Crystallization of ADP-ribosyl cyclase from Aplysia californica

ADP-ribosyl cyclase synthesizes the secondary messenger cyclic ADP-ribose from NAD⁺. Diffraction quality crystals of the enzyme from ovotestes of Aplysia californica have been obtained. Crystallographic analysis of this enzyme will yield insight into the mode of binding of the novel cyclic nucleotide and the mechanism by which NAD⁺ is cyclized.     

Inhibitors and activators of ADP-ribosylation reactions

ADP-ribosylation reaction, that is the transfer of the ADP-ribose moiety of NAD⁺ to acceptor protein, is catalyzed by two classes of ADP-ribosyltransferases,i.e., poly(ADP-ribose) synthetase and mono (ADP-ribosyl)transferases. These two types differ not only in the number of transferring ADP-ribose units but also in the acceptor amino acid(s) and protein. Their in hibitors, particularly those of poly(ADP-ribose) synthetase, have been successfully employed in studies on biological functions of the enzymes and other related fields of research. Recently, we found many potent and specific inhibitors of poly-(ADP-ribose) synthetase, and broadened their chemical as well as biochemical variety. More recently, we found several potent inhibitors of arginine-specific mono(ADP-ribosyl)transferases and activators of poly(ADP-ribose) synthetase.     

Mapping the enzymatic active site of Pseudomonas aeruginosa exotoxin A

Pseudomonas aeruginosa exotoxin A is representative of a class of enzymes, the monoADP-ribosyl, which catalyze the covalent transfer of an ADP-ribose moiety of NAD⁺ to a target substrate. Availability of the three-dimensional structure of exotoxin A provides the opportunity for mapping substrate binding sites and suggesting which amino acid residues may be involved in catalysis. Data from several sources have been combined to develop a proposal for the NAD⁺ binding site of exotoxin A: the binding of NAD⁺ fragments adenosine, AMP, and ADP have been delineated crystallographically to 6.0, 6.0, and 2.7 Å, respectively; significant sequence homology spanning 60 residues has been found between exotoxin A and diphtheria toxin, which has the identical enzymatic activity; iodination of exotoxin A, under conditions in which only tyrosine 481 is iodinated in the enzymatic domain, abolishes ADP-ribosyl transferase activity.     

Discovery of novel poly(ADP-ribose) glycohydrolase inhibitors by a quantitative assay system using dot-blot with anti-poly(ADP-ribose)

Poly(ADP-ribosyl)ation, which is mainly regulated by poly(ADP-ribose) polymerase (PARP) and poly(ADP-ribose) glycohydrolase (PARG), is a unique protein modification involved in cellular responses such as DNA repair and replication. PARG hydrolyzes glycosidic linkages of poly(ADP-ribose) synthesized by PARP and liberates ADP-ribose residues. Recent studies have suggested that inhibitors of PARG are able to be potent anti-cancer drug. In order to discover the potent and specific Inhibitors of PARG, a quantitative and high-throughput screening assay system is required. However, previous PARG assay systems are not appropriate for high-throughput screening because PARG activity is measured by radioactivities of ADP-ribose residues released from radioisotope (RI)-labeled poly(ADP-ribose). In this study, we developed a non-RI and quantitative assay system for PARG activity based on dot-blot assay using anti-poly(ADP-ribose) and nitrocellulose membrane. By our method, the maximum velocity (V_max) and the michaelis constant (k_m) of PARG reaction were 4.46 μM and 128.33 μmol/min/mg, respectively. Furthermore, the IC50 of adenosine diphosphate (hydroxymethyl) pyrrolidinediol (ADP-HPD), known as a non-competitive PARG inhibitor, was 0.66 μM. These kinetics values were similar to those obtained by traditional PARG assays. By using our assay system, we discovered two novel PARG inhibitors that have xanthene scaffold. Thus, our quantitative and convenient method is useful for a high-throughput screening of PARG specific inhibitors.     

