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Adenosine-to-inosine (A-to-I) editing of eukaryotic cellular RNAs is essential for protection against auto-immune disorders. Editing is carried out by ADAR1, whose innate immune response-specific cytoplasmic isoform possesses a Z-DNA binding domain (Zα) of unknown function. Zα also binds to CpG repeats in RNA, which are a hallmark of Z-RNA formation. Unexpectedly, Zα has been predicted - and in some cases even shown - to bind to specific regions within mRNA and rRNA devoid of such repeats. Here, we use NMR, circular dichroism, and other biophysical approaches to demonstrate and characterize the binding of Zα to mRNA and rRNA fragments. Our results reveal a broad range of RNA sequences that bind to Zα and adopt Z-RNA conformations. Binding is accompanied by destabilization of neighboring A-form regions which is similar in character to what has been observed for B-Z-DNA junctions. The binding of Zα to non-CpG sequences is specific, cooperative and occurs with an affinity in the low micromolar range. This work allows us to propose a model for how Zα could influence the RNA binding specificity of ADAR1.

Adenosine deaminase (ADA), which catalyzes the irreversible deamination of adenosine to inosine, is related to various human diseases such as tuberculous peritonitis and leukemia. Therefore, the method used to detect ADA activity and screen the effectiveness of various inhibitor candidates has important implications for the diagnosis treatment for various human diseases. A simple and rapid assay method for ADA, based on the enzymatic formation of a luminescent lanthanide complex, is proposed in this study. Inosine, an enzymatic product of ADA with stronger sensitization efficiency for Tb 3+ than adenosine, produced a strong luminescence by forming an inosine-Tb 3+ complex, and it enabled the direct monitoring of ADA activity in real-time. By introducing only Tb 3+ to adenosine and ADA in the buffer, the enhancement of luminescence enabled the detection of a low concentration of ADA (detection limit 1.6 U/L). Moreover, this method could accurately determine the inhibition efficiency (IC 50 ) of the known ADA inhibitor, erhythro-9-(2-hydroxy-3-nonyl)adenine (EHNA), and the inhibition of ADA could be confirmed by the naked eye. Considering its simplicity, this assay could be extended to the high-throughput screening of various ADA inhibitor candidates.

Transposable elements are viewed as 'selfish genetic elements', yet they contribute to gene regulation and genome evolution in diverse ways. More than half of the human genome consists of transposable elements. Alu elements belong to the short interspersed nuclear element (SINE) family of repetitive elements, and with over 1 million insertions they make up more than 10% of the human genome. Despite their abundance and the potential evolutionary advantages they confer, Alu elements can be mutagenic to the host as they can act as splice acceptors, inhibit translation of mRNAs and cause genomic instability. Alu elements are the main targets of the RNA-editing enzyme ADAR and the formation of Alu exons is suppressed by the nuclear ribonucleoprotein HNRNPC, but the broad effect of massive secondary structures formed by inverted-repeat Alu elements on RNA processing in the nucleus remains unknown. Here we show that DHX9, an abundant nuclear RNA helicase, binds specifically to inverted-repeat Alu elements that are transcribed as parts of genes. Loss of DHX9 leads to an increase in the number of circular-RNA-producing genes and amount of circular RNAs, translational repression of reporters containing inverted-repeat Alu elements, and transcriptional rewiring (the creation of mostly nonsensical novel connections between exons) of susceptible loci. Biochemical purifications of DHX9 identify the interferon-inducible isoform of ADAR (p150), but not the constitutively expressed ADAR isoform (p110), as an RNA-independent interaction partner. Co-depletion of ADAR and DHX9 augments the double-stranded RNA accumulation defects, leading to increased circular RNA production, revealing a functional link between these two enzymes. Our work uncovers an evolutionarily conserved function of DHX9. We propose that it acts as a nuclear RNA resolvase that neutralizes the immediate threat posed by transposon insertions and allows these elements to evolve as tools for the post-transcriptional regulation of gene expression.

Riboswitches are complex folded RNA domains that serve as receptors for specific metabolites which identified in prokaryotes. They are comprised of a biosensor that includes the binding site for a small ligand and they respond to association with this ligand by undergoing a conformational change. In the present study, we report on the integration of silver nanoclusters (AgNCs) and riboswitches for the development of a kissing complexes-induced aptasensor (KCIA). We specifically apply the tunable riboswitches properties of this strategy to demonstrate the multiplexes analysis of adenosine and adenosine deaminase (ADA). This strategy allows for simple tethering of the specific oligonucleotides stabilizing the AgNCs to the nucleic acid probes. This is a new concept for aptasensors, and opens an opportunity for design of more novel biosensors based on the kissing complexes-induced strategy., (Copyright © 2015 Elsevier B.V. All rights reserved.)

We demonstrated a sensitive and selective adenosine deaminase (ADA) detection by modulating the fluorescence resonance energy transfer (FRET) between cationic conjugated poly(9,9-bis(6'-N,N,N-trimethylammonium) hexyl)fluorine phenylene) (PFP) and the deoxyguanosine-tailored hairpin aptamer. The hairpin aptamer was labeled with a fluorophore FAM at one end and three deoxyguanosines (Gs) at the other end as a quencher. In the absence of ADA, aptamer forms hairpin-like conformation with adenosines making close affinity of Gs and FAM, which results in the weak FRET from PFP to FAM because of FAM fluorescence being quenched by Gs via photoinduced electron transfer (PET). After addition of ADA, adenosine was hydrolyzed by ADA, followed by the release of free aptamer. In this case, FAM being far away from Gs, the strong FRET thus was obtained due to the quenching process being blocked. Therefore, the new strategy based on the FRET ratio enhancement is reasonably used to detect the ADA sensitively, combining the fluorescence signal amplification of conjugated polymers with the initiative signal decreasing by Gs. The detection limit of the ADA assay is 0.3 U/L in both buffer solution and human serum, which is more sensitive than most of those previously documented methods. Importantly, the assay is rapid, homogeneous, and simple without a complicated treating process. The ADA inhibitor, erythro-9-(2-hydroxy-3-nonyl) adenine hydrochloride (EHNA), was also studied based on this assay, and the detection limit of EHNA is 10 pM. This strategy provides a new platform for the detection of other biomolecules and enzymes.

