Adenine Deaminase Research Articles

Gene Duplication in Pseudomonas aeruginosa Improves Growth on Adenosine.

The laboratory strain of Pseudomonas aeruginosa, PAO1, activates genes for catabolism of adenosine using quorum sensing (QS). However, this strain is not well-adapted for growth on adenosine, with doubling times greater than 40 h. We previously showed that when PAO1 is grown on adenosine and casein, variants emerge that grow rapidly on adenosine. To understand the mechanism by which this adaptation occurs, we performed whole-genome sequencing of five isolates evolved for rapid growth on adenosine. All five genomes had a gene duplication-amplification (GDA) event covering several genes, including the quorum-regulated nucleoside hydrolase gene, nuh, and PA0148, encoding an adenine deaminase. In addition, two of the growth variants also exhibited a nuh promoter mutation. We recapitulated the rapid growth phenotype with a plasmid containing six genes common to all the GDA events. We also showed that nuh and PA0148, the two genes at either end of the common GDA, were sufficient to confer rapid growth on adenosine. Additionally, we demonstrated that the variant nuh promoter increased basal expression of nuh but maintained its QS regulation. Therefore, GDA in P. aeruginosa confers the ability to grow efficiently on adenosine while maintaining QS regulation of nucleoside catabolism.IMPORTANCEPseudomonas aeruginosa thrives in many habitats and is an opportunistic pathogen of humans. In these diverse environments, P. aeruginosa must adapt to use myriad potential carbon sources. P. aeruginosa PAO1 cannot grow efficiently on nucleosides, including adenosine; however, it can acquire this ability through genetic adaptation. We show that the mechanism of adaptation is by amplification of a specific region of the genome and that the amplification preserves the regulation of the adenosine catabolic pathway by quorum sensing. These results demonstrate an underexplored mechanism of adaptation by P. aeruginosa, with implications for phenotypes such as development of antibiotic resistance.

A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.

Saccharomyces cerevisiae responds to changes in extracellular inorganic phosphate (Pi) availability by regulating the activity of the phosphate-responsive (PHO) signaling pathway, enabling cells to maintain intracellular levels of the essential nutrient Pi. Pi-limitation induces upregulation of inositol heptakisphosphate (IP7) synthesized by the inositol hexakisphosphate kinase Vip1, triggering inhibition of the Pho80/Pho85 cyclin-cyclin dependent kinase (CDK) complex by the CDK inhibitor Pho81, which upregulates the PHO regulon through the CDK target and transcription factor Pho4. To identify genes that are involved in signaling upstream of the Pho80/Pho85/Pho81 complex and how they interact with each other to regulate the PHO pathway, we performed genome-wide screens with the synthetic genetic array method. We identified more than 300 mutants with defects in signaling upstream of the Pho80/Pho85/Pho81 complex, including AAH1, which encodes an adenine deaminase that negatively regulates the PHO pathway in a Vip1-dependent manner. Furthermore, we showed that even in the absence of VIP1, the PHO pathway can be activated under prolonged periods of Pi starvation, suggesting complexity in the mechanisms by which the PHO pathway is regulated.

Purine salvage in Methanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminase.

Adenine deaminases (Ade) and hypoxanthine/guanine phosphoribosyltransferases (Hpt) are widely distributed enzymes involved in purine salvage. Characterization of the previously uncharacterized Ade (MJ1459 gene product) and Hpt (MJ1655 gene product) are discussed here and provide insight into purine salvage in Methanocaldococcus jannaschii. Ade was demonstrated to use either Fe(II) and/or Mn(II) as the catalytic metal. Hpt demonstrated no detectable activity with adenine, but was equally specific for hypoxanthine and guanine with a kcat /KM of 3.2 × 10(7) and 3.0 × 10(7) s(- 1) M(- 1) , respectively. These results demonstrate that hypoxanthine and IMP are the central metabolites in purine salvage in M. jannaschii for AMP and GMP production. A conserved cysteine (C127, M. jannaschii numbering) was examined due to its high conservation in bacterial and archaeal homologues. To assess the role of this highly conserved cysteine in M. jannaschii Ade, site-directed mutagenesis was performed. It was determined that mutation to serine (C127S) completely abolished Ade activity and mutation to alanine (C127A) exhibited 10-fold decrease in kcat over the wild type Ade. To further investigate the role of C127, detailed molecular docking and dynamics studies were performed and revealed adenine was unable to properly orient in the active site in the C127A and C127S Ade model structures due to distinct differences in active site conformation and rotation of D261. Together this work illuminates purine salvage in M. jannaschii and the critical role of a cysteine residue in maintaining active site conformation of Ade. Proteins 2016; 84:828-840. © 2016 Wiley Periodicals, Inc.

