Multiple respiratory bursts as a response to veratrate stress in Rhodococcus erythropolis cells

Although Rhodococcus spp. strains are able to degrade methoxyphenols by enzymatic means, the contact with veratric acid (3, 4-dimethoxybenzoic acid, hereafter called veratrate) is very stressful for the cells of Rhodococcus erythropolis DSM 1069 (Rh). Within 5 min of contact veratrate in phosphate buffer, the emergence of many vacuoles was observed in the cell body and respiratory bursts, with violent endogenous oxygen uptake, took place several times during the 24 h incubation. During these peaks (where the cells were in their MAX states), increased activity of NADH oxidase was noted, accompanied by maximal accumulation of vanillic and isovanillic acids (3-methoxy-4-hydroxybenzoic acid and 4-hydroxy-3-methoxybenzoic acid respectively, hereafter called vanillates) in the incubation medium, which appeared to be products of veratrate demethylation. At the troughs (cell in their MIN state), the vacuoles disappeared from the cell body, oxygen uptake was normal, and the pool of vanillates decreased while the veratrate level in the medium increased. The cells from MAX and MIN states reacted in opposite ways in the presence of either formaldehyde and GSH, or paraquate and cAMP. The NADH oxidase activity, measured as oxygen uptake against NADH in the membrane pellets of MAX and MIN stage cells, differed in their response to the exogenous presence of FAD, ATP, cAMP, catalase, GSH, H(2)O(2)and methoxyphenolic substrates. The periodic character of these events is described here. Co-operation between two multiprotein membrane complexes (NAD(P)H oxidase and 3-O/4-O-demethylases) in Rhodococcus erythropolis cells and their competition for two common substrates-NAD(P)H and O(2)-is proposed as an explanation for rhythmical nature of these reactions.     

Nonlinear changes in the activity of the oxygen-dependent demethylase system in Rhodococcus erythropolis cells in the presence of low and very low doses of formaldehyde

ABSTRACT: The effect of exogenous, highly diluted formaldehyde on the rate of demethylation/re-methylation of veratric acid by the bacteria Rhodococcus erythropolis was studied using electrophoretic and microscopic techniques. The activity of 4-O-demethylase, responsible for accumulation of vanillic acid, and the levels of veratric and vanillic acids were determined using capillary electrophoresis. Formaldehyde was serially diluted at 1:100 ratios, and the total number of iterations was 20. After incubation of the successive dilutions of formaldehyde with the bacteria, demethylase activity oscillated in a sinusoidal manner. It was established using capillary electrophoresis that methylation of vanillic acid to veratric acid occurred at a double rate, as shown by the doubled fluctuation in the concentration of veratrate. There were also changes in the NADH oxidase activity, which is associated with methylation processes. Microscopic observations revealed the presence of numerous enlarged vacuoles in bacterial cells during the accumulation of large amounts of vanillic acid, and their disappearance together with a decrease in 4-O-demethylase activity. The presented results give evidence for the ability of living cells to detect the presence of submolecular concentrations of biological effectors in their environment and provide a basis for a scientific explanation of the law of hormesis and the therapeutic effect of homeopathic dilutions.     