A general and reliable fluorescent molecular beacon is proposed in this work utilizing DNA-templated silver nanoclusters (AgNCs). The fluorescent molecular beacon has been employed for sensitive determination of the concentration of adenosine deaminase (ADA) and its inhibition. A well-designed oligonucleotide containing three functional regions (an aptamer region for adenosine assembly, a sequence complementary to the region of the adenosine aptamer, and an inserted six bases cytosine-loop) is adopted as the core element in the strategy. The enzymatic reaction of adenosine catalyzed by ADA plays a key role as well in the regulation of the synthesis of the DNA-templated AgNCs, i.e. the signal indicator. The intensity of the fluorescence signal may thereby determine the concentration of the enzyme and its inhibitor. The detection limit of the ADA can be lowered to 0.05 UL(-1). Also, 100 fM of a known inhibitor erythro-9-(2-hydroxy-3-nonyl) adenine hydrochloride (EHNA) is enough to present distinguishable fluorescence emission. Moreover, since the fluorescent signal indicator is not required to be bound with the oligonucleotide, this fluorescent molecular beacon may integrate the advantages of both the label-free and signal-on strategies., (© 2013 Elsevier B.V. All rights reserved.)

An inherited disorder, adenosine deaminase deficiency is a form of severe combined immunodeficiency, which is ultimately caused by an absence of adenosine deaminase (ADA), a key enzyme of the purine salvage pathway. The absence of ADA-activity in sufferers eventually results in a dysfunctional immune system due to the build-up of toxic metabolites. To date, this has been treated with mixed success, using PEG-ADA, made from purified bovine ADA coupled to polyethylene glycol. It is likely, however, that an enzyme replacement therapy protocol based on recombinant human ADA would be a more effective treatment for this disease. Therefore, as a preliminary step to produce biologically active human ADA in transgenic tobacco plants a human ADA cDNA has been inserted into a plant expression vector under the control of the CaMV 35S promoter and both human and TMV 5' UTR control regions. Plant vector expression constructs have been used to transform tobacco plants via Agrobacterium-mediated transformation. Genomic DNA, RNA and protein blot analyses have demonstrated the integration of the cDNA construct into the plant nuclear genome and the expression of recombinant ADA mRNA and protein in transgenic tobacco leaves. Western blot analysis has also revealed that human and recombinant ADA have a similar size of approximately 41 kDa. ADA-specific activities of between 0.001 and 0.003 units per mg total soluble protein were measured in crude extracts isolated from transformed tobacco plant leaves.

In this work, we report an enzyme substrate binding aptamer complex based fluorescence sensor for an enzyme activity detection of adenosine deaminase (ADA). The sensor employs a DNA probe containing an adenosine aptamer region dually labeled with biotin and digoxigenin (DIG). The probe is immobilized in a streptavidin-modified 96-well micro plate via biotin-avidin bridge, and the DIG serves as an affinity tag for an Anti-DIG antibody conjugated with horseradish peroxidase (anti-DIG-HRP). The principle of our sensor is as follows: the aptamer forms a coiled structure making the DNA in a "closed" state in the presence of adenosine, which shields the DIG tag from the bulky anti-DIG-HRP due to a proper steric effect. After adding ADA in the test solution, adenosine will be converted to inosine regardless of the aptamer binding. Then, the inosine release causes the DNA to relax and consequently, the DIG becomes accessible to the bulky anti-DIG-HRP which will further conjugate a Eu³⁺ labeled anti-horseradish peroxidase (Eu-anti-HRP). The Eu-anti-HRP can give a fluorescence signal when an enhancement solution is added. In the result of the experiment, we found the sensor signal can reflect the enzyme activity accurately and the detection limit is lowered to 0.5 U L⁻¹ of ADA not only in buffer solution, but also in serum, and an enzyme inhibitor erythro-9-(2-hydroxy-3-nonyl) adenine hydrochloride is studied. With a concentration of 0.01 nM it is enough to cause a distinct difference of the sensor response., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Plasmodium lacks the de novo pathway for purine biosynthesis and relies exclusively on the salvage pathway. Adenosine deaminase (ADA), first enzyme of the pathway, was purified and characterized from Plasmodium yoelii, a rodent malarial species, using ion exchange and gel exclusion chromatography. The purified enzyme is a 41 kDa monomer. The enzyme showed K(m) values of 41 μM and 34 μM for adenosine and 2'-deoxyadenosine, respectively. Erythro-9-(2-hydroxy-3-nonyl) adenine competitively inhibited P. yoelii ADA with K(i) value of 0.5 μM. The enzyme was inhibited by DEPC and protein denaturing agents, urea and GdmCl. Purine analogues significantly inhibited ADA activity. Inhibition by p-chloromercuribenzoate (pCMB) and N-ethylmaleimide (NEM) indicated the presence of functional -SH groups. Tryptophan fluorescence maxima of ADA shifted from 339 nm to 357 nm in presence of GdmCl. Refolding studies showed that higher GdmCl concentration irreversibly denatured the purified ADA. Fluorescence quenchers (KI and acrylamide) quenched the ADA fluorescence intensity to the varied degree. The observed differences in kinetic properties of P. yoelii ADA as compared to the erythrocyte enzyme may facilitate in designing specific inhibitors against ADA., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The sequencing of the genome of Streptomyces coelicolor A3(2) identified seven putative adenine/adenosine deaminases and adenosine deaminase-like proteins, none of which have been biochemically characterized. This report describes recombinant expression, purification and characterization of SCO4901 which had been annotated in data bases as a putative adenosine deaminase. The purified putative adenosine deaminase gives a subunit Mr=48,400 on denaturing gel electrophoresis and an oligomer molecular weight of approximately 182,000 by comparative gel filtration. These values are consistent with the active enzyme being composed of four subunits with identical molecular weights. The turnover rate of adenosine is 11.5 s⁻¹ at 30 °C. Since adenine is deaminated ∼10³ slower by the enzyme when compared to that of adenosine, these data strongly show that the purified enzyme is an adenosine deaminase (ADA) and not an adenine deaminase (ADE). Other adenine nucleosides/nucleotides, including 9-β-D-arabinofuranosyl-adenine (ara-A), 5'-AMP, 5'-ADP and 5'-ATP, are not substrates for the enzyme. Coformycin and 2'-deoxycoformycin are potent competitive inhibitors of the enzyme with inhibition constants of 0.25 and 3.4 nM, respectively. Amino acid sequence alignment of ScADA with ADAs from other organisms reveals that eight of the nine highly conserved catalytic site residues in other ADAs are also conserved in ScADA. The only non-conserved residue is Asn317, which replaces Asp296 in the murine enzyme. Based on these data, it is suggested here that ADA and ADE proteins are divergently related enzymes that have evolved from a common α/β barrel scaffold to catalyze the deamination of different substrates, using a similar catalytic mechanism., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Dipeptidyl peptidase II (DPPII) from bovine kidney cortex and lung was purified to the electrophoretically homogeneous state. The molecular and catalytic characteristics of the enzyme were determined. It was revealed that DPPII preparations possess adenosine deaminase (ADA) activity at all purification steps. For the first time, the ADA-binding ability of DPPII has been shown similar to the well-known ADA-binding enzyme, DPPIV. The dissociation constant of the DPPII-ADA complex was estimated using a resonant mirror biosensor (80 nM), fluorescence polarization (60 nM), and differential spectroscopy (36 nM) techniques. The data demonstrate that DPPII can form a complex with ADA, but with one order of magnitude higher dissociation constant than that of DPPIV (7.8 nM).