The Epitranscriptome and Innate Immunity.

Our knowledge of the variety and abundances of RNA base modifications is rapidly increasing. Modified bases have critical roles in tRNAs, rRNAs, translation, splicing, RNA interference, and other RNA processes, and are now increasingly detected in all types of transcripts. Can new biological principles associated with this diversity of RNA modifications, particularly in mRNAs and long non-coding RNAs, be identified? This review will explore this question by focusing primarily on adenosine to inosine (A-to-I) RNA editing by the adenine deaminase acting on RNA (ADAR) enzymes that have been intensively studied for the past 20 years and have a wide range of effects. Over 100 million adenosine to inosine editing sites have been identified in the human transcriptome, mostly in embedded Alu sequences that form potentially innate immune-stimulating dsRNA hairpins in transcripts. Recent research has demonstrated that inosine in the epitranscriptome and ADAR1 protein establish innate immune tolerance for host dsRNA formed by endogenous sequences. Innate immune sensors that detect viral nucleic acids are among the readers of epitranscriptome RNA modifications, though this does preclude a wide range of other modification effects.

CECR1 p.Gly47Arg mutations are not increased in frequency in Turkish Behçet's disease patients compared with healthy controls

Question In Behcet’s disease (BD), vasculitis involving blood vessels of nearly all sizes and types may underlie the diverse tissue and organ involvement. Loss of function mutations in the CECR1 gene (encoding adenosine deaminase 2) have recently been shown to cause a recessive genetic disease, deficiency of adenine deaminase 2 (DADA2). Patients with DADA2 exhibit systemic vasculopathy characterized by intermittent fevers, skin rash, and neurovascular manifestations along with other features that can lead to a diagnosis of polyarteritis nodosa. Patients homozygous for the CECR1 p.Gly47Arg mutation are reported in two nonconsanguineous Turkish families and this mutation is found at low frequency in the Turkish population. We therefore attempted to determine whether some BD cases may be explained by adenosine deaminase 2 deficiency and whether this mutation contributes to BD risk in patients of Turkish ancestry.

Effects of iron supplementation on blood adenine deaminase activity and oxidative stress in Trypanosoma evansi infection of rats

The aim of this study was to assess the effects of iron supplementation on oxidative stress and on the activity of the adenosine deaminase (ADA) in rats experimentally infected by Trypanosoma evansi. For this purpose, 20 rats were divided into four experimental groups with five animals each as follows: groups A and B were composed by healthy animals, while animals from groups C and D were infected by T. evansi. Additionally, groups B and D received two subcutaneous doses of iron (60 mg kg-1) within an interval of 5 days. Blood samples were drawn on day 8 post infection in order to assess hematological and biochemical variables. Among the main results are: (1) animals from group C showed reduced erythrogram (with tendency to anemia); however the same results were not observed for group D; this might be a direct effect of free iron on trypanosomes which helped to reduce the parasitemia and the damage to erythrocytes caused by the infection; (2) iron supplementation was able to reduce NOx levels by inhibiting iNOS, and thus, providing an antioxidant action and, indirectly, reducing the ALT levels in groups Band D; (3) increase FRAP levels in group D; (4) reduce ADA activity in serum and erythrocytes in group C; however, this supplementation (5) increased the protein oxidation in groups B and D, as well as group C (positive control). Therefore, iron showed antioxidant and oxidant effects on animals that received supplementation; and it maintained the activity of E-ADA stable in infected/supplemented animals.