Enzymatic demethylation of lignin for potential biobased polymer applications

Lignin is a highly methylated, recalcitrant biopolymer available aplenty in nature, and is highly heteropolymer in nature, but yet it has been an under-utilized biopolymer. Modifying it chemically, biologically or enzymatically could render it a good candidate for phenol formaldehyde resin or into fine chemicals, fuels, and plastics applications. Lignin demethylation is facilitated by the enzymes called the O-demethylases, which are able to strip-off of the –OCH₃ group in lignin, that give rise to the more widely accessible phenolic hydroxyls groups. Biological demethylation of lignins can be accomplished by means of the microorganisms, such as the white-rot, soft-rot and brown-rot fungi, besides some species of bacteria. Although the enzymes responsible for the lignin demethylation process have not been identified and purified adequately, it is perhaps possible that the O-demethylases, which have the ability to remove the O-methyl groups at the C-3 and (or) C-4 positions of the benzyl ring of low molecular weight lignin-like model compounds (LMCs) and lignin makes them the suitable candidate. These LMCs resemble the aromatic moieties inherent in the molecular structure of lignins, such as the vanillate, syringate, and veratrate. Thus, these enzymes are known as vanillate-O-demethylases, syringate O-demethylases, veratrate O-demethylases and Tetrahydrofolate (THF)-dependent O-demethylase (LigM), respectively. Whereas, some ligninolytic enzymes are known to cause damage to the structure of lignins (e.g., laccases, manganese-dependent peroxidase and lignin peroxidases). The O-demethylase enzymes are believed to be capable of removing the O-methyl groups from the lignins without affecting the complex backbone structure of the lignins. The mechanism of action of O-demethylases on lignin degradation is still largely unexplored, and their ability to remove the O-methyl groups from lignins has not been elucidated sufficiently. In this review, the recent advances made on the molecular approaches in the lignin demethylation (O-demethylases and ligninolytic enzymes), degradation and the probable strategies to tone up the lignin quality have been discussed in detail. The demethylation process of lignins by means of enzymes is envisaged to open up new vistas for its application as a biopolymer in various bioprocess and biorefinery process.     

An affinity-column procedure for the purification of veratrate O-demethylase from fungi.

An affinity column procedure is reported for purifying veratrate O-demethylase from higher fungi. The procedure is based on the affinity of the fungal demethylases for veratrate, which was coupled to AH-Sepharose 4B. An over 300-fold purification of the enzyme from an Ascomycete (Chaetomium piluliferum), and a lower degree of purification (20-fold) from a Basidiomycete (Xerocomus badius), were obtained. The O-demethylases from higher fungi require NADH and oxygen. The enzyme activity is sensitive to exposure to oxygen. The pH optima are 5 for enzyme from Chaetomium, and 7 for demethylase from Xerocomus, respectively. The enzymes are not specific for veratrate. They also demethylate p- and m-anisate and 3,4-dimethoxycinnamate, but to a lower degree.     

Microsomal electron transport reactions. II. The use of reduced triphosphopyridine nucleotide and-or reduced diphosphopyridine nucleotide for the oxidative N-demethylation of aminopyrine and other drug substrates

The ratio of formaldehyde formed to TPNH oxidized during aminopyrine oxidative demethylation as catalyzed by rabbit liver microsomes was found to be about 0.5. This is less than the expected 1:1 ratio for a mixed function oxidase reaction and may reflect the oxidation of TPNH by other reactions. Similar results were obtained when measuring the oxidative demethylation of codeine and ethylmorphine. In all cases the addition of DPNH significantly increased the yield of formaldehyde formed in the presence of TPNH. The stimulatory effect of DPNH was a linear function of the DPNH concentration added until the initial concentrations of DPNH and TPNH were equal. Increasing the DPNH concentration above a DPNH:TPNH ratio of 1:1 had no further effect upon the final concentration of formaldehyde formed. This observation, as well as the inhibition of DPNH-supported aminopyrine metabolism by TPN⁺, argue against the role of a transhydrogenase mechanism for the DPNH effect. The rate of DPNH oxidation catalyzed by liver microsome was also observed to increase markedly in the presence of TPNH.     

Aerobic and Anaerobic Catabolism of Vanillic Acid and Some Other Methoxy-Aromatic Compounds by Pseudomonas sp. Strain PN-1