Nucleotidase cascades (apyrase, 5' nucleotidase, and adenosine deaminase (ADA) were investigated in the parasitic trematode Fasciola gigantica. ADA had the highest activity in the nucleotidase cascades. Adenosine deaminase was purified from F. gigantica through acetone precipitation and chromatography on CM-cellulose. Two forms of enzyme (ADAI, ADAII) were separated. ADAII was purified to homogeneity after chromatography on Sephacryl S-200. The molecular mass was 29 KDa for the native and denatured enzyme using gel filtration and SDS-PAGE, respectively. The enzyme (ADAII) had a pH optimum at 7.5 and a K(m) 1.0 mM adenosine, a temperature optimum at 40 degrees C and heat stability up to 40 degrees C. The order of effectiveness of metals as inhibitors was found to be Hg(2+)>Mn(2+)>Cu(2+)>Ca(2+)>Zn(2+)>Ni(2+)>Ba(2+).

Bacterial tRNA-specific adenosine deaminase (TadA) catalyzes the essential deamination of adenosine to inosine at the wobble position of tRNAs and is necessary to permit a single tRNA species to recognize multiple codons. The transition state structure of Escherichia coli TadA was characterized by kinetic isotope effects (KIEs) and quantum chemical calculations. A stem loop of E. coli tRNA(Arg2) was used as a minimized TadA substrate, and its adenylate editing site was isotopically labeled as [1'-(3)H], [5'-(3)H2], [1'-(14)C], [6-(13)C], [6-(15)N], [6-(13)C, 6-(15)N] and [1-(15)N]. The intrinsic KIEs of 1.014, 1.022, 0.994, 1.014 and 0.963 were obtained for [6-(13)C]-, [6-(15)N]-, [1-(15)N]-, [1'-(3)H]-, [5'-(3)H2]-labeled substrates, respectively. The suite of KIEs are consistent with a late SNAr transition state with a complete, pro-S-face hydroxyl attack and nearly complete N1 protonation. A significant N6-C6 dissociation at the transition state of TadA is indicated by the large [6-(15)N] KIE of 1.022 and corresponds to an N6-C6 distance of 2.0 A in the transition state structure. Another remarkable feature of the E. coli TadA transition state structure is the Glu70-mediated, partial proton transfer from the hydroxyl nucleophile to the N6 leaving group. KIEs correspond to H-O and H-N distances of 2.02 and 1.60 A, respectively. The large inverse [5'-(3)H] KIE of -3.7% and modest normal [1'-(3)H] KIE of 1.4% indicate that significant ribosyl 5'-reconfiguration and purine rotation occur on the path to the transition state. The late SNAr transition-state established here for E. coli TadA is similar to the late transition state reported for cytidine deaminase. It differs from the early SNAr transition states described recently for the adenosine deaminases from human, bovine, and Plasmodium falciparum sources. The ecTadA transition state structure reveals the detailed architecture for enzymatic catalysis. This approach should be readily transferable for transition state characterization of other RNA editing enzymes.

We have purified and investigated the role of adenosine ecto-deaminase (ecto-ADA) in porcine brain synaptic membranes and found a low activity of ecto-ADA in synaptic preparations from the cerebral cortex, hippocampus, striatum and medulla oblongata in the presence of purine transport inhibitors (NBTI, dipyridamole and papaverine). The purification procedure with affinity chromatography on epoxy-Toyopearl gel/purine riboside column as a crucial step of purification allowed a 214-fold purification of synaptic ecto-ADA with a yield of 30%. Gel filtration chromatography revealed a molecular mass estimated at 42.4+/-3.9 kDa. The enzyme had a broad optimum pH and was not affected by mono- and divalent cations. Ecto-ADA revealed a low affinity to adenosine (Ado) and 2'-deoxyadenosine (2'-dAdo) (K(M)=286.30+/-40.38 microM and 287.14+/-46.50 microM, respectively). We compared the affinity of ecto-ADA to the substrates with the physiological and pathological concentrations of the extracellular Ado in brains that do not exceed a low micromolar range even during ischemia and hypoxia, and with the affinity of adenosine receptors to Ado not exceeding a low nanomolar (A(1) and A(2A) receptors) or low micromolar (A(2B) and A(3)) range. Taken together, our data suggest that the role of synaptic ecto-ADA in the regulation of the ecto-Ado level in the brain and in the termination of adenosine receptor signaling is questionable. The porcine brain synapses must have other mechanisms for the ecto-Ado removal from the synaptic cleft and synaptic ecto-ADA may also play an extra-enzymatic role in cell adhesion and non-enzymatic regulation of adenosine receptor activity.

