Enzymatic assays for NAD-dependent deacetylase activities

The NAD-dependent deacetylases are a new class of enzymes responsible for the removal of acetyl groups from lysines on proteins. Instead of water, the NAD-dependent deacetylases use a highly reactive ADP-ribose intermediate as a recipient for the acetyl group. The products of the reaction are nicotinamide, acetyl-ADP-ribose, and a deacetylated substrate. Many assays have been developed for the measurement of NAD-dependent deacetylase activity. In this review we present assays based on each of the two reactions catalyzed by these enzymes, deacetylation and NAD hydrolysis. First we describe methods for the production of acetylated protein and peptide substrates for use in deacetylation reactions. Then we describe four methods for assaying deacetylation, three of which directly measure the loss of acetyl groups from a protein or peptide substrate, and one that measures acetate production. We also describe two indirect methods for following enzyme activity, NAD hydrolysis and a novel NAD-nicotinamide exchange reaction. Finally, a quantitative method using a monoacetylated peptide as a substrate and HPLC to measure products is described.     

Kinetic and chemical mechanism of arylamine N-acetyltransferase from Mycobacterium tuberculosis

Arylamine N-acetyltransferases (NATs) are cytosolic enzymes that catalyze the transfer of the acetyl group from acetyl coenzyme A (AcCoA) to the free amino group of arylamines and hydrazines. Previous studies have reported that overexpression of NAT from Mycobacterium smegmatis and Mycobacterium tuberculosis may be responsible for increased resistance to the front-line antitubercular drug, isoniazid, by acetylating and hence inactivating the prodrug. We report the kinetic characterization of M. tuberculosis NAT which reveals that substituted anilines are excellent substrates but that isoniazid is a very poor substrate for this enzyme. We propose that the expression of NAT from M. tuberculosis (TBNAT) is unlikely to be a significant cause of isoniazid resistance. The kinetic parameters for a variety of TBNAT substrates were examined, including 3-amino-4-hydroxybenzoic acid and AcCoA, revealing K m values of 0.32 +/- 0.03 and 0.14 +/- 0.02 mM, respectively. Steady-state kinetic analysis of TBNAT reveals that the enzyme catalyzes the reaction via a bi-bi ping-pong kinetic mechanism. The pH dependence of the kinetic parameters reveals that one enzyme group must be deprotonated for optimal catalytic activity and that two amino acid residues at the active site of the free enzyme are involved in binding and/or catalysis. Solvent kinetic isotope effects suggest that proton transfer steps are not rate-limiting in the overall reaction for substituted aniline substrates but become rate-limiting when poor hydrazide substrates are used.     

Removal of H(2)S by Thiobacillus denitrificans immobilized on different matrices

Biological removal of high concentrations of H(2)S was studied using the immobilized Thiobacillus denitrificans with peat moss, wood chip, ceramic and granular activated carbon (GAC) separately. Experiments on the physical adsorption capacity of matrix, retention time and pressure drop were carried out; the ability of bioreactor to buffer shock loading and the removal efficiency with different packing materials were also investigated. Besides, the kinetics of single-stage biodesulfuration was analyzed. The results showed that GAC provided higher bacteria adsorption capacity, showed a more resistance to shock loading and allowed better operational control with respect to pressure drop than other inert carriers. When the retention time was changed from 30 to 100 s at an influent concentration of 100 mg/L of H(2)S, the removal efficiencies were above 98%; when the inlet concentration of H(2)S were changed from 110 to 120 mg/L, an average 96.8% removal efficiency was achieved during the long-term operation for GAC bioreactor. Next to GAC, wood chip was found to be a good packing material; however, peat moss and ceramic had limited effectiveness and their removal efficiencies were less of 90%. The kinetic analysis showed that the maximum removal rate and the half-saturation constant of the GAC bioreactor were 666.7 mg (H(2)S)/(L.d) and 20.8 mg/L, respectively.     

