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.     

GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7

The packaging of eukaryotic genomic DNA into chromatin is modulated through a range of posttranslational histone modifications. Among these, the role of histone ubiquitylation remains poorly understood. Here, we show that the essential Drosophila ubiquitin-specific protease 7 (USP7) contributes to epigenetic silencing of homeotic genes by Polycomb (Pc). We purified USP7 from embryo nuclear extracts as a stable heteromeric complex with guanosine 5'-monophosphate synthetase (GMPS). The USP7-GMPS complex catalyzed the selective deubiquitylation of histone H2B, but not H2A. Biochemical assays confirmed the tight association between USP7 and GMPS in Drosophila embryo extracts. Similar to USP7, mutations in GMPS acted as enhancers of Pc in vivo. USP7 binding to GMPS was required for histone H2B deubiquitylation and strongly augmented deubiquitylation of the human tumor suppressor p53. Thus, GMPS can regulate the activity of a ubiquitin protease. Collectively, these results implicate a biosynthetic enzyme in chromatin control via ubiquitin regulation.     

Oligonucleotide-based assays for integrase activity

Oligonucleotide assays have been invaluable for elucidation of the molecular mechanisms of retroviral integrases. A suite of rapid and sensitive fluorescence assays to measure the DNA binding, processing, and joining activities of integrase (IN) is described here. The assays are especially useful for characterizing the major activities of the enzyme, and for handling large numbers of samples efficiently. They can greatly facilitate further biochemical and structural analyses for HIV-1 and other IN proteins. The assays can also be adapted for moderate-high throughput testing of various inhibitory compounds.     

Enzymatic assays of L-serine in biological material

Affinity chromatography of adenosine deaminase (EC 3.5.4.4.) on agarose-bound inosine with biospecific elution of the enzyme using linear gradients of adenosine or inosine leads via chromatographic parameters to a dissociation constant of the binary complex of K_diss = 3.5 × 10^?3m and to a binding enthalpy of ΔH = ?3.9 kcal mol^?1. These values can be explained by formation of two hydrogen bonds between immobilized inosine and the enzyme. The measurement of height equivalents of theoretical plates of the affinity column with dependence on the flow rate leads to the assumption that the velocity with which the equilibrium is reached is high compared with the flow rate; the high specificity of the affinity resin is not first of all due to a high number of theoretical plates but to the selectivity of the heterogenous enzymic reaction.     

Development of homogeneous luminescence assays for histone demethylase catalysis and binding

Covalent modifications to histones play important roles in chromatin dynamics and the regulation of gene expression. The JumonjiC (JmjC)-containing histone demethylases (HDMs) catalyze the demethylation of methylated lysine residues on histone tails. Here we report the development of homogeneous luminescence-based assay methods for measuring the catalytic activity and the binding affinities of peptides to HDMs. The assays use amplified luminescent proximity homogeneous assay (ALPHA) technology, are sensitive and robust, and can be used for small molecule inhibitor screening of HDMs. We have profiled known inhibitors of JMJD2E and demonstrate a correlation between the inhibitor potencies determined by the ALPHA and other types of assays. Although this study focuses on the JMJD2E isoform, the catalytic turnover and binding assays described here can be used in studies on other HDMs. The assays should be useful for the development of small molecule inhibitors selective for HDM isoforms.     

TR-FRET cellular assays for interrogating posttranslational modifications of histone H3

Posttranslational modifications such as phosphorylation, acetylation, and methylation play important roles in regulating the structures and functions of histones, which in turn regulate gene expression and DNA repair and replication. Histone-modifying enzymes, such as deacetylases, methyltransferases and demethylases, have been pursued as therapeutic targets for various diseases. However, detection of the activities of these enzymes in high-throughput cell-based formats has remained challenging. The authors have developed high-throughput LanthaScreen cellular assays for Histone H3 site-specific modifications. These assays use cells expressing green fluorescence protein-tagged Histone H3 transiently delivered via BacMam and terbium-labeled anti-Histone H3 modification-specific antibodies. Robust time-resolved F?rster resonance energy transfer signals were detected for H3 lysine-9 acetylation and dimethylation (H3K9me2), serine-10 phosphorylation, K4 di- and trimethylation, and K27 trimethylation. Consistent with previous reports, hypoxic stress increased K4 methylation levels, and methyltransferase G9a inhibitor UNC-0638 decreased K9me2 levels significantly, with little effects on other modifications. To demonstrate the utility of this assay platform in screening, the K9 acetylation assay was used to profile the Enzo Epigenetics Library. Twelve known HDAC inhibitors were identified as hits and followed up in a dose-response format. In conclusion, this assay platform enables high-throughput cell-based analysis of diverse types of posttranslational modifications of Histone H3.     

Cell-free assays for gamma-secretase activity.