ADAR editing enzymes are found in all multicellular animals and are conserved in sequence and protein organization. The number of ADAR genes differs between animals, ranging from three in mammals to one in Drosophila. ADAR is also alternatively spliced to generate isoforms that can differ significantly in enzymatic activity. Therefore, to study the enzyme in vitro, it is essential to have an easy and reliable method of expressing and purifying recombinant ADAR protein. To add to the complexity of RNA editing, the number of transcripts that are edited by ADARs differs in different organisms. In humans there is extensive editing of Alu sequences, whereas in invertebrates transcripts expressed in the central nervous system are edited and this editing increases during development. It is possible to quantify site-specific RNA editing by sequencing of clones derived from RT-PCR products. However, for routine assaying of an edited position within a particular transcript, this is both expensive and time consuming. Therefore, a nonradioactive method based on poison primer extension assay is an ideal alternative.

Many biochemical and biophysical analyses of enzymes require quantities of protein that are difficult to obtain from expression in an endogenous system. To further complicate matters, native adenosine deaminases that act on RNA (ADARs) are expressed at very low levels, and overexpression of active protein has been unsuccessful in common bacterial systems. Here we describe the plasmid construction, expression, and purification procedures for ADARs overexpressed in the yeast Saccharomyces cerevisiae. ADAR expression is controlled by the Gal promoter, which allows for rapid induction of transcription when the yeast are grown in media containing galactose. The ADAR is translated with an N-terminal histidine tag that is cleaved by the tobacco etch virus protease, generating one nonnative glycine residue at the N-terminus of the ADAR protein. ADARs expressed using this system can be purified to homogeneity, are highly active in deaminating RNA, and are produced in quantities (from 3 to 10mg of pure protein per liter of yeast culture) that are sufficient for most biophysical studies.

The essential tRNA-specific adenosine deaminase catalyzes the deamination of adenosine to inosine at the wobble position of tRNAs. This modification allows for a single tRNA species to recognize multiple synonymous codons containing A, C, or U in the last (3'-most) position and ensures that all sense codons are appropriately decoded. We report the first combined structural and kinetic characterization of a wobble-specific deaminase. The structure of the Escherichia coli enzyme clearly defines the dimer interface and the coordination of the catalytically essential zinc ion. The structure also identifies the nucleophilic water and highlights residues near the catalytic zinc likely to be involved in recognition and catalysis of polymeric RNA substrates. A minimal 19 nucleotide RNA stem substrate has permitted the first steady-state kinetic characterization of this enzyme (k(cat) = 13 +/- 1 min(-)(1) and K(M) = 0.83 +/- 0.22 microM). A continuous coupled assay was developed to follow the reaction at high concentrations of polynucleotide substrates (>10 microM). This work begins to define the chemical and structural determinants responsible for catalysis and substrate recognition and lays the foundation for detailed mechanistic analysis of this essential enzyme.

Adenosine deaminase (ADA) plays an important role in the immune system, and its activity is composed of two kinetically distinct isozymes, ADA1 and ADA2. ADA2 is a major component of human plasma total ADA activity and ADA2 activity is significantly elevated in patients with various diseases such as HIV infection and chronic hepatitis. However, relatively little is known about ADA2 because of difficulties in purifying this enzyme. In this study we succeeded in purifying human plasma ADA2 and demonstrate the extracellular secretion of ADA2 from human peripheral blood monocytes stimulated with phorbol 12-myristate 13-acetate and calcium ionophore.

Adenosine deaminase is involved in purine metabolism and is a key enzyme for the control of the cellular levels of adenosine. Adenosine deaminase activity showed significant changes during embryogenesis of the camel tick Hyalomma dromedarii. From the elution profile of chromatography on DEAE-sepharose, three forms of enzyme (ADAI, ADAII and ADAIII) were separated. ADAII was purified to homogeneity after chromatography on Sephacryl S-200. The molecular mass of adenosine deaminase ADAII was 42 kDa for the native enzyme and represented a monomer of 42 kDa by SDS-PAGE. The enzyme had a pH optimum at 7.5 and temperature optimum at 40 degrees C with heat stability up to 40 degrees C. ADAII had a K (m) of 0.5 mM adenosine with higher affinity toward deoxyadenosine and adenosine than other purines. Ni(2+), Ba(2+), Zn(2+), Li(2+), Hg(2+) and Mg(2+) partially inhibited the ADAII. Mg(2+) was the strongest inhibitor by 91% of the enzyme's activity.

Site-selective adenosine (A) to inosine (I) RNA editing by the ADAR enzymes has been found in a variety of metazoan from fly to human. Here we describe a method to detect novel site-selective A to I editing that can be used on various tissues as well as species. We have shown previously that there is a preference for ADAR2-binding to selectively edited sites over non-specific interactions with random sequences of double-stranded RNA. The method utilizes immunoprecipitation (IP) of intrinsic RNA-protein complexes to extract substrates subjected to site-selective editing in vivo, in combination with microarray analyses of the captured RNAs. We show that known single sites of A to I editing can be detected after IP using an antibody against the ADAR2 protein. The RNA substrates were verified by RT-PCR, RNase protection and microarray. Using this method it is possible to uniquely identify novel single sites of selective A to I editing.

Two distinct isoenzymes of ADA (adenosine deaminase), ADA1 and ADA2, have been found in humans. Inherited mutations in ADA1 result in SCID (severe combined immunodeficiency). This observation has led to extensive studies of the structure and function of this enzyme that have revealed an important role for it in lymphocyte activation. In contrast, the physiological role of ADA2 is unknown. ADA2 is found in negligible quantities in serum and may be produced by monocytes/macrophages. ADA2 activity in the serum is increased in various diseases in which monocyte/macrophage cells are activated. In the present study, we report that ADA2 is a heparin-binding protein. This allowed us to obtain a highly purified enzyme and to study its biochemistry. ADA2 was identified as a member of a new class of ADGFs (ADA-related growth factors), which is present in almost all organisms from flies to humans. Our results suggest that ADA2 may be active in sites of inflammation during hypoxia and in areas of tumour growth where the adenosine concentration is significantly elevated and the extracellular pH is acidic. Our finding that ADA2 co-purified and concentrated together with IgG in commercially available preparations offers an intriguing explanation for the observation that treatment with such preparations leads to non-specific immune-system stimulation.