The Role of Potassium in Active Transport of Sodium by the Toad Bladder

Studies were carried out on the isolated urinary bladder of the toad, Bufo marinus, in order to explain the dependence of active sodium transport on the presence of potassium, in the serosal medium. Attempts to obtain evidence for coupled sodium-potassium transport by the serosal pump were unsuccessful; no relation between sodium transport and uptake of K⁴² from the serosal medium was demonstrable. Rather, the predominant effect of serosal potassium appeared to be operative at the mucosal permeability barrier, influencing the permeability of this surface to sodium. The mucosal effects of serosal potassium were correlated with effects on cellular cation content. When sodium Ringer's solution was used as serosal medium, removal of potassium resulted in significant decrease in tissue potassium content, commensurate increase in tissue sodium content, and marked depression of mucosal permeability and sodium transport. When choline replaced sodium in the serosal medium, removal of potassium resulted in only slight alterations of tissue electrolyte content, and effects on mucosal permeability and sodium transport were minimal.     

N-Iodoacetyl-d-glucosamine, an inhibitor of growth and glycoside uptake in Escherichia coli

1. Synthesis of N-iodoacetyl-d-glucosamine and its N-iodo[1,2-(14)C(2)]acetyl form has been achieved from the tetra-O-acetyl amino sugar and iodoacetic acid in the presence of dicyclohexylcarbodi-imide followed by catalytic deacetylation. 2. N-Iodoacetylglucosamine (up to 0.1mm) linearly inhibits uptake (up to 1min) of methyl alpha-d-glucoside by Escherichia coli ML308 and K12. Uptake of methyl beta-d-thiogalactoside and glycerol is also inhibited. 3. Growth of the organism (strain ML308) on glucose, succinate and glycerol is strongly inhibited by the iodoacetyl compound. The inhibition is relieved by N-acetylglucosamine. 4. The inhibitor has multiple effects, some of which are considered to be intracellular. 5. A separate transport pathway exists for N-acetylglucosamine by means of which the iodoacetyl analogue may enter the cell.     

Effects of bacterial treatments on wood extractives

Bacterial strains were isolated from spruce wood chips and their ability to reduce the content of wood extractives was studied. Strains were screened by cultivation on liquid media containing wood extractives as the major nutrient. Some bacterial species could decrease remarkably the amount of extractives in the liquid media and reduced the amount of triglycerides, steryl esters and total extractives by 100, 20 and 39%, respectively. Spruce wood chips were treated in controlled conditions with selected bacteria to test their effects on the chips. All the bacteria grew well on wood chips. The effect of bacterial metabolism on wood extractives was significant. Bacterial treatments reduced the amount of lipophilic extractives by 16-38% in 1 week of treatment and up to 67% in 2 weeks. The most efficient strain removed 90, 66 and 50% of triglycerides, steryl esters and resin acids, respectively, in 2 weeks. These results indicate that bacteria may be promising agents for the removal of extractives for improved pulping and papermaking processes.     

The kinetic mechanism of AAC3-IV aminoglycoside acetyltransferase from Escherichia coli

The aminoglycoside 3-N-acetyltransferase AAC(3)-IV from Escherichia coli exhibits a very broad aminoglycoside specificity, causing resistance to a large number of aminoglycosides, including the atypical veterinary antibiotic, apramycin. We report here on the characterization of the substrate specificity and kinetic mechanism of the acetyl transfer reaction catalyzed by AAC(3)-IV. The steady-state kinetic parameters revealed a narrow specificity for the acyl-donor and broad range of activity for aminoglycosides. AAC(3)-IV has the broadest substrate specificity of all AAC(3)'s studied to date. Dead-end inhibition and ITC experiments revealed that AAC(3)-IV follows a sequential, random bi-bi kinetic mechanism. The analysis of the pH dependence of the kinetic parameters revealed acid- and base-assisted catalysis and the existence of three additional ionizable groups involved in substrate binding. The magnitude of the solvent kinetic isotope effects suggests that a chemical step is at least partially rate limiting in the overall reaction.     

代谢酶乙酰化修饰对新陈代谢的调控

蛋白质的赖氨酸乙酰化修饰可以定义为在蛋白质的赖氨酸残基上添加或移除一个乙酰基团,这个过程是由乙酰化酶和脱乙酰酶调控的.真核生物细胞核内组蛋白和转录因子的可逆乙酰化修饰对基因表达调控的机制早已研究得比较清楚.1996年以来,一些独立的研究也陆续发现,参与到其他生命活动中的蛋白质存在着乙酰化修饰情况,表明乙酰化可能在生命活动中发挥着广泛的调节作用.然而直到2009年,高通量的蛋白质质谱分析技术才使得在蛋白质组水平上研究乙酰化修饰成为可能,并发现蛋白质乙酰化普遍存在.学者们发现,乙酰化修饰是一个在细胞核或细胞质的亚细胞器内广泛存在的翻译后修饰调控机制,可能参与了染色体重塑、细胞周期调控、细胞骨架的大分子运输、新陈代谢等多种生命活动.本文详细总结代谢酶的乙酰化修饰对新陈代谢调控的关键作用,并说明代谢酶的乙酰化修饰是一个从原核生物到真核生物进化上高度保守的调控机制.     

