f/G_f-ratio, and biofilm community could metabolically respond to changes in growth and detachment forces. A proper balance between growth and detachment forces is crucial for development of a compact and stable biofilm. The proposed D_f/G_f concept provides a theoretical basis for experimental data obtained at different growth and detachment forces to be interpreted in a unified sense. Biofilm structure may be manipulated by controlling the D_f/G_f ratio.     

Model of energy uncoupling for substrate-sufficient culture

The growth yields (Y(obs)) are greater under substrate-limited conditions than those under substrate-sufficient conditions in continuous cultures. This indicates that the excess substrate should cause uncoupling between anabolism and catabolism, which leads to energy spilling. Although the uncoupling between anabolism and catabolism has already been recognized in the microbiology literature, how to quantitatively describe such uncoupling remains unclear. Based on a balance on substrate reaction, a growth yield model was developed in relation to residual substrate concentration for substrate-sufficient continuous cultures. On the basis of that yield model, the concept of an uncoupling coefficient between anabolism and catabolism is defined in this work. A model describing the effect of the residual substrate concentration on the uncoupling coefficient of anabolism to catabolism is proposed. This model agrees very well with literature data. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 571-576, 1997.     

Simple generic model for dynamic experiments with Saccharomyces cerevisiae in continuous culture: decoupling between anabolism and catabolism

The dynamic behavior of a continuous culture of Saccharomyces cerevisiae subjected to a sudden increase in the dilution rate has been successfully modelled for anaerobic growth on glucose, and for aerobic growth on acetate, on ethanol, and on glucose. The catabolism responded by an immediate jump whereas biosynthesis did not. Thus catabolism was in excess to anabolism. The model considers the decoupling between biosynthesis and catabolism, both types of reactions being modelled by first-order kinetic expressions evolving towards maximal values. Yield parameters and maximal reaction rates were identified in steady state continuous cultures or during batch experiments. Only the time constant of biosynthesis regeneration, tauX, and the time constant of catabolic capacity regeneration, taucat, had to be identified during transient experiments. In most experiments tauX was around 3 h, and taucat varied between 2 and 2.5 h for the different metabolisms investigated.     

Metabolic aspects of the growth of a pink-pigmented facultative methylotroph in carbon-limited chemostat culture

Summary The regulation of carbon metabolism in a pink-pigmented facultative methylotroph has been studied. In methanol-limited chemostat culture a pH optimum at 7.0 with a narrow growth rate optimum with respect to growth yield and metabolic uncoupling was revealed. The average growth yield was 14±0.036 g·mol^–1 and the organism displayed a low maintenance energy and high maximum specific growth rate. When the carbon concentration in the feed remained constant and the dilution rate increased a deviation from linearity between substrate consumption and growth rate was found at higher growth rates. The addition of a pulse of methanol to a carbon-limited culture showed that anabolism could be dissociated from catabolism with the resulting accumulation of formaldehyde in concentrations which were not lethal. Offprint requests to: F. M. Girio     

Charges of nicotinamide adenine nucleotides and adenylate energy charge as regulatory parameters of the metabolism in Escherichia coli.

Methods for measurements of catabolic reduction charge (defined as NADH/(NADH+NAD+)) and anabolic reduction charge (defined as NADPH/(NADPH + NADP+)) are described using [14C]nicotinamide labeling of Escherichia coli cultures. Together with these parameters the adenylate energy charge (ATP + 1/2ADP)/(ATP + ADP + AMP) was measured using labeling with [2-3H]adenine. These three charges were found under different exponential growth conditions to have values independent of the growth conditions: catabolic reduction charge, 0.05; anabolic reduction charge, 0.45; and adenylate energy charge, 0.9. The charges were examined during interruption of growth primarily affecting catabolism, respiration, or anabolism, leading to changes of the charges. The changes of charges are evaluated as a possible regulation of the metabolic rates utilizing or producing the nucleotides by their respective charges.     

Simulation of growth and detachment in biofilm systems under defined hydrodynamic conditions

Detachment from biofilms was evaluated using a mixed culture biofilm grown on primary wastewater in a tube reactor. The growth of biofilms and the detachment of biomass from biofilms are strongly influenced by hydrodynamic conditions. In a long-term study, three biofilms were cultivated in a biofilm tube reactor. The conducted experiments of biofilm growth and detachment can be divided into three phases: 1) an exponential phase with a rapid increase of the biofilm thickness, 2) a quasi-steady-state with spontaneous fluctuation of the biofilm thickness between 500 and 1,200 microm in the investigated biofilm systems, and 3) a washout experiment with increased shear stress in three to four steps after several weeks of quasi-steady-state. Whereas the biofilm thickness during the homogeneous growth phase can be regarded constant throughout the reactor, it was found to be very heterogeneous during the quasi-steady-state and the washout experiments. Growth and detachment during all three phases was simulated with the same one-dimensional biofilm model. For each of the three phases, a different detachment rate model was used. During the homogeneous growth phase, detachment was modeled proportional to the biofilm growth rate. During the quasi-steady-state phase, detachment was described by random detachment events assuming a base biofilm thickness. Finally, the washout experiment was simulated with detachment being a function of the biofilm thickness before the increase of the shear stress.     