Adenine deaminase is encoded by Tad1 and participates in copper accumulation in Trichoderma reesei

We cloned a novel Tad1 gene and demonstrated that this gene is closely involved in copper bioaccumulation in Trichoderma reesei. Tad1 gene encodes a 510 amino acids protein of the amidohydrolase superfamily which belongs to COG0402. We found that adenine was the most efficient substrate of Tad1 protein among the substrates used in this study. Gene function was also investigated by overexpression and RNA interference. Results showed that copper accumulation increased in mutant cells when Tad1 was overexpressed; by contrast, copper accumulation significantly decreased when Tad1 was inhibited. To investigate the function of Tad1 in copper bioaccumulation, we determined adenine, hypoxanthine, and xanthine concentrations by reversed phase HPLC. Tad1 overexpression induced a substantial production of xanthine, which functions in binding numerous copper ions and reducing copper concentration. We further compared the gene expression profile of AT01 with that of a wild-type T. reesei strain grown in a medium containing 1.0mM Cu2+ by performing DNA microarray. Several upregulated genes in the mutant were associated with adenine or copper metabolism.

Arxula adeninivoransrecombinant adenine deaminase and its application in the production of food with low purine content

Construction of a transgenic Arxula adeninivorans strain that produces a high concentration of adenine deaminase and investigation into the application of the enzyme in the production of food with low purine content. The A. adeninivorans AADA gene, encoding adenine deaminase, was expressed in this yeast under the control of the strong inducible nitrite reductase promoter using the Xplor(®) 2 transformation/expression platform. The recombinant enzyme was biochemically characterized and was found to have a pH range of 5.5-7.5 and temperature range of 34-46 °C with medium thermostability. A beef broth was treated with the purified enzyme resulting in the concentration of adenine decreasing from 70.4 to 0.4 mg l(-1). It was shown that the production of adenine deaminase by A. adeninivorans can be increased and that the recombinant adenine deaminase can be used to lower the adenine content in the food. Adenine deaminase is one component of an enzymatic system that can reduce the production of uric acid from food constituents. This study gives details on the expression, characterization and application of the enzyme and thus provides evidence that supports the further development of the system.

Adenine and adenosine salvage in Leishmania donovani

6-aminopurine metabolism in Leishmania is unique among trypanosomatid pathogens since this genus expresses two distinct routes for adenine salvage: adenine phosphoribosyltransferase (APRT) and adenine deaminase (AAH). To evaluate the relative contributions of APRT and AAH, adenine salvage was evaluated in Δaprt, Δaah, and Δaprt/Δaah null mutants of L. donovani. The data confirm that AAH plays the dominant role in adenine metabolism in L. donovani, although either enzyme alone is sufficient for salvage. Adenosine salvage was also evaluated in a cohort of null mutants. Adenosine is also primarily converted to hypoxanthine, either intracellularly or extracellularly, but can also be phosphorylated to the nucleotide level by adenosine kinase when the predominant pathways are genetically or pharmacologically blocked. These data provide genetic verification for the relative contributions of 6-aminopurine metabolizing pathways in L. donovani and demonstrate that all of the pathways can function under appropriate conditions of genetic or pharmacologic perturbation.

RNA Targets and Specificity of Staufen, a Double-stranded RNA-binding Protein in Caenorhabditis elegans

The Staufen family consists of proteins that possess double-stranded RNA-binding domains (dsRBDs). Staufen proteins of Drosophila and mammals regulate mRNA localization, translation, and decay. We report analysis of Staufen in Caenorhabditis elegans, which we have designated STAU-1. We focus on its biochemical properties, mRNA targets, and possible role in RNAi. We show that STAU-1 is expressed as mRNA and protein at all stages of C. elegans development. The wild-type, full-length protein, purified from bacteria, binds duplex RNA with high affinity in vitro. Purified, mutant proteins lacking single dsRBDs still bind RNA efficiently, demonstrating that no single domain is required for binding to duplex RNA (although dsRBD2 could not be tested). STAU-1 mRNA targets were identified via immunoprecipitation with specific anti-STAU-1 antibodies, followed by microarray analysis (RIP-Chip). These studies define a set of 418 likely STAU-1 mRNA targets. Finally, we demonstrate that stau-1 mutants enhance exogenous RNAi and that stau-1;eri-1 double mutants exhibit sterility and synthetic germ line defects.