Vanillic acid (4-hydroxy-3-methoxybenzoic acid) supported the anaerobic (nitrate respiration) but not the aerobic growth of Pseudomonas sp. strain PN-1. Cells grown anaerobically on vanillate oxidized vanillate, p-hydroxybenzoate, and protocatechuic acid (3,4-dihydroxybenzoic acid) with O₂ or nitrate. Veratric acid (3,4-dimethoxybenzoic acid) but not isovanillic acid (3-hydroxy-4-methoxybenzoic acid) induced cells for the oxic and anoxic utilization of vanillate, and protocatechuate was detected as an intermediate of vanillate breakdown under either condition. Aerobic catabolism of protocatechuate proceeded via 4,5-meta cleavage, whereas anaerobically it was probably dehydroxylated to benzoic acid. Formaldehyde was identified as a product of aerobic demethylation, indicating a monooxygenase mechanism, but was not detected during anaerobic demethylation. The aerobic and anaerobic systems had similar but not identical substrate specificities. Both utilized m-anisic acid (3-methoxybenzoic acid) and veratrate but not o- or p-anisate and isovanillate. Syringic acid (4-hydroxy-3,5-dimethoxybenzoic acid), 3-O-methylgallic acid (3-methoxy-4,5-dihydroxybenzoic acid), and 3,5-dimethoxybenzoic acid were attacked under either condition, and formaldehyde was liberated from these substrates in the presence of O₂. The anaerobic demethylating system but not the aerobic enzyme was also active upon guaiacol (2-methoxyphenol), ferulic acid (3-[4-hydroxy-3-methoxyphenyl]-2-propenoic acid), 3,4,5-trimethoxycinnamic acid (3-[3,4,5-trimethoxyphenyl]-2-propenoic acid), and 3,4,5-trimethoxybenzoic acid. The broad specificity of the anaerobic demethylation system suggests that it probably is significant in the degradation of lignoaromatic molecules in anaerobic environments.     

核酸(脱)甲基化与内源甲醛及认知损伤

核酸(DNA和RNA)甲基化/脱甲基是表观遗传调控的重要机制.甲醛参与DNA、RNA的甲基化/脱甲基过程,从而影响表观遗传的调节,包括学习记忆等认知功能.然而,甲醛代谢失调将影响核酸的甲基化与脱甲基,使动物的学习记忆能力下降,造成认知损伤.对北京地区604名老人(≥60岁)的调查显示,内源甲醛含量与被试受教育的年限相关,受教育程度越高,内源甲醛含量越低,反之亦然.这些结果表明,内源甲醛在人类学习记忆中扮演重要的角色,"活到老,学到老"可以延缓甲醛代谢失调引起的老年认知损伤.因此,研究内源甲醛代谢与核酸甲基化修饰之间的关系,对探索记忆储存及认知损伤等表观遗传学相关疾病的发生发展机制,具有一定的启示.     

Oxygen gradients correlate with cell density and cell viability in engineered cardiac tissue

For clinical utility, cardiac grafts should be thick and compact, and contain physiologic density of metabolically active, differentiated cells. This involves the need to control the levels of nutrients, and most critically oxygen, throughout the construct volume. Most culture systems involve diffusional transport within the constructs, a situation associated with gradients of oxygen concentration, cell density, cell viability, and function. The goal of our study was to measure diffusional gradients of oxygen in statically cultured cardiac constructs, and to correlate oxygen gradients to the spatial distributions of cell number and cell viability. Using microelectrodes, we measured oxygen distribution in a disc-shaped constructs (3.6 mm diameter, 1.8 mm thickness) based on neonatal rat cardiomyocytes cultured on collagen scaffolds for 16 days in static dishes. To rationalize experimental data, a mathematical model of oxygen distribution was derived as a function of cell density, viability, and spatial position within the construct. Oxygen concentration and cell viability decreased linearly and the live cell density decreased exponentially with the distance from the construct surface. Physiological density of live cells was present only within the first 128 microm of the construct thickness. Medium flow significantly increased oxygen concentration within the construct, correlating with the improved tissue properties observed for constructs cultured in convectively mixed bioreactors.     

Effects of cell density and glucose and glutamine levels on the respiration rates of hybridoma cells