Metabolic behavior of immobilized aggregates of Escherichia coli under conditions of varying mechanical stress.

Experiments were conducted on immobilized aggregates of Escherichia coli cells. Mechanical stress was applied by forcing a convective stream of nutrient medium through the aggregate. It was shown to be possible to maintain uniform exponential growth with this convective supply of nutrients. Analysis of effluent from the system allowed investigation of metabolic responses unambiguously attributable to mechanical stress. A reversible increase in catabolic activity was observed after an increase in mechanical stress. Changes in the level of catabolism were accompanied by an alteration in the total acid yield on glucose and in the spectrum of organic acids produced during glucose fermentation. The behavior observed here was likely due to an osmoregulatory response induced by the mechanically stressed bacteria to counteract changes in shape.     

Metabolic behavior of immobilized aggregates of Escherichia coli under conditions of varying mechanical stress

Experiments were conducted on immobilized aggregates of Escherichia coli cells. Mechanical stress was applied by forcing a convective stream of nutrient medium through the aggregate. It was shown to be possible to maintain uniform exponential growth with this convective supply of nutrients. Analysis of effluent from the system allowed investigation of metabolic responses unambiguously attributable to mechanical stress. A reversible increase in catabolic activity was observed after an increase in mechanical stress. Changes in the level of catabolism were accompanied by an alteration in the total acid yield on glucose and in the spectrum of organic acids produced during glucose fermentation. The behavior observed here was likely due to an osmoregulatory response induced by the mechanically stressed bacteria to counteract changes in shape.     

A statistical analysis of the effect of substrate utilization and shear stress on the kinetics of biofilm detachment

One of the least understood processes affecting biofilm accumulation is detachment. Detachment is the removal of cells and cell products from an established biofilm and subsequent entrainment in the bulk liquid. The goal of this research was to determine the effects of shear stress and substrate loading rate on the rate of biofilm detachment.Monopopulation Pseudomonas aeruginosa and undefined mixed population biofilms were grown on glucose in a RotoTorque biofilm reactor. Three levels of shear stress and substrate loading rate were used to determine their effects on the rate of detachment. Suspended cell concentrations were monitored to determine detachment rates, while other variables were measured to determine their influence on the detachment rate. Results indicate that detachment rate is directly related to biofilm growth rate and that factors which limit growth rate will also limit detachment rate. No significant influence of shear on detachment rate was observed.A new kinetic expression that incorporates substrate utilization rate, yield, and biofilm thickness was compared to published detachment expressions and gives a better correlation of data obtained both in this research and from previous research projects, for both mono- and mixed-population biofilms. (c) John Wiley & Sons, Inc.     

Textural fingerprints: a comprehensive descriptor for biofilm structure development

Automated tools to determine biofilm structure are necessary to interpret large time series of biofilm images. Image analysis based on the evaluation of Spatial Gray Level Dependence Matrices (SGLDM) enabled us to monitor biofilm structure development in response to external disturbances (i.e., periodic increases of wall shear stress) at a large scale (i.e., >1 mm). We applied our method to an experiment conducted in an annular reactor over a 10-week period. Six states of biofilm development were differentiated by their unique structure. Previous exposure to rapidly increased shear influenced the resulting biofilm structure after additional shear increases. In addition, on the scale of the biofilm images, the biofilm structure after a shear increase was spatially heterogeneous and resulted in spatially differentiated regrowth after detachment at different locations in the biofilm. SGLDM was developed further as an alternative to approaches based on image binarization as binarization leads to information loss for low-magnification and low-resolution images. During post-processing of image data, structural states of biofilm development were identified by K-means clustering and data display in Principal Component plots. Quantitatively selected representative images were used to illustrate the meaning of the clusters. Post-treatment of image data was essential for managing several thousands of raw biofilm images and therefore improved the usefulness of the image analysis.     

Microbiology and performance of a methanogenic biofilm reactor during the start-up period

Aims:  To understand the interactions between anaerobic biofilm development and process performances during the start-up period of methanogenic biofilm reactor.
Methods and Results:  Two methanogenic inverse turbulent bed reactors have been started and monitored for 81 days. Biofilm development (adhesion, growth, population dynamic) and characteristics (biodiversity, structure) were investigated using molecular tools (PCR–SSCP, FISH-CSLM). Identification of the dominant populations, in relation to process performances and to the present knowledge of their metabolic activities, was used to propose a global scheme of the degradation routes involved. The inoculum, which determines the microbial species present in the biofilm influences bioreactor performances during the start-up period. FISH observations revealed a homogeneous distribution of the Archaea and bacterial populations inside the biofilm.
Conclusion:  This study points out the link between biodiversity, functional stability and methanogenic process performances during start-up of anaerobic biofilm reactor. It shows that inoculum and substrate composition greatly influence biodiversity, physiology and structure of the biofilm.
Significance and Impact of the Study:  The combination of molecular techniques associated to a biochemical engineering approach is useful to get relevant information on the microbiology of a methanogenic growing biofilm, in relation with the start-up of the process.     