Membrane-bound form of ADP-ribosyl cyclase in rat cortical astrocytes in culture

ADP-ribosyl cyclase activities in cultured rat astrocytes were examined by using TLC for separation of enzymatic products. A relatively high rate of [3H]cyclic ADP-ribose production converted from [3H]NAD+ by ADP-ribosyl cyclase (2.015+/-0.554 nmol/min/mg of protein) was detected in the crude membrane fraction of astrocytes, which contained approximately 50% of the total cyclase activity in astrocytes. The formation rate of [3H]ADP-ribose from cyclic ADP-ribose by cyclic ADP-ribose hydrolase and/or from NAD+ by NAD glycohydrolase was low and enriched in the cytosolic fraction. Although NAD+ in the extracellular medium was metabolized to cyclic ADP-ribose by incubating cultures of intact astrocytes, the presence of Triton X-100 in the medium for permeabilizing cells increased cyclic ADP-ribose production three times as much. Isoproterenol and GTP increased [3H]cyclic ADP-ribose formation in crude membrane-associated cyclase activity. This isoproterenol-induced stimulation of membrane-associated ADP-ribosyl cyclase activity was confirmed by cyclic GDP-ribose formation fluorometrically. This stimulatory action was blocked by prior treatment of cells with cholera toxin but not with pertussis toxin. These results suggest that ADP-ribosyl cyclase in astrocytes has both extracellular and intracellular actions and that signals of beta-adrenergic stimulation are transduced to membrane-bound ADP-ribosyl cyclase via G proteins within cell surface membranes of astrocytes.     

ADP-ribosyl cyclase and abscisic acid are involved in the seasonal growth and in post-traumatic tissue regeneration of Mediterranean sponges

In previous papers it has been demonstrated that the plant hormone abscisic acid (ABA) is responsible for the stimulation of water filtration and oxygen consumption elicited by a temperature increase in the Mediterranean demosponge Axinella polypoides. The signal transduction pathway triggered by ABA involves activation of ADP-ribosyl cyclase (ADPRC), leading to an increase of the intracellular concentration of cyclic ADP-ribose (cADPR), a universal and potent intracellular calcium mobilizer. These data prompted us to investigate the possible involvement of the ABA/ADPRC/cADPR system in the sponge life cycle and in post-traumatic tissue regeneration of Mediterranean sponges. ADPRC activity was detected in the cell lysate from several common Mediterranean sponge species, including Calcarea and Demospongiae. Specimens were collected monthly over a 2-year period, from January 2002 to April 2004. All species studied showed a peak of ADPRC activity during July and August 2003, concomitant with an anomalous heat wave that struck the whole Mediterranean basin during these months. In the aquarium, during spontaneous tissue regeneration, an increase of the [ABA]_i and of the ADPRC activity over time zero values was consistently observed. In conclusion, these results indicate that an increase of ABA content and of ADPRC activity correlates with the growth and with post-traumatic tissue regeneration in several Mediterranean sponge species, indicating that the ABA/ADPRC/cADPR system is involved in the response to environmental stress in sponges. Determination of ADPRC activity/ABA content may provide a means to assess metabolic activation of sponge populations under conditions of environmental stress.     

ADP-Ribosylation of Highly Purified Rat Brain Mitochondria

Highly purified synaptic and nonsynaptic mitochondria were prepared from rat brain, and their ADP-ribosyl transferase and NAD glycohydrolase activities were investigated. Data show that there is no significant difference in ADP-ribosyl transferase activity between these two types of subcellular preparations. However, NAD glycohydrolase activity appeared to be much higher in nonsynaptic mitochondria. The specific activity of both enzymes was investigated in the presence of the inhibitor nicotinamide or its analogue 3-aminobenzamide or other adenine nucleotides, such as ATP or ADP-ribose. The inhibitory effect of nicotinamide or 3-aminobenzamide on ADP-ribosyl transferase appears rather weak compared with their effect on NAD glycohydrolase activity. However, ADP-ribose and ATP appeared more effective in inhibiting ADP-ribosyl transferase. Our results provide evidence for the existence of ADP-ribosyl transferase activity in rat brain mitochondria. When NAD glycohydrolase was inhibited totally by nicotinamide, the transfer of ADP-ribose from NAD to mitochondrial proteins still occurred. The chain length determinations show that the linkage of ADP-ribose to mitochondrial proteins is oligomeric.     

Ultraviolet radiation and Vitamin D3 in amphibian health, behaviour, diet and conservation

Amphibians are currently suffering a period of mass extinction with approximately 20% of species under severe threat and more than 120 species already extinct. In light of this crisis there is an urgency to establish viable ex situ populations and also find the causes of in situ declines. The role of ultraviolet radiation and Vitamin D₃ in amphibian health directly influences both ex situ and in situ populations. Vitamin D₃ can be photosynthesised endogenously via UV-B radiation (UV-B), or acquired through the diet, and then metabolised to calcitriol the biologically active hormonal form. Although, there is a lack of literature concerning Vitamin D₃ requirements and calcitriol synthesis in amphibians, amphibians are likely to have similar Vitamin D₃ requirements and metabolic processes as other vertebrates due to the phylogenetically conservative nature of calcitriol biosynthesis. Deficiencies in calcitriol in amphibians result in nutritional metabolic bone disease (NMBD) and could compromise reproduction and immunity. However, excess biologically active UV radiation has also proven detrimental across all three amphibian life stages and therefore could impact both in situ and ex situ populations. Here we review the role and necessity of UV-B and calcitriol in amphibians and the potential for negative impacts due to excessive exposure to UV radiation. We also identify priorities for research that could provide critical information for maintaining healthy in ex situ and in situ populations of amphibians.     