Adenosine deaminase isoenzyme 2 (ADA2) was isolated from human pleural fluid for the first time. Molecular and kinetic properties were characterized. It was shown that the inhibitors of adenosine deaminase isoenzyme 1 (ADA1), adenosine, and erithro-9-(2-hydroxy-3-nonyl)adenine (EHNA) derivatives are poor inhibitors of ADA2. Comparison of the interaction of ADA2 and ADA1 with adenosine and its derivative, 1-deazaadenosine, indicates that the isoenzymes have similar active centers. The absence of ADA2 inhibition by EHNA is evidence of a difference of these active centers in a close environment. The possible role of Zn2+ ions and the participation of acidic amino acids Glu and Asp in adenosine deamination catalyzed by ADA2 were shown.

In this review is summarized my research in the adenosine field from the beginning of my carrier to day. My research began preparing the degree thesis with Prof. Carlo Alfonso Rossi, about the purification and characterization of adenosine deaminase. My scientific interest for adenosine has spread during the years and I have been interested in the study of ARs and their related transduction and in the study of molecular mechanisms involved in homologous and heterologous AR receptor regulation.

Adenosine deaminase (ADA) is involved in purine metabolism and plays an important role in the mechanism of the immune system. ADA activity is composed of two kinetically distinct isozymes, which are referred to as ADA1 and ADA2. ADA1 is widely distributed in many animals and well characterized. On the contrary, relatively little is known about ADA2. In this study, we first purified ADA2 to homogeneity from chicken liver. The purified enzyme had a molecular mass of approximately 110 kDa on gel filtration. Also, the enzyme was shown to be a homodimer with an estimated molecular mass of 61 kDa on SDS-PAGE. Following treatment with N-glycosidase, the molecular mass of ADA2 changed to 55 kDa. Several properties of the highly purified ADA2 were also investigated in this study. Furthermore, the N-terminal amino acid sequence of ADA2 was determined.

Adenosine deaminase was purified (780-fold) from skeletal muscle of camel (Camelus Dormedarius) to homogeneity level by using DEAE Sephadex chromatography, ammonium sulfate precipitation, gel filtration and ion exchange chromatography. The enzyme appeared to be monomeric with subunit molecular weight of 43kDa and isoelectric point of 4.85. The enzyme showed specificity for adenosine and exhibited Michaelis-Menten Kinetics with kappa(cat) of 1112.41 min(-1) and K(m) of 14.7 microM at pH 7.5. The pH and temperature optima for enzyme activity were 7-7.5 and 25 degrees C, respectively. Free energy (DeltaG*), enthalpy (DeltaH*) and entropy (DeltaS*) of activation for denaturation of adenosine deaminase at 50 degrees C were 88.94, 99.65 kJmol(-1) and 33.16 Jmol(-1), respectively. The purified enzyme had half-lives of 636 and 61 min at 25 and 50 degrees C, respectively. The activation energy for catalysis of camel skeletal muscle adenosine deaminase was 9.13 kJmol(-1). Free energy (DeltaG#), enthalpy (DeltaH#) and entropy (DeltaS#) of activation for hydrolysis of adenosine deaminase at 25 degrees C were 50.35, 6.65 kJmol(-1) and -146.62 Jmol(-1), respectively. Purine riboside inhibited the enzyme competitively with K(i) of 16 microM.

Adenosine deaminase 1 (ADA1) was purified from human and chicken liver. The purified enzyme had a molecular weight of approximately 42,000 Da on SDS-PAGE. In humans, ADA1 was mainly purified concomitant with ADA-binding protein, dipeptidyl peptidase IV (DPP IV)/CD26; however, in chickens, only ADA1 without DPP IV was purified. Both human and chicken ADA1s showed similar properties on substrate specificities, sensitivities on inhibitors, and pH profile. However, they had different affinities with adenosine-Sepharose and IgG anti-ADA1-Sepharose. Human ADA1 was not adsorbed in adenosine-Sepharose column, but chicken ADA1 was adsorbed. As for IgG anti-ADA1-Sepharose column, the results were converse. Furthermore, human ADA1 could bind to DPP IV whereas chicken ADA1 could not.

The goal was to optimise a purification procedure of adenosine deaminase from human erythrocytes for the preparation of a European Reference Material. Adenosine deaminase was purified from human erythrocytes with a specific activity of 4.46 microkat/mg of protein and a catalytic concentration of 133 microkat/l. The isolation and purification procedure involved ion-exchange chromatography (STREAMLINE DEAE), and two purine riboside affinity chromatographies. The purified enzyme exhibits a single band in SDS-PAGE with a molecular weight of 41600 g/mol, and three bands in PAGE, isoelectric focusing and two-dimensional electrophoresis with pI 4.7, 4.85 and 5.0.

Adenosine deaminase (ADA) was isolated from small intestine of mice and purified to utmost homogeneity. SDS-PAGE of purified ADA gave a molecular weight of 41 kDa. Western blot analyses gave a single reactive band at 41 kDa and the other band was an associated ADA binding protein. The purified enzyme was more stable in the alkaline pH. The optimum pH and the pI values were about 7.0 and 4.96, respectively. Km values of the small intestinal ADA for adenosine and 2'-deoxyadenosine were 23 and 16 microM, respectively. Purine riboside was a competitive inhibitor with Ki of 5 microM, whereas 2'-3'-o-isopropylidene adenosine acted as an uncompetitive inhibitor (Ki 66 microM). Activity of ADA was inhibited by the presence of theophylline (-40%), caffeine (-30%), and L-cysteine (-50%). Significantly, Hg2+ (100 microM) inhibited 98% of the initial ADA activity. In addition, various purine analogs such as inosine, purine, alpha-adenosine and adenine showed variable inhibitions on the activity of ADA. Relative ADA activity towards 3'-deoxyadenosine and 6-chloropurine riboside was lower by 30% and 40%, respectively. However, the activity towards 2'-o-methyl adenosine was higher (30%) compared to the activity obtained using adenosine.

Adenosine deaminase (ADA) from bovine intestine was crystallized with purine riboside by vapour diffusion using ammonium sulfate as precipitant. The crystals are tetragonal and have unit-cell parameters a = b = 80.03, c = 141.68 A. They belong to space group P4(1)2(1)2 or P4(3)2(1)2 and diffract to at least 2.0 A resolution. The structure is being solved by molecular replacement.