The amyloid b-protein (Ab) deposited in Alzheimer's disease (AD) is a normally secreted proteolytic product of the amyloid b-protein precursor (APP). Generation of Ab from the APP requires two sequential proteolytic events: an initial b-secretase cleavage at the amino terminus of the Ab sequence followed by g-secretase cleavage at the carboxyl terminus of Ab. We describe the development of a robust in vitro assay for g-secretase cleavage by showing de novo Ab production in vitro and establish that this assay monitors authentic gamma-secretase activity by documenting the production of a cognate g-CTF, confirming the size of the Ab produced by mass spectrometry, and inhibiting cleavage in this system with multiple inhibitors that alter g-secretase activity in living cells. Using this assay, we demonstrate that the g-secretase activity 1) is tightly associated with the membrane, 2) can be solubilized, 3) has a pH optimum of 6.8 but is active from pH 6.0 to pH >8.4, and 4) ascertain that activities of the g-40 and g-42 are indeed pharmacologically distinct. These studies should facilitate the purification of the protease or proteases that are responsible for this unusual activity, which is a major therapeutic target for the treatment of AD.     

Enzymatic amplification for spectrophotometric and electrochemical assays of NAD+ and NADH

Five different procedures are presented for the enzymatic assay of the sum of NAD+ and NADH concentrations. They are based on the principle of amplification by cycling. The reactions involve oxidation of the formate ion, ethanol, glucose, or carnitine catalyzed by the corresponding dehydrogenases. The detection reactions are based on the 2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyltetrazolium chloride (INT)/INT-formazan and ferricyanide/ferrocyanide couples and use a diaphorase. Two of the systems presented--with formate ion and ethanol--were coupled with spectrophotometric detection. The absorbance measurement values were multiplied by 3 in the first case and by 20 in the second, with respect to the values that would have been obtained in the same conditions without the amplification system. The accessible concentration ranges were between 0.05 and 100 microM approximately. Three systems--with formate ion, carnitine, and glucose--used an electrochemical detection based on oxidation of the ferrocyanide ion. The response times were of the order of 10 min and the precision of about 5%. The first brought to light some difficulties concerning the design of such devices. For the second, the proportionality constant had a value of the order of 0.25 microA.microM-1 and an accessible concentration range between 0.2 and 40 microM. The third allowed more precise assays for lower concentration values: between 0.02 and 1.5 microM, with a proportionality constant of 0.49 microA.microM-1. Emphasis was placed on the adaptation possibilities of these systems as a function of the assay requirements.     

Continuous spectrometric assays for glutaminyl cyclase activity

A high-throughput mass spectrometric immunoassay system for the analysis of proteins directly from plasma is reported. A 96-well format robotic workstation was used to prepare antibody-derivatized affinity pipette tips for subsequent use in the extraction of specific proteins from plasma and deposition onto 96-well format matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) targets. Samples from multiple individuals were screened with regard to the plasma protein transthyretin (TTR), followed by analysis of the same plasma samples for the transthyretin-associated transport protein, retinol-binding protein (RBP). Analyses were able to detect the presence of posttranslationally modified TTR and RBP, as well as a mutation present in the TTR of one individual. Subsequent analyses of wild-type and mutated TTR using enzymatically active MALDI-TOF MS targets were able to identify the site and nature of the point mutation. The approach represents a rapid (approximately 100 samples/2 h, reagent preparation-to-data) and accurate means of characterizing specific proteins present in large numbers of individuals for proteomic and clinical/diagnostic purposes.     

Enzymatic activity in basidiomycetes

The oxidation-reduction activity of the basidiomyceteOudemansiella mucida was studied in relation to its growth in a laboratory fermentor. Cytochromes were detected in the mycelium destroyed by sonication, flavin diaphorase, polyphenoloxidase, peroxidase and catalase were found to be present in the mycelial homogenate from Waring-blendor. The obtained values of the enzymatic activity were dependent on the method of preparation of the mycelium. Homogenization in a Waring-blendor was the most appropriate. Certain interrelationships between the appearance and activity of the enzymes followed and the phase of submerged growth of the fungus were shown. The results document the succession of cytochromes, flavins and polyphenoloxidase and the specific time differences of the activity of catalase and that of peroxidase.     

New generation QuIC assays for prion seeding activity

The ability of abnormal TSE-associated forms of PrP to seed the formation of amyloid fibrils from recombinant PrP^Sen has served as the basis for several relatively rapid and highly sensitive tests for prion diseases. These tests include rPrP-PMCA (rPMCA), standard quaking-induced conversion (S-QuIC), amyloid seeding assay (ASA), real-time QuIC (RT-QuIC) and enhanced QuIC (eQuIC). Here, we summarize recent improvements in the RT-QuIC-based assays that enhance the practicality, sensitivity and quantitative attributes of assays QuIC and promote the detection of prion seeding activity in dilute, inhibitor-laden fluids such as blood plasma.     

Enzymatic activity of aphroproteins.

Chitinase and proteinase activities were found in aphroproteins excreted by larvae of the cicada Aphrophora costalis Mats; this accounts for their fungicidal effect. Aphroproteins did not show DNase or RNase activities and did not exhibit properties of proteinase inhibitors. The data suggest that larval foam protects the larva and host plant from entomogenous and phytopathogenic fungi.