Genetic diversity and similarity revealed via molecular analysis among and within an in situ population and ex situ accessions of chiltepín (Capsicum annuum var. glabriusculum)

Molecular analysis of genetic diversity amongand within phenotypically similar wild Capsicum annuum var. glabriusculum(chile) populations revealed geneticdifferences among accessions spread over abroad geographic range. These chiles areregionally known as chiltepíns and are a 50metric ton per year wild harvest for the spiceindustry, as well as a genetic resource forcrop improvement. Understanding geneticvariability in this species providesinformation related to conservation efforts. The objective of this research was to surveygenetic diversity among and within an insitu population and ex situ accessionsof chiltepíns. Random AmplifiedPolymorphic DNA (RAPD) molecular markers wereused to study the genetic structure of an in situ population found at the nothernmostrange of this species and ex situaccessions collected from Mexico and Guatemala. Novel genetic variation was found in both thein situ northern disjunct population, aswell as some ex situ accessions, thussupporting conservation of this species viaboth in situ and ex situ strategies The evidence presented here supports effortsto conserve outlier populations via insitu management practices.     

Activation of Cysteine Proteases in Cowpea Plants during the Hypersensitive Response-A Form of Programmed Cell Death

There is increasing evidence that the hypersensitive response during plant–pathogen interactions is a form of programmed cell death. In an attempt to understand the biochemical nature of this form of programmed cell death in the cowpea–cowpea rust fungus system, proteolytic activity in extracts of fungus-infected and uninfected cowpea plants was investigated, using exogenously added poly(ADP-ribose) polymerase as a marker. Unlike the proteolytic cleavage pattern of endogenous poly(ADP-ribose) polymerase in apoptotic animal cells, exogenously added poly(ADP-ribose) polymerase in extracts of fungus-infected plants was proteolytically cleaved into fragments of molecular masses 77, 52, 47, and 45 kDa.In vitroandin vivoprotease inhibitor experiments revealed the activation of cysteine proteases, and possibly a regulatory role, during the hypersensitive response.     

Raman–deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota

Human intestinal microbiota is important to host health and is associated with various diseases. It is a challenge to identify the functions and metabolic activity of microorganisms at the single-cell level in gut microbial community. In this study, we applied Raman microspectroscopy and deuterium isotope probing (Raman–DIP) to quantitatively measure the metabolic activities of intestinal bacteria from two individuals and analysed lipids and phenylalanine metabolic pathways of functional microorganisms in situ. After anaerobically incubating the human faeces with heavy water (D₂O), D₂O with specific substrates (glucose, tyrosine, tryptophan and oleic acid) and deuterated glucose, the C–D band in single-cell Raman spectra appeared in some bacteria in faeces, due to the Raman shift from the C–H band. Such Raman shift was used to indicate the general metabolic activity and the activities in response to the specific substrates. In the two individuals' intestinal microbiota, the structures of the microbial communities were different and the general metabolic activities were 76 ± 1.0% and 30 ± 2.0%. We found that glucose, but not tyrosine, tryptophan and oleic acid, significantly stimulated metabolic activity of the intestinal bacteria. We also demonstrated that the bacteria within microbiota preferably used glucose to synthesize fatty acids in faeces environment, whilst they used glucose to synthesize phenylalanine in laboratory growth environment (e.g. LB medium). Our work provides a useful approach for investigating the metabolic activity in situ and revealing different pathways of human intestinal microbiota at the single-cell level.     

Rapamycin inhibits poly(ADP-ribosyl)ation in intact cells

Rapamycin is an immunosuppressive drug, which inhibits the mammalian target of rapamycin (mTOR) kinase activity inducing changes in cell proliferation. Synthesis of poly(ADP-ribose) (PAR) is an immediate cellular response to genotoxic stress catalyzed mostly by poly(ADP-ribose) polymerase 1 (PARP-1), which is also controlled by signaling pathways. Therefore, we investigated whether rapamycin affects PAR production. Strikingly, rapamycin inhibited PAR synthesis in living fibroblasts in a dose-dependent manner as monitored by immunofluorescence. PARP-1 activity was then assayed in vitro, revealing that down-regulation of cellular PAR production by rapamycin was apparently not due to competitive PARP-1 inhibition. Further studies showed that rapamycin did not influence the cellular NAD pool and the activation of PARP-1 in extracts of pretreated fibroblasts. Collectively, our data suggest that inhibition of cellular PAR synthesis by rapamycin is mediated by formation of a detergent-sensitive complex in living cells, and that rapamycin may have a potential as therapeutic PARP inhibitor.     