The effects of cell density as well as the concentration levels of glucose and glutamine on the specific respiration rate of a hybridoma cell line were investigated. The experimental oxygen consumption rate was found to be constant over a wide range of dissolved oxygen levels if the suspension medium contained glutamine. In glutamine-free medium, however, the rate of oxygen consumption decreased slowly with time.In a stationary flask batch culture, the specific respiration rate decreased from about 7 to 2.9 mumol/min per 10(9) cells as the cell density increased exponentially from 1 x 10(5) to 1.2 x 10(6)/mL. To isolate the effect of cell density, cells were re suspended in fresh culture medium so that nutrient concentrations were the same for all experiments. The specific respiration rate decreased with increasing cell density in the same manner as in the stationary flask culture, falling from 8 to 4 mumol/min per 10(9) cells as the cell density increased from 10(5) to 10(6) cells/mL, then declining to 2 mumol/min per 10(9) cells when the cell density reached 10(7) cells/mL.Cells suspended in Hanks balanced sale solution (HBSS) were used to elucidate the effect of glucose and glutamine levels on respiration. The addition of glucose in concentrations of 0.25, 0.50, and 0.75 g/L had no observable effect on the specific oxygen uptake rate; however, a glucose concentration of 1 g/L reduced the uptake rate by 22%. Glutamine in a concentration of 0.30 g/L increased the specific respiration rate in HBSS containing 0 and 1 g/L glucose by approximately 13%.     

The separation of vanillate o-demethylase from protocatechuate 3,4-oxygenase by ultracentrifugation

1. Protocatechuate 3,4-oxygenase in the soluble part of a cell-free extract of Pseudomonas fluorescens (strain T) sedimented more rapidly than vanillate O-demethylase under specified conditions in a preparative ultracentrifuge. 2. The supernatant from this process contained vanillate O-demethylase and formaldehyde dehydrogenase, and when supplemented with NADH oxidized vanillate with an uptake of 1 mole of oxygen/mole of substrate and accumulation of protocatechuate. 3. This uptake was decreased to 0.5mole/mole of substrate in the presence of semicarbazide as trapping agent for formaldehyde. 4. Reasons are presented for the process of methyl group removal from vanillate being oxidative demethylation.     

Bacterial degradation of p-methoxybenzoic acid

Summary A cell-free system from a Pseudomonas sp., strain PM3, catalysed the oxidative demethylation, hydroxylation and subsequent ring cleavage of p-methoxybenzoate. Demethylation, to yield p-hydroxybenzoate, involved absorption of 1.0 mole of oxygen/mole of p-methoxybenzoate, and required reduced pyridine nucleotide (either NADH or NADPH) as cofactor. p-Hydroxybenzoate was hydroxylated to yield protocatechuate with the absorption of 1 mole of oxygen/mole of substrate, and required NADPH as cofactor. Protocatechuate was oxidized, with absorption of 1 mole of oxygen/mole of substrate, to 3-oxoadipate. The methyl group of p-methoxybenzoate was removed as formaldehyde, and oxidized to formate and carbon dioxide by formaldehyde dehydrogenase, which required GSH and NAD⁺, and formate dehydrogenase, which required NAD⁺.     

Formaldehyde,as its dimedone adduct,fromAscophyllum nodosum

Formaldehyde, as its dimedone adduct (formaldemethone), has been isolated fromAscophyllum nodosum and characterised by thin-layer and overpressured layer chromatography, and from proton nuclear magnetic resonance spectroscopic and electron impact mass spectrometric data. Formaldemethone was detected in extracts of both fresh and dry alga. It is postulated that during dynamic methylation and demethylation processes in the cells, hydroxymethyl groups may be formed, which dependent on pH, are in equilibrium with either free formaldehyde or ions such as iminium, oxonium and thionium; these species will react with dimedone to form formaldemethone. The amount of formaldehyde captured by the dimedone reagent increases as the concentration of dimedone is increased, until a maximum is reached.     

Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation

The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) α-ketoglutarate-dependent dioxygenase superfamily, which removes the alkyl group through oxidation eliminating a methyl group as formaldehyde. We have developed a fluorescence-based assay for the dealkylation activity of this family of enzymes. It uses formaldehyde dehydrogenase to convert formaldehyde to formic acid and monitors the creation of an NADH analog using fluorescence. This assay is a great improvement over the existing assays for DNA demethylation in that it is continuous, rapid and does not require radioactively labeled material. It may also be used to study other demethylation reactions including demethylation of histones. We used it to determine the kinetic constants for AlkB and found them to be somewhat different than previously reported values. The results show that AlkB demethylates 1mA and 3mC with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart.     