The ecto form of adenosine deaminase isolated from human placental membrane was tested towards its sensitivity against adenosine deaminase inhibitors, such as aza and deaza analogues of adenosine and erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA). Ki values of the inhibitors observed were similar to these obtained for the small form of adenosine deaminase purified from human erythrocytes, indicating that the presence of the binding protein on placental adenosine deaminase does not produce alteration in the binding of these inhibitors on the enzyme active site. The inhibition rate of 2'-deoxycoformycin, one of the most potent ADA inhibitors is affected by the presence of the binding protein on human placental adenosine deaminase, that probably modulates the rearrangement of the active site produced by the binding with this tight-binding inhibitor.

ADAR1 and ADAR2 are members of a family of enzymes that catalyze the conversion of adenosine to inosine in double-stranded RNA. Unlike the other types of RNA editing that involve multiprotein editing complexes, the site-specific deamination of an adenosine to inosine is catalyzed by single enzymes. ADAR1 and ADAR2 have been purified and the genes cloned from various sources. Each gene encodes multiple splice variants. As it is crucial to have an adequate supply of pure protein to investigate this type of RNA editing, we describe in this article methods for both the purification and the overexpression of either full-length or partial ADAR1 and ADAR2 isoforms.

Grb3-3 is an isoform of Grb2, thought to arise by alternative splicing, that lacks a functional SH2 domain but retains functional SH3 domains, which allow interaction with other proteins through binding to prolinerich sequences. Several evidences suggest that besides common partners for Grb2 and Grb3-3, specific targets could exist. In order to find specific partners for Grb3-3, we have screened a human cDNA library by the yeast two-hybrid system with Grb3-3 as a bait. We have identified adenosine deaminase, an enzyme involved in purine metabolism whose deficiency is associated with severe combined immunodeficiency, as a Grb3-3 binding protein that is not able to bind to Grb2. This interaction has been confirmed in vitro with GST fusion proteins and in vivo by coimmunoprecipitation experiments in NIH3T3 cells stably transfected with Grb3-3. The functional significance of this finding is discussed.

The glutamate receptor subunit B (GluR-B) pre-mRNA is edited at two adenosine residues, resulting in amino acid changes that alter the electrophysiologic properties of the glutamate receptor. Previous studies showed that these amino acid changes are due to adenosine to inosine conversions in two codons resulting from adenosine deamination. Here, we describe the purification and characterization of an activity from human HeLa cells that efficiently and accurately edits GluR-B pre-mRNA at both of these sites. The purified activity contains a human homolog of the recently reported rat RED1 (rRED1) protein, a member of the family of double-stranded RNA-dependent deaminase proteins. Recombinant human RED1 (hRED1), but not recombinant dsRAD, another member of the family, efficiently edits both the Q/R and R/G sites of GluR-B RNA. We conclude that the GluR-B editing activity present in HeLa cell extracts and the recombinant hRED1 protein are indistinguishable.

RNAs encoding subunits of glutamate-gated ion channel receptors are posttranscriptionally modified by RNA editing and alternative splicing. The change in amino acid sequence caused by RNA editing can affect both the kinetics and the permeability of the ion channel receptors to cations. Here, we report the purification of a 90-kDa double-stranded RNA-specific adenosine deaminase from HeLa cell nuclear extract that specifically edits the glutamine codon at position 586 in the pre-mRNA of the glutamate receptor B subunit. Site-specific deamination of an adenosine to an inosine converts the glutamine codon to that of arginine. Recently, a gene encoding a double-stranded-specific editase (RED1) was cloned from a rat brain cDNA library. Antibodies generated against the deaminase domain of its human homolog specifically recognized and inhibited the activity of the 90-kDa enzyme, indicating that we have purified hRED1 the human homolog of rat RED1. This enzyme is distinct from double-stranded RNA-specific adenosine deaminase which we and others have previously purified and cloned.

His 238, a conserved amino acid located in hydrogen-bonding distance from C-6 of the substrate in the active site of murine adenosine deaminase (mADA) and postulated to play an important role in catalysis, was altered into an alanine, a glutamate, and an arginine using site-directed mutagenesis. The Ala and Glu substitutions did not result in changes of the secondary or tertiary structure, while the Arg mutation caused local perturbations in tertiary structure and quenched the emission of one or more enzyme tryptophans. Neither the Glu or Arg mutations affected substrate binding affinity. By contrast, the Ala mutation enhanced substrate and inhibitor binding by 20-fold. The most inactive of the mutants, Glu 238, had a kcat/K(m) 4 x 10(-6) lower than the wild-type value, suggesting that a positive charge on His 238 is important for proper catalytic function. The Ala 238 mutant was the most active ADA, with a kcat/K(m) 2 x 10(-3) lower than the wild-type value. NMR spectroscopy and crystallography revealed that this mutant is able to catalyze hydration of purine riboside, a ground-state analog of the reaction. These results collectively show that His 238 is not required for formation of the hydroxylate used in the deamination and may instead have an important electrostatic role.

To investigate the diagnostic utility of adenosine deaminase as a test for tuberculosis, molecular forms of the enzyme indicative of cell-mediated immunity were studied in tuberculosis pleural effusion, peritonitis and meningitis. Twenty-six pleural, 21 peritoneal, and 24 cerebrospinal tuberculous and non-tuberculous fluids were examined for adenosine deaminase and the large and small forms of the enzyme were differentiated on immunoblots. Adenosine deaminase levels ranged from zero to 81 units/L, zero to 31 units/L and zero to 31 units/L in the pleural, peritoneal and cerebrospinal fluids, respectively. The large form of adenosine deaminase (280 kDa) was detected in one of 14 proved tuberculous cases, a peritoneal fluid. The small form of the enzyme (35-39 kDa) was seen in both tuberculous and non-tuberculous conditions in 6 pleural, 7 peritoneal and 8 cerebrospinal fluids. Molecular forms of adenosine deaminase did not appear to help in the diagnosis of tuberculosis in this patient population and may not be suited for analysis in fluids with low enzyme activity.