Can allelopathically active submerged macrophytes stabilise clear-water states in shallow lakes?

Inhibition of phytoplankton by allelochemicals released by submerged macrophytes is supposed to be one of the mechanisms that contribute to the stabilisation of clear-water states in shallow lakes. The relevance of this process at ecosystem level, however, is debated because in situ evidence is difficult to achieve. Our literature review indicates that allelopathically active species such as Myriophyllum, Ceratophyllum, Elodea and Najas or certain charophytes are among the most frequent submerged macrophytes in temperate shallow lakes. The most common experimental approach for allelopathic interference between macrophytes and phytoplankton has been the use of plant extracts or purified plant compounds. Final evidence, however, requires combination with more realistic in situ experiments. Such investigations have successfully been performed with selected species. In situ allelopathic activity is also influenced by the fact that phytoplankton species exhibit differential sensitivity against allelochemicals both between and within major taxonomic groups such as diatoms, cyanobacteria and chlorophytes. In general, epiphytic species apparently are less sensitive towards allelochemicals than phytoplankton despite living closely attached to the plants and being of key importance for macrophyte growth due to their shading. Light and nutrient availability potentially influence the sensitivity of target algae and cyanobacteria. Whether or not additional stressors such as nutrient limitation enhance or dampen allelopathic interactions still has to be clarified. We strongly propose allelopathy as an important mechanism in the interaction between submerged macrophytes and phytoplankton in shallow lakes based on the frequent occurrence of active species and the knowledge of potential target species. The role of allelopathy interfering with epiphyton development is less well understood. Including further levels of complexity, such as nutrient interference, grazing and climate, will extend this ecosystem-based view of in situ allelopathy.     

Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential

Viral macrodomains possess the ability to counteract host ADP-ribosylation, a post-translational modification implicated in the creation of an antiviral environment via immune response regulation. This brought them into focus as promising therapeutic targets, albeit the close homology to some of the human macrodomains raised concerns regarding potential cross-reactivity and adverse effects for the host. Here, we evaluate the structure and function of the macrodomain of SARS-CoV-2, the causative agent of COVID-19. We show that it can antagonize ADP-ribosylation by PARP14, a cellular (ADP-ribosyl)transferase necessary for the restriction of coronaviral infections. Furthermore, our structural studies together with ligand modelling revealed the structural basis for poly(ADP-ribose) binding and hydrolysis, an emerging new aspect of viral macrodomain biology. These new insights were used in an extensive evolutionary analysis aimed at evaluating the druggability of viral macrodomains not only from the Coronaviridae but also Togaviridae and Iridoviridae genera (causing diseases such as Chikungunya and infectious spleen and kidney necrosis virus disease, respectively). We found that they contain conserved features, distinct from their human counterparts, which may be exploited during drug design.     

Poly(ADP-ribose)-binding promotes Exo1 damage recruitment and suppresses its nuclease activities

Exonuclease 1 (Exo1) has important roles in DNA metabolic transactions that are essential for genome maintenance, telomere regulation and cancer suppression. However, the mechanisms for regulating Exo1 activity in these processes remain incompletely understood. Here, we report that Exo1 activity is regulated by a direct interaction with poly(ADP-ribose) (PAR), a prominent posttranslational modification at the sites of DNA damage. This PAR-binding activity promotes the early recruitment of Exo1 to sites of DNA damage, where it is retained through an interaction with PCNA, which interacts with the C-terminus of Exo1. The effects of both PAR and PCNA on Exo1 damage association are antagonized by the 14-3-3 adaptor proteins, which interact with the central domain of Exo1. Although PAR binding inhibits both the exonuclease activity and the 5′ flap endonuclease activity of purified Exo1, the pharmacological blockade of PAR synthesis does not overtly affect DNA double-strand break end resection in a cell free Xenopus egg extract. Thus, the counteracting effects of PAR on Exo1 recruitment and enzymatic activity may enable appropriate resection of DNA ends while preventing unscheduled or improper processing of DNA breaks in cells.     