Bacterial attack on phenolic ethers: An enzyme system demethylating vanillic acid

1. A cell-free system from Pseudomonas fluorescens catalysed the oxidative demethylation and subsequent ring-cleavage of vanillate, with uptake of 2·5 moles of oxygen/mole of substrate. 2. Demethylation involved absorption of 0·5 mole of oxygen/mole, and required reduced glutathione (GSH) and nucleotide (probably NADPH) as cofactors, with further possible requirements, the natures of which are discussed. 3. Incomplete evidence suggested that the aromatic ring was opened via protocatechuate and the appropriate oxygenase, with absorption of 1 mole of oxygen/mole of substrate, eventually yielding β-oxoadipate. 4. The methyl group was removed sequentially as formaldehyde, formate and carbon dioxide, the steps catalysed respectively by formaldehyde dehydrogenase, which required GSH and NAD⁺, and formate dehydrogenase. Each enzyme was cytochrome-linked and accounted for absorption of 0·5mole of oxygen/mole of substrate. 5. All enzymes except formate dehydrogenase, which was a cell-wall enzyme, resided in the soluble fraction of the extract. The demethylase could not be resolved because of unknown cofactor requirements.     

Online detection of feed demand in high cell density cultures of Escherichia coli by measurement of changes in dissolved oxygen transients in complex media

A starvation-based dissolved oxygen (DO) transient controller was developed to supply growth-limiting substrate to high cell density fed-batch cultures of recombinant Escherichia coli. The algorithm adjusted a preexisting feed rate in proportion to the culture's oxygen demand, which was estimated from transients in the DO concentration after short periods of feed interruption. In this manner, the addition of glucose feed was precisely controlled at a rate that did not exceed the acetate production threshold, thus preventing acetate accumulation. In comparison to exponential feed algorithms commonly used in industry, the implementation of the new feeding strategy increased the final cell density from 32 to 44 g (dry cell weight).L(-1), with less than 16 mM acetate accumulated, producing an ideal culture for subsequent induction. Despite a constant starvation level and relatively low levels of acetate, experimental cultivations still tended to produce acetate towards the end of the process. The use of a simple Monod model provided an explanation as to why this may occur in high cell density cultivations and suggests how it may be overcome.     

Metabolic regulation adapting to high methanol environment in the methylotrophic yeast Ogataea methanolica

Since methylotrophic yeasts such as Ogataea methanolica can use methanol as a sole carbon feedstock, they could be applied to produce valuable products from methanol, a next-generation energy source synthesized from natural gases, using genetic engineering tools. In this study, metabolite profiling of O. methanolica was conducted under glucose (Glc) and low and high methanol (L- and H-MeOH) conditions to show the adaptation mechanism to a H-MeOH environment. The yeast strain responded not only to the presence of methanol but also to its concentration based on the growth condition. Under H-MeOH conditions, O. methanolica downregulated the methanol utilization, glycolytic pathway and alcohol oxidase (AOD) isozymes and dihydroxyacetone synthase (DAS) expression compared with L-MeOH-grown cells. However, levels of energy carriers, such as ATP, were maintained to support cell survival. In H-MeOH-grown cells, reactive oxygen species (ROS) levels were significantly elevated. Along with increasing ROS levels, ROS scavenging system expression was significantly increased in H-MeOH-grown cells. Thus, we concluded that formaldehyde and H₂O₂, which are products of methanol oxidation by AOD isozymes in the peroxisome, are overproduced in H-MeOH-grown cells, and excessive ROS derived from these cells is generated in the cytosol, resulting in upregulation of the antioxidant system and downregulation of the methanol-utilizing pathway to suppress overproduction of toxic intermediates.     