A logistic model for the prediction of the influence of water on the solid waste methanization in landfills

This article deals with the impact of water content of solid waste on biogas production kinetics in landfills. This impact has been proved in the laboratory thanks to anaerobic biodegradation experiments on paper/cardboard waste samples. A strong dependence with the moisture level was observed for both kinetic rates and maximum methane production. In this article, a logistic model is proposed to simulate the biogas production rate. It is chosen as simple as possible in order to allow for a correct identification of the model parameters given the experimental data available. The moisture dependency is introduced through a linear weighing of the biomass specific growth rate and of the amount of accessible organic substrate. It is directly linked to physical properties of the waste: the holding capacity and the minimal moisture level allowing the presence of free water.     

Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers

Nutrient depletion, which is one of the physiological triggers of autophagy, results in the depletion of intracellular acetyl coenzyme A (AcCoA) coupled to the deacetylation of cellular proteins. We surmise that there are 3 possibilities to mimic these effects, namely (i) the depletion of cytosolic AcCoA by interfering with its biosynthesis, (ii) the inhibition of acetyltransferases, which are enzymes that transfer acetyl groups from AcCoA to other molecules, mostly leucine residues in cellular proteins, or (iii) the stimulation of deacetylases, which catalyze the removal of acetyl groups from leucine residues. There are several examples of rather nontoxic natural compounds that act as AcCoA depleting agents (e.g., hydroxycitrate), acetyltransferase inhibitors (e.g., anacardic acid, curcumin, epigallocatechin-3-gallate, garcinol, spermidine) or deacetylase activators (e.g., nicotinamide, resveratrol), and that are highly efficient inducers of autophagy in vitro and in vivo, in rodents. Another common characteristic of these agents is their capacity to reduce aging-associated diseases and to confer protective responses against ischemia-induced organ damage. Hence, we classify them as “caloric restriction mimetics” (CRM). Here, we speculate that CRM may mediate their broad health-improving effects by triggering the same molecular pathways that usually are elicited by long-term caloric restriction or short-term starvation and that imply the induction of autophagy as an obligatory event conferring organismal, organ- or cytoprotection.     

Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers

Nutrient depletion, which is one of the physiological triggers of autophagy, results in the depletion of intracellular acetyl coenzyme A (AcCoA) coupled to the deacetylation of cellular proteins. We surmise that there are 3 possibilities to mimic these effects, namely (i) the depletion of cytosolic AcCoA by interfering with its biosynthesis, (ii) the inhibition of acetyltransferases, which are enzymes that transfer acetyl groups from AcCoA to other molecules, mostly leucine residues in cellular proteins, or (iii) the stimulation of deacetylases, which catalyze the removal of acetyl groups from leucine residues. There are several examples of rather nontoxic natural compounds that act as AcCoA depleting agents (e.g., hydroxycitrate), acetyltransferase inhibitors (e.g., anacardic acid, curcumin, epigallocatechin-3-gallate, garcinol, spermidine) or deacetylase activators (e.g., nicotinamide, resveratrol), and that are highly efficient inducers of autophagy in vitro and in vivo, in rodents. Another common characteristic of these agents is their capacity to reduce aging-associated diseases and to confer protective responses against ischemia-induced organ damage. Hence, we classify them as “caloric restriction mimetics” (CRM). Here, we speculate that CRM may mediate their broad health-improving effects by triggering the same molecular pathways that usually are elicited by long-term caloric restriction or short-term starvation and that imply the induction of autophagy as an obligatory event conferring organismal, organ- or cytoprotection.     