Evolution of amino acid metabolism inferred through cladistic analysis

Because free amino acids were most probably available in primitive abiotic environments, their metabolism is likely to have provided some of the very first metabolic pathways of life. What were the first enzymatic reactions to emerge? A cladistic analysis of metabolic pathways of the 16 aliphatic amino acids and 2 portions of the Krebs cycle was performed using four criteria of homology. The analysis is not based on sequence comparisons but, rather, on coding similarities in enzyme properties. The properties used are shared specific enzymatic activity, shared enzymatic function without substrate specificity, shared coenzymes, and shared functional family. The tree shows that the earliest pathways to emerge are not portions of the Krebs cycle but metabolisms of aspartate, asparagine, glutamate, and glutamine. The views of Horowitz (Horowitz, N. H. (1945) Proc. Natl. Acad. Sci. U. S. A. 31, 153-157) and Cordón (Cordón, F. (1990) Tratado Evolucionista de Biologia, Aguilar, Madrid, Spain), according to which the upstream reactions in the catabolic pathways and the downstream reactions in the anabolic pathways are the earliest in evolution, are globally corroborated; however, with some exceptions. These are due to later opportunistic connections of pathways (actually already suggested by these authors). Earliest enzymatic functions are mostly catabolic; they were deaminations, transaminations, and decarboxylations. From the consensus tree we extracted four time spans for amino acid metabolism development. For some amino acids catabolism and biosynthesis occurred at the same time (Asp, Glu, Lys, Leu, Ala, Val, Ile, Pro, Arg). For others ultimate reactions that use amino acids as a substrate or as a product are distinct in time, with catabolism preceding anabolism for Asn, Gln, and Cys and anabolism preceding catabolism for Ser, Met, and Thr. Cladistic analysis of the structure of biochemical pathways makes hypotheses in biochemical evolution explicit and parsimonious.     

Prostaglandin biosynthesis and catabolism in the developing fetal sheep lung.

The prostaglandin biosynthetic and catabolic capacity of homogenates of lungs from fetal sheep of various gestational ages was measured. Prostaglandin biosynthesis was assayed by the deuterium-isotope dilution technique making use of mass fragmentography whereas prostaglandin catabolism was measured by the radioisotope-dilution method described previous (Pace-Asciak, C.R. and Rangaraj, G. (1976) J. Biol. Chem. 251, 3381-3385). Homogenates of lungs from fetuses of all ages tested (40 days to term) formed both prostaglandins E2 and F2alpha; although prostaglandin F2alpha was formed to a greater extent than prostaglandin E2 by the 40 days lung, prostaglandin E2 increased with increasing age until at term the ratio of both prostaglandins approached unity. Total prostaglandin biosynthesis (E2 + F2alpha) rose gradually with age (approx. 3 fold increase between 40 days and term). Prostaglandin F2alpha catabolism occurred mainly by the prostaglandin 15-hydroxy dehydrogenase pathway; this activity was detectable even at 40 days and remained unchanged up to 80 days. Prostaglandin catabolic activity rose sharply at 90 days (approx. 3 fold) with a maximum around 110 days (approx. 4 fold) decreasing back to 40 day levels by term (143 days). The increasing prostaglandin catabolic activity around 90-100 days in this species is discussed in relation to the hemodynamic changes in the lungs starting around this age and the appearance of surfactant. Prostaglandin catabolism might play an important role in the developing organ controlling steady state concentrations of prostaglandins during certain periods of organogenesis.     

Shear stress effects on production of exopolymeric substances and biofilm characteristics during phenol biodegradation by immobilized Pseudomonas desmolyticum (NCIM2112) cells in a pulsed plate bioreactor

This article reports studies on a continuous pulsed plate bioreactor (PPBR) with the cells of Pseudomonas desmolyticum (NCIM2112) immobilized on granular activated carbon (GAC) used as a biofilm reactor for biodegradation of phenol. Almost complete removal of 200 ppm phenol could be achieved in this bioreactor. Biofilm structure and characteristics are influenced by hydrodynamic and shear conditions in bioreactors. In this article, the effect of shear stress induced by frequency of pulsation on biofilm characteristics during the startup period in the PPBR is reported. The startup time decreased with the increase in frequency of pulsation. The formation of biofilm in PPBR was found to have three phases: accumulation, compaction, and plateau. The effect of frequency on production of exoploymeric substances (EPS) such as, protein, carbohydrate, and humic substance is reported. An increase in shear stress induced by the frequency of pulsation increased the production of exopolymeric substances in the biofilm during startup of the bioreactor. Increase in shear stress caused a decrease in biofilm thickness and an increase in dry density of the biofilm. Increase in shear stress resulted in a smoother and thinner biofilm surface with more compact and dense structure.