High cell density induces spontaneous bifurcations of dissolved oxygen controllers during CHO cell fermentations

High cell density cultures of CHO cells growing in a bioreactor under dissolved oxygen control were found to undergo spontaneous bifurcations and a subsequent loss of stability some time into the fermentation. This loss of stability was manifested by sustained and amplified oscillations in the bioreactor dissolved oxygen concentration and in the oxygen gas flow rate to the reactor. To identify potential biological and operational causes for the phenomenon, linear stability analysis was applied in a neighborhood of the experimentally observed bifurcation point. The analysis revealed that two steady state process gains, K(P1) and K(P2), regulated k(l)a and gas phase oxygen concentration inputs, respectively, and the magnitude of K(P1) was found to determine system stability about the bifurcation point. The magnitude of K(P1), and hence the corresponding open-loop steady state gain K(OL1), scaled linearly with the bioreactor cell density, increasing with increasing cell density. These results allowed the generation of a fermentation stability diagram, which partitioned K(C)-N operating space into stable and unstable regions separated by the loci of predicted critically stable controller constants, K(C,critical), as a function of bioreactor cell density. This consistency of this operating diagram with experimentally observed changes in system stability was demonstrated. We conclude that time-dependent increases in cell density are the cause of the observed instabilities and that cell density is the critical bifurcation parameter. The results of this study should be readily applicable to the design of a more robust controller.     

Effect of elevated oxygen and glutamine levels on foreign protein production at high cell densities using the insect cell-baculovirus expression system

Per cell protein expression in virally-infected insect cells declines significantly at high cell density resulting in a decrease in volumetric productivity. Specific protein expression levels in Spodoptera frugiperda (Sf-21) cells could be increased at high cell densities by increasing the oxygen supply and by supplementing the medium with glutamine post-infection. beta-Galactosidase yield was increased from 411 to 855 IU/ml by increasing the glutamine concentration in the medium by 46% and increasing the gas phase oxygen concentration from 21 to 80%. Similarly, the yield of a secreted alkaline phosphatase was increased from 14.2 to 26.2 IU/mL using the same conditions. Part of the increase in production with Sf-21 culture was due to increased release to the extra-cellular compartment at the higher oxygen concentrations. Increasing the gas phase oxygen concentration to 95% in conjunction with a 100% increase in glutamine and glucose concentrations did not improve the yield any further. Peak production under elevated oxygen and nutrient conditions occurred at 72 h about 24-48 h earlier than under normal conditions. In a Trichoplusia ni cell line (BTI-TN-5B1-4), the maximum secreted alkaline phosphatase activity was increased from 10 to 27.2 IU/mL by similarly manipulating the oxygen supply. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 142-152, 1997.     

Survival,growth and physiological responses of juvenile Japanese flounder (Paralichthys olivaceus,Temminck & Schlegel, 1846) exposed to different dissolved oxygen concentrations and stocking densities

The aim of this study was to determine to what extent juvenile Japanese flounder can adapt to different stocking densities in captivity and to examine whether growth and some physiological parameters critical for welfare might be affected by different dissolved oxygen levels. Japanese flounder (Paralichthys olivaceus) juveniles (initial weight 1.27 ± 0.04 g/fish) were reared at five stocking densities (500, 1,000, 1,500, 2,000, 2,500 ind/m³) and two levels of dissolved oxygen (DO) concentration (5.5 ± 0.5 mg/L or 14 ± 2 mg/L) with duplicate tanks for each treatment in water‐recirculating systems for 40 days. Survival and activity of superoxide dismutase (SOD) were not affected either by stocking density or dissolved oxygen, whereas final body weight, specific growth rate (SGR) and feed conversion efficiency (FCE) of fish under low DO concentration decreased significantly with increasing stocking density. In contrast, growth of fish reared in high DO levels were unaffected by the stocking density. Furthermore, fish in this group had a higher feed intake and, consequently, grew faster (SGR) and achieved a higher final weight than fish reared at the low DO level. A significant reduction in hemoglobin (Hb) concentration and red blood cell (RBC) count of fish were recorded as DO concentration increased. Furthermore, the activity of protease decreased significantly with increasing stocking density and increased significantly with increasing DO concentration. The ventilation frequency results indicate that gill ventilation decreased significantly as DO levels increased. This study demonstrates that stocking density can affect the growth performance and physiological parameters critical for welfare of juvenile Japanese flounder. Also shown is that pure oxygen supplementation is an effective way to improve the growth of juvenile Japanese flounder when reared at a high stocking density.