Pyridine Nucleotide Changes In Hepatocytes Exposed To Quinones

Quinones may be toxic by a number of mechanisms. including arylation and oxidative stress caused by redox cycling. Using isolated hepatocytes, we have studied the cytotoxicity of four quinones. with differing abilities to arylate cellular nucleophiles and redox cycle. in relation to their effects on cellular pyridine nucleotides. High concentrations of menadione (redox cycles and arylates). 2-hydroxy-1,4-naphthoquinone (neither arylates nor redox cycles via a one electron reduction) 2.3-dimethoxy-1.4-naphthoquinone (a pure redox cycler) and p-benzoquinone (a pure arylator) caused an initial decrease in NAD⁺ and loss of viability, which was not prevented by 3-aminobenzamide. an inhibitor of poly(ADP-ribose)polymerase. In contrast. 3-aminobenzamide inhibited the loss of NAD' and viability caused by dimethyl sulphate so implicating poly(ADP-ribose)polymerase in its toxicity but not that of the quinones. Non-toxic concentrations of menadione. 2.3-dimethoxy-1.4-naphthoquinone and 2-hydroxy-1.4-naphthoquinone all caused markedly similar changes in cellular pyridine nucleotides. An initial decrease in NAD⁺ was accompanied by a small. transient increase in NADP⁺ and followed by a larger. prolonged increase in NADPH and total NADP⁺ + NADPH. Nucleotide changes were not observed with non-toxic concentrations of p-benzoquinone. Our findings suggest that a primary event in the response of the cell to redox cycling quinones is to bring about an interconversion of pyridine nucleotides. in an attempt to combat the effects of oxidative stress     

A new glycation product ‘norpronyl-lysine,’ and direct characterization of cross linking and other glycation adducts: NMR of model compounds and collagen

NMR is ideal for characterizing non-enzymatic protein glycation, including AGEs (advanced glycation endproducts) underlying tissue pathologies in diabetes and ageing. Ribose, R5P (ribose-5-phosphate) and ADPR (ADP-ribose), could be significant and underinvestigated biological glycating agents especially in chronic inflammation. Using [U-¹³C]ribose we have identified a novel glycoxidation adduct, 5-deoxy-5-desmethylpronyl-lysine, ‘norpronyl-lysine’, as well as numerous free ketones, acids and amino group reaction products. Glycation by R5P and ADPR proceeds rapidly with R5P generating a brown precipitate with PLL (poly-L-lysine) within hours. ssNMR (solid-state NMR) ¹³C–¹³C COSY identifies several crosslinking adducts such as the newly identified norpronyl-lysine, in situ, from the glycating reaction of ¹³C₅-ribose with collagen. The same adducts are also identifiable after reaction of collagen with R5P. We also demonstrate for the first time bio-amine (spermidine, N-acetyl lysine, PLL) catalysed ribose 2-epimerization to arabinose at physiological pH. This work raises the prospect of advancing understanding of the mechanisms and consequences of glycation in actual tissues, in vitro or even ex vivo, using NMR isotope-labelled glycating agents, without analyses requiring chemical or enzymatic degradations, or prior assumptions about glycation products.     

LACK OF DEFENSE OR PHLOROTANNIN INDUCTION BY UV RADIATION OR MESOGRAZERS IN DESMARESTIA ANCEPS AND D. MENZIESII (PHAEOPHYCEAE)1

Phlorotannins are polyphenoloic metabolites occurring only in the Phaeophyceae that have numerous putative primary roles (e.g. cell‐wall construction and storage) as well as secondary metabolic roles, which include herbivore feeding deterrence and protection from UV radiation. The proposed role of phlorotannins in the defense against UV radiation is of particular importance in the Antarctic due to depletion of the stratospheric ozone layer in that area. Several studies of brown algae have found evidence of an induction response (the production of defensive metabolites, including phlorotannins) after grazing by various mesograzers, after simulated grazing/wounding, and after exposure to increases in UV radiation. This study aimed to determine if phlorotannin production or other defenses in two dominant, endemic Antarctic species (Desmarestia menziesii Montagne and Desmarestia anceps J. Agardh) could be induced by an increase in exposure to UV radiation or by natural and artificial grazing. An in situ experiment failed to detect any effect of UV radiation on phlorotannin concentrations in either species or on subsequent palatability in feeding bioassays. A laboratory‐based experiment did not detect any effect of mesoherbivore grazing or simulated grazing (wounding) on palatability or the concentration of phlorotannins in D. menziesii. Instead, phlorotannin concentrations increased in all treatments in both experiments, consistent with an increase in overall resource availability due to an increase in available PAR compared with the in situ irradiance at the algal collection sites.