Choline Uptake in Cultured Human Y79 Retinoblastoma Cells: Effect of Polyunsaturated Fatty Acid Compositional Modifications

Abstract: Choline uptake in Y79 human retinoblastoma cells occurs through two kinetically distinguishable processes. The high-affinity system shows little sodium or energy dependence, and it does not appear to be linked to acetyl CoA: choline O -acetyltransferase. When the cells are grown in a culture medium containing 10% fetal bovine serum, the high-affinity system has a K' _m= 2.16 ± 0.13 μ m and V' _max= 27.0 ± 2.9 pmol min⁻¹ mg⁻¹, whereas the low-affinity system has K' _m= 20.4 ± 1.3 μ m and V' _max= 402 ± 49 pmol min⁻¹ mg⁻¹. Under these conditions, the polyunsaturated fatty acid content of the cell membranes is relatively low. When the polyunsaturated fatty acid content of the microsomal membrane fraction was increased by supplementing the culture medium with linolenic or docosahexaenoic acids (n-3 polyunsaturated fatty acids) or arachidonic acid (n-6 polyunsaturated fatty acid), the K' ^m of the high-affinity choline transport system was reduced by 40–60%. The V' _max also was reduced by 20–40%. Supplementation with oleic acid, the most prevalent monounsaturated fatty acid, did not affect either kinetic parameter. The results suggest that one functional effect of the high unsaturated fatty acid content of neural cell membranes is to facilitate the capacity of the high-affinity choline uptake system to transport low concentrations of choline. This effect appears to be specific for polyunsaturated fatty acids but not for a single type, for it is produced by members of both the n-3 and n-6 classes of polyunsaturated fatty acids.     

Sir2 regulation by nicotinamide results from switching between base exchange and deacetylation chemistry

Life span regulation and inhibition of gene silencing in yeast have been linked to nicotinamide effects on Sir2 enzymes. The Sir2 enzymes are NAD(+)-dependent protein deacetylases that influence gene expression by forming deacetylated proteins, nicotinamide and 2'-O-acetyl-ADPR. Nicotinamide is a base-exchange substrate as well as a biologically effective inhibitor. Characterization of the base-exchange reaction reveals that nicotinamide regulates sirtuins by switching between deacetylation and base exchange. Nicotinamide switching is quantitated for the Sir2s from Archeaglobus fulgidus (Sir2Af2), Saccharomyces cerevisiae (Sir2p), and mouse (Sir2alpha). Inhibition of deacetylation was most effective for mouse Sir2 alpha, suggesting species-dependent development of this regulatory mechanism. The Sir2s are proposed to form a relatively stable covalent intermediate between ADPR and the acetyl oxygen of the acetyllysine-protein substrate. During the lifetime of this intermediate, nicotinamide occupation of the catalytic site determines the fate of the covalent complex. Saturation of the nicotinamide site for mouse, yeast, and bacterial Sir2s causes 95, 65, and 21% of the intermediate, respectively, to return to acetylated protein. The fraction of the intermediate committed to deacetylation results from competition between the nicotinamide and the neighboring 2'-hydroxyl group at the opposite stereochemical face. Nicotinamide switching supports the previously proposed Sir2 catalytic mechanism and the existence of a 1'-O-peptidyl-ADPR.Sir2 intermediate. These findings suggest a strategy for increasing Sir2 enzyme catalytic activity in vivo by inhibition of chemical exchange but not deacetylation.     

N-lysine propionylation controls the activity of propionyl-CoA synthetase

Reversible protein acetylation is a ubiquitous means for the rapid control of diverse cellular processes. Acetyltransferase enzymes transfer the acetyl group from acetyl-CoA to lysine residues, while deacetylase enzymes catalyze removal of the acetyl group by hydrolysis or by an NAD(+)-dependent reaction. Propionyl-coenzyme A (CoA), like acetyl-CoA, is a high energy product of fatty acid metabolism and is produced through a similar chemical reaction. Because acetyl-CoA is the donor molecule for protein acetylation, we investigated whether proteins can be propionylated in vivo, using propionyl-CoA as the donor molecule. We report that the Salmonella enterica propionyl-CoA synthetase enzyme PrpE is propionylated in vivo at lysine 592; propionylation inactivates PrpE. The propionyl-lysine modification is introduced by bacterial Gcn-5-related N-acetyltransferase enzymes and can be removed by bacterial and human Sir2 enzymes (sirtuins). Like the sirtuin deacetylation reaction, sirtuin-catalyzed depropionylation is NAD(+)-dependent and produces a byproduct, O-propionyl ADP-ribose, analogous to the O-acetyl ADP-ribose sirtuin product of deacetylation. Only a subset of the human sirtuins with deacetylase activity could also depropionylate substrate. The regulation of cellular propionyl-CoA by propionylation of PrpE parallels regulation of acetyl-CoA by acetylation of acetyl-CoA synthetase and raises the possibility that propionylation may serve as a regulatory modification in higher organisms.     