Functional Annotation and Three-Dimensional Structure of an Incorrectly Annotated Dihydroorotase from cog3964 in the Amidohydrolase Superfamily

The substrate specificities of two incorrectly annotated enzymes belonging to cog3964 from the amidohydrolase superfamily were determined. This group of enzymes are currently misannotated as either dihydroorotases or adenine deaminases. Atu3266 from Agrobacterium tumefaciens C58 and Oant2987 from Ochrobactrum anthropi ATCC 49188 were found to catalyze the hydrolysis of acetyl-(R)-mandelate and similar esters with values of k(cat)/K(m) that exceed 10(5) M(-1) s(-1). These enzymes do not catalyze the deamination of adenine or the hydrolysis of dihydroorotate. Atu3266 was crystallized and the structure determined to a resolution of 2.62 Å. The protein folds as a distorted (β/α)(8) barrel and binds two zincs in the active site. The substrate profile was determined via a combination of computational docking to the three-dimensional structure of Atu3266 and screening of a highly focused library of potential substrates. The initial weak hit was the hydrolysis of N-acetyl-D-serine (k(cat)/K(m) = 4 M(-1) s(-1)). This was followed by the progressive identification of acetyl-(R)-glycerate (k(cat)/K(m) = 4 × 10(2) M(-1) s(-1)), acetyl glycolate (k(cat)/K(m) = 1.3 × 10(4) M(-1) s(-1)), and ultimately acetyl-(R)-mandelate (k(cat)/K(m) = 2.8 × 10(5) M(-1) s(-1)).

Target Enrichment and High-Throughput Sequencing of 80 Ribosomal Protein Genes to Identify Mutations Associated with Diamond-Blackfan Anaemia.

AbstractAbstract 2369Diamond-Blackfan anaemia (DBA) is a rare autosomal dominant disorder associated with inactivating mutations in ribosomal protein (RP) genes, causing defects in erythroid progenitor and precursor cell development. Many cases are due to de novo mutations and in family cases there is often clinical heterogeneity due to variable penetrance. Mutations in RPS19 account for 25% of all DBA cases and single nucleotide variations (SNV), indels and allele-loss deletions have been found in 11 other RP genes in a further ∼50% of patients. Around 25% of patients with DBA have no identifiable mutations. Given that (with the exception of 2 cases with GATA1 mutations) all mutations in DBA characterised so far affect RP genes, it is likely that mutations in one of the 80 RP genes will be eventually identified in a significant proportion of the patients. Current screening methods are primarily based on Sanger sequencing on a per-exon/per-gene basis, with the associated time, labour and cost restrictions. We therefore aimed to evaluate high-throughput sequencing technology, including a bespoke target enrichment platform, to screen all 80 known RP genes to facilitate rapid, cost-effective identification of DBA associated mutations. DNA was extracted from peripheral blood samples that had been referred to Imperial Molecular Pathology for DBA screening from 10 individuals, including 3 family pairs: affected mother and daughter; 2 affected siblings; and another sibling pair, one of whom was unaffected/low-penetrance (no defining clinical symptoms, except for high adenine deaminase). Only one patient had a known mutation (RPS19 c.280C>T) and was included as a control. Agilent SureSelect XP was used for the target enrichment, which employed a custom designed tiled-RNA bait hybridisation solution to capture the target genes, including non-masked intronic regions and 500bp of flanking sequence. The DNA was sheared using a Covaris e220, QC was performed via QIAxcel capillary electrophoresis and the hybridisation was carried out at 65°C for 48h. Individual libraries were quantified using qPCR against the supplied standard curve and pooled proportionally. The sequencing was performed on an Illumina MiSeq, using 150bp paired-end reads and multiplexed using the supplied ScriptSeq barcodes. The sequencing reads were aligned to the build 37 reference genome using BWA software, and the variant calls made using GATK. Annovar was used for functional annotations of the variants. Protein truncating mutations were found in RP genes in 7 of the 10 samples, including the positive control and 6 of the 8 clinically confirmed DBA patient samples., All mutations were in RP genes previous described as being involved in DBA, although 3 affected novel codons: RPL5 c.G244T (stop-gain SNV; novel; mother-daughter pair); RPL5 c.166_169delACAA (frameshift); RPS10 c.C337T (stop-gain SNV); RPL11 c.472–473delAA (frameshift; novel); RPS26 c.212–213insA (frameshift; novel). Validation was by Sanger sequencing and further confirmation testing will include unaffected family members. The remaining 2 DBA patients, a brother-sister pair, showed no definable mutations in the captured regions and neither did the unaffected/low-penetrance sibling of the RPS10 patient. In summary, a rapid and cost effective methodology for screening genetic lesions associated with the causation of DBA is warranted, especially given the magnitude of attaining global coverage by conventional techniques. Whole-gene enrichment followed by multiplexed runs on a bench-top class high-throughput sequencing platform is arguably the approach of choice; although as the cost of exome and even genome sequencing continues to fall, these may well become realistic options in the coming few years. This work is ongoing, with a second group of 10 samples already sequenced and undergoing analysis, and bioinformatic refinements, especially for the detection of larger deletions, may yet yield results for the two undetected samples. These preliminary results suggest that high throughput sequencing technology with a bespoke target enrichment platform for RP genes is a feasible, efficient and relatively rapid diagnostic tool for detection of causative mutations DBA. Disclosures:No relevant conflicts of interest to declare.