Two adjacent aspartates, Asp 295 and Asp 296, playing major roles in the reaction catalyzed by mouse adenosine deaminase (mADA) were altered using site-directed mutagenesis. These mutants were expressed and purified from an ADA-deficient bacterial strain and characterized. Circular dichroism spectroscopy shows the mutants to have unperturbed secondary structure. Their zinc content compares well to that of wild-type enzyme. Changing Asp 295 to a glutamate decreases the kcat but does not alter the Km for adenosine, confirming the importance of this residue in the catalytic process and its minimal role in substrate binding. The crystal structure of the D295E mutant reveals a displacement of the catalytic water from the active site due to the longer glutamate side chain, resulting in the mutant's inability to turn over the substrate. In contrast, Asp 296 mutants exhibit markedly increased Km values, establishing this residue's critical role in substrate binding. The Asp 296->Ala mutation causes a 70-fold increase in the Km for adenosine and retains 0.001% of the wild-type kcat/Km value, whereas the ASP 296->Asn mutant has a 10-fold higher Km and retains 1% of the wild-type kcat/Km value. The structure of the D296A mutant shows that the impaired binding of substrate is caused by the loss of a single hydrogen bond between a carboxylate oxygen and N7 of the purine ring. These results and others discussed below are in agreement with the postulated role of the adjacent aspartates in the catalytic mechanism for mADA.

Gel filtration of human thyroid extract with Sephadex G-200 revealed two molecular forms of adenosine deaminase differing in their molecular sizes. The smaller form of adenosine deaminase was purified over 120-fold by precipitation of the protein impurities at pH5.6 and chromatography on DEAE-Sephadex A-50, Sephadex G-100 and adenosine-Sepharose. The purified enzyme was specific towards adenosine. The Michaelis constant was 5.2 X 10(-5) M. The optimum pH was about 7.0 and molecular weight 42000.

A M(r) 140,000 protein has been purified from chicken lungs to apparent homogeneity. The protein binds with high affinity to a non-BNA conformation, which is most likely to the Z-DNA. The protein also has a binding site for double-stranded RNA (dsRNA). Peptide sequences from this protein show similarity to dsRNA adenosine deaminase, an enzyme that deaminates adenosine in dsRNA to form inosine. Assays for this enzyme confirm that dsRNA adenosine deaminase activity and Z-DNA binding are properties of the same molecule. The coupling of these two activities in a single molecule may indicate a distinctive mechanism of gene regulation that is, in part, dependent on DNA topology. As such, DNA topology, through its effects on the efficiency and extent of RNA editing may be important in the generation of new phenotypes during evolution.

Extracts of liver and spleen were used to isolate opossum adenosine deaminase isoenzymes (ADA1 and ADA2) and to determine their activities with adenosine and 2'-deoxyadenosine as substrates. Km values (microM) for adenosine and 2'-deoxyadenosine, respectively, as substrates for partially purified opossum liver adenosine deaminase isoenzymes were ADA1: 57 +/- 7 vs. 26 +/- 4 and ADA2: 285 +/- 25 vs. 580 +/- 92. In crude spleen extract, ADA2 activity was stable at 56 degrees C during 40 min of incubation. ADA1 activity declined in a linear fashion under the above conditions with an apparent T1/2 of 80 min. Sephadex G-150 column chromatography of crude spleen extract showed the apparent molecular weight of the ADA activity not inhibited by (+/-)-EHNA (i.e. ADA2) to be 170 kDa; ADA activity fully inhibited by (+/-)-EHNA (i.e. ADA1) eluted in the fractions corresponding to a molecular weight of 35 kDa.

Double-stranded RNA (dsRNA)-specific adenosine deaminase converts adenosine to inosine in dsRNA. The protein has been purified from calf thymus, and here we describe the cloning of cDNAs encoding both the human and rat proteins as well as a partial bovine clone. The human and rat clones are very similar at the amino acid level except at their N termini and contain three dsRNA binding motifs, a putative nuclear targeting signal, and a possible deaminase motif. Antibodies raised against the protein encoded by the partial bovine clone specifically recognize the calf thymus dsRNA adenosine deaminase. Furthermore, the antibodies can immunodeplete a calf thymus extract of dsRNA adenosine deaminase activity, and the activity can be restored by addition of pure bovine deaminase. Staining of HeLa cells confirms the nuclear localization of the dsRNA-specific adenosine deaminase. In situ hybridization in rat brain slices indicates a widespread distribution of the enzyme in the brain.

A Z-DNA binding protein of 140,000 M(r) has been purified from chicken lungs by sedimentation through 40%(w/w) sucrose and Z-DNA affinity chromatography. Specificity of the protein for Z-DNA was confirmed by competition with polyd(CG) that had been stabilized in the Z-DNA conformer by chemical bromination and also with a supercoiled plasmid that contains a Z-DNA-forming insert. In addition to a Z-DNA binding site, the protein also has a separate binding site for double-stranded RNA. Peptide sequence of the protein shows that it has high similarity to the RNA editing enzyme double-stranded RNA adenosine deaminase (dsRAD), which deaminates adenosine in dsRNA to form inosine. The Z-DNA binding protein has this enzymatic activity, confirming its identity to dsRAD. Recombinant human dsRAD also binds to Z-DNA. Z-DNA is stabilized in a sequence-dependent manner by negative supercoiling, which occurs in actively transcribed genes upstream to RNA polymerase. It is proposed that Z-DNA links editing to transcription by localizing dsRAD to a particular region of a gene and thus determines the efficiency with which an RNA is edited. The presence of Z-DNA forming elements in many genes raises the possibility that RNA editing by dsRAD is far more prevalent than is currently thought.

A double-stranded RNA-specific adenosine deaminase, which converts adenosine to inosine, has been purified to homogeneity from calf thymus. The enzyme was purified approximately 340,000-fold by a series of column chromatography steps. The enzyme consists of a single polypeptide with a molecular mass of 116 kDa as determined by electrophoresis on a SDS/polyacrylamide gel. The native protein sediments at 4.2 s in glycerol gradients and has a Stokes radius of 42 A upon gel-filtration chromatography. This leads to an estimate of approximately 74,100 for the native molecular weight, suggesting that the enzyme exists as a monomer in solution. Enzyme activity is optimal at 0.1 M KCl and 37 degrees C. Divalent metal ions or ATP is not required for activity. The Km for double-stranded RNA substrate is approximately 7 x 10(-11) M. The Vmax is approximately 10(-9) mol of inosine produced per min per mg and the Kcat is 0.13 min-1.