木质素生物合成途径及其基因调控的研究进展

木质素是植物体内含量仅次于纤维素的一类高分子有机物质,在植物体的机械支持、水分运输及抵抗外界不良环境的侵袭方面起着重要的作用。然而,它的存在严重影响植物材料在造纸工业、纺织业、畜牧业生产中的应用。木质素代谢过程中存在多基因现象使得木质素的合成途径出现多样性,利用共抑制、反义抑制等转基因技术开发低木质素含量的优良新品种具有重要的意义。     

Control of the heparosan <Emphasis Type="Italic">N</Emphasis>-deacetylation leads to an improved bioengineered heparin

The production of the anticoagulant drug heparin from non-animal sources has a number of advantages over the current commercial production of heparin. These advantages include better source material availability, improved quality control, and reduced concerns about animal virus or prion impurities. A bioengineered heparin would have to be chemically and biologically equivalent to be substituted for animal-sourced heparin as a pharmaceutical. In an effort to produce bioengineered heparin that more closely resembles pharmaceutical heparin, we have investigated a key step in the process involving the N-deacetylation of heparosan. The extent of N-deacetylation directly affects the N-acetyl/N-sulfo ratio in bioengineered heparin and also impacts its molecular weight. Previous studies have demonstrated that the presence and quantity of N-acetylglucosamine in the nascent glycosaminoglycan chain, serving as the substrate for the subsequent enzymatic modifications (C5 epimerization and O-sulfonation), can impact the action of these enzymes and, thus, the content and distribution of iduronic acid and O-sulfo groups. In this study, we control the N-deacetylation of heparosan to produce a bioengineered heparin with an N-acetyl/N-sulfo ratio and molecular weight that is similar to animal-sourced pharmaceutical heparin. The structural composition and anticoagulant activity of the resultant bioengineered heparin was extensively characterized and compared to pharmaceutical heparin obtained from porcine intestinal mucosa.     

A new colorimetric method for dosage of lignin

Summary A quantitative colorimetric method to measure lignin content in wood has been developed. Red colored complex formed in presence of phloroglucinol-HCl was solubilised by addition of acetic acetyl bromide. Linearity was demonstrated between the absorption values at 545 nm of this complex and 0.5 to 2 mg of lignin of spruce or poplar wood, in presence or absence of ligninolytic fungi.     

Mechanism of copper transport from plasma to hepatocytes

The effects of plasma components on the kinetics of copper transport by rat hepatocytes were examined in an attempt to determine how copper is mobilized from plasma for uptake by the liver. Specific protein-facilitated transport was indicated by saturation kinetics, competition by related substrates, and similar kinetic parameters for uptake and efflux. For copper uptake, Km = 11 +/- 0.6 microM and Vmax = 2.7 +/- 0.6 nmol Cu/(min X mg protein). Zinc is a competitive inhibitor of copper uptake, and copper competes for zinc uptake. Copper efflux from preloaded cells is biphasic. The kinetic parameters for the initial rapid phase are similar to the parameters for uptake. Copper transport by hepatocytes is strictly passive. A variety of metabolic inhibitors have no effect on uptake and initial rates are solely dependent on extracellular-intracellular concentration gradients. Albumin markedly inhibits copper uptake by a substrate removal mechanism, and histidine facilitates albumin-inhibited copper uptake. The active species that delivers copper to hepatocytes under conditions of excess albumin and excess histidine is the His2Cu complex. Experiments with [3H]His2 64Cu showed that the transported species is free ionic copper. The kinetic parameters of copper transport by hepatocytes isolated from the brindled mouse model of Menkes' disease are normal. However, these cells show a decreased capacity to accumulate copper on prolonged incubation. An intracellular metabolic defect seems to be involved.