Enzyme Based Amperometric Biosensor for Adenine Determination

AbstractAn enzyme‐based amperometric biosensor was developed for the rapid determination of adenine in biological and food samples. Recombinant adenine deaminase (EC 3.5.4.2) from Schizosaccharomyces pombe was co‐immobilized on graphite electrode with xanthine oxidase (EC 1.17.3.2), peroxidase (EC 1.11.1.7) and an Os mediator. Optimal working conditions were pH 7.0 and −150 mV vs. Ag/AgCl. The novel method was characterized by a detection limit of 1 µM and a linear measuring range of 0.005–0.1 mM. Different beer and tea samples were analyzed by the newly elaborated adenine biosensor. The results obtained correlate with the adenine content measured by the reference HPLC method.

Stem Cell Selection In Vivo Using Foamy Vectors Cures Canine Pyruvate Kinase Deficiency

BackgroundHematopoietic stem cell (HSC) gene therapy has cured immunodeficiencies including X-linked severe combined immunodeficiency (SCID-X1) and adenine deaminase deficiency (ADA). For these immunodeficiencies corrected cells have a selective advantage in vivo, and low numbers of gene-modified cells are sufficient to provide therapeutic benefit. Strategies to efficiently transduce and/or expand long-term repopulating cells in vivo are needed for treatment of diseases that require higher levels of corrected cells, such as hemoglobinopathies. Here we expanded corrected stem cells in vivo in a canine model of a severe erythroid disease, pyruvate kinase deficiency.Methodology/Principal FindingsWe used a foamy virus (FV) vector expressing the P140K mutant of methylguanine methyltransferase (MGMTP140K) for in vivo expansion of corrected hematopoietic repopulating cells. FV vectors are attractive gene transfer vectors for hematopoietic stem cell gene therapy since they efficiently transduce repopulating cells and may be safer than more commonly used gammaretroviral vectors. Following transplantation with HSCs transduced ex vivo using a tri-cistronic FV vector that expressed EGFP, R-type pyruvate kinase, and MGMTP140K, we were able to increase marking from approximately 3.5% to 33% in myeloid long-term repopulating cells resulting in a functional cure.Conclusions/SignificanceHere we describe in one affected dog a functional cure for a severe erythroid disease using stem cell selection in vivo. In addition to providing a potential cure for patients with pyruvate kinase deficiency, in vivo selection using foamy vectors with MGMTP140K has broad potential for several hematopoietic diseases including hemoglobinopathies.

Reduction of dADAR activity affects the sensitivity of Drosophila melanogaster to spinosad and imidacloprid

The insecticides spinosad and imidacloprid cause toxicity by acting at the nicotinic acetylcholine receptor (nAChR), but at distinct sites on the receptor. Mutations or deletions of specific nAChR subunits cause resistance to these compounds. Transcripts of nAChR subunits are subject to A-to-I RNA editing by adenine deaminase acting on RNA (ADAR), which may result in