An extracellular adenosine deaminase was isolated from the culture supernatant of Nocardioides sp. J-326TK and purified 193-fold to homogeneity. It had a specific activity of 4677 units/mg at 37 degrees C, was a monomeric protein as judged by SDS/PAGE, and was characterized with respect to M(r) (80,000 and 72,000 by gel filtration on Sephadex G-200 and SDS/PAGE respectively), pH optimum (6.0), temperature optimum (50 degrees C) and pI (7.6). The adsorption spectrum of the enzyme had a maximum at 280 nm and a minimum at 250 nm. The enzyme was stable at pH 6.5-7.5 and at temperatures below 30 degrees C. Adenosine and 2'-deoxyadenosine were deaminated and the respective Km values were 0.22 and 0.20 mM, but the enzyme was not active on adenine and 6-(gamma gamma'-dimethylallylamino)purine riboside. The enzyme reaction was promoted by Fe3+ and Sn2+, but potently inhibited by Hg2+, Ag2+, o-phenanthroline and pentachlorophenol, and noticeably inhibited by 8-bromoadenosine, theobromine and theophylline.

The double-stranded RNA (dsRNA) adenosine deaminase (DRADA) deaminates adenosine residues to inosines and creates I-U mismatched base pairs in dsRNAs. Its involvement in RNA editing of glutamate-gated ion channel gene transcripts in mammalian brains has been proposed as one of the biological functions for this recently identified cellular enzyme. We purified a mixture of three forms, 93, 88, and 83 kDa, of bovine DRADA proteins, all likely to be active enzymes. We determined that DRADA has a native molecular mass of approximately 100 kDa, suggesting that the enzyme exists as a monomer. The purified enzyme was not inhibited by 2'-deoxycoformycin, a transition state analog inhibitor of adenosine deaminase and AMP deaminase, suggesting that the catalytic mechanism of DRADA might be different from that of other deaminases. DRADA binds specifically to dsRNA with a dissociation constant of 0.23 nM for a synthetic dsRNA, and the Michaelis constant is 0.85 nM. These values indicate that DRADA has a much higher affinity for its substrate than other deaminases such as adenosine deaminase and AMP deaminase. DRADA may need this extremely high affinity to catalyze efficiently the modification of relatively rare substrate RNAs in the cell nucleus.

A double-stranded RNA adenosine deaminase that catalyzes the conversion of adenosines to inosines in duplex RNA substrates was purified to near homogeneity from Xenopus laevis eggs. The final specific activity was approximately 2.0 nmol of inosine min-1 mg-1 at 25 degrees C and pH 7.9 with a 794-base pair RNA substrate. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single major approximately 120-kDa protein band by silver staining. The purified enzyme migrated with an apparent molecular mass of 90 +/- 10 kDa during high performance liquid chromatography. Gel filtration of the partially purified enzyme gave an apparent molecular mass of 210 +/- 20 kDa, suggesting that the enzyme may dimerize or associate with other cellular components. Substrate modification was inhibited by excess substrate, thiol reagents, heparin, and moderate concentrations of monovalent cations.

Adenosine deaminase from the white and gray matter of the large hemispheres, cerebellum, medulla oblongata and pituitary anterior lobe has been isolated and purified. The pH optimum, Km, molecular mass, yield and specific activities for all the enzyme preparations have been determined. Gel filtration and electrophoresis data point to the heterogeneity of the enzyme. The lack of effects of SH-reagents suggests the absence of an essential SH-group. Among five bivalent metal ions, only Cu2+ irreversibly inhibited the enzyme activity in all the preparations.

Adenosine deaminase was overexpressed in a baculovirus system. The pure recombinant and native enzymes were identical in size, Zn2+ content, and activity. Five amino acids, in proximity to the active site, were replaced by mutagenesis. The altered enzymes were purified to homogeneity and compared to wild-type adenosine deaminase with respect to zinc content, enzymatic activity, and kinetic parameters. All but one of the alterations produced significant activity perturbations. Replacement of Cys262 produced a protein that retained at least 30-40% of wild-type activity. In contrast, replacements of His17, His214, His238, and Glu217 resulted in dramatic losses of enzyme activity. None of these mutants exhibited large variations in Km. The proteins produced from alterations of amino acids implicated in metal coordination were slightly activated by inclusion of Zn2+ throughout purification. These experiments confirm that in the active enzyme Zn2+ plays a critical role in catalysis, that a histidine or glutamate residue plays a mechanistic role in the hydrolytic deamination step, and that cysteine is not involved in the catalytic mechanism of adenosine deaminase. These data support the roles for these amino acid residues suggested from the x-ray structure of murine adenosine deaminase (Wilson, D. K., Rudolf, F. B., and Quicho, F. A. (1991) Science 252, 1278-1284).

Adenosine deaminase from Aspergillus oryzae resembles mammalian adenosine deaminases in its ability to catalyze the hydrolytic removal of many substituents from C-6, and in the chirality at C-6 of the active isomer of the transition-state-analogue inhibitor 6-hydroxymethyl-1,6-dihydropurine ribonucleoside. The 5'-OH group of adenosine has been found to contribute a factor of 5.10(4) to transition-state stabilization by calf intestinal adenosine deaminase, and crystallographic observations suggest that a zinc-histidine 'bridge' is formed between the 6-OH and the 5'-OH groups of the substrate in the transition state for its deamination. The present paper describes experiments indicating that this bridge is not present during the action of adenosine deaminase from Aspergillus oryzae. We find (1), that the fungal enzyme catalyzes deamination of adenosine and 5'-deoxyadenosine with kcat/Km values that are almost identical; (2), that the Ki value of the transition-state-analogue inhibitor 2'-deoxycoformycin is much higher for the fungal enzyme (2.7.10(-9) M) than for the mammalian enzyme (2.10(-12) M) and (3), that this difference in binding affinities arises mainly from a difference in rates of enzyme-inhibitor association. Thus, the onset of inhibition was markedly slower for the fungal enzyme (kon = 1.3.10(4) M-1 s-1) than for the calf intestinal enzyme (kon = 2.6.10(6) M-1 s-1). Effects of chelating agents and divalent cations suggest that the fungal enzyme, like other deaminases for adenosine and cytidine, contains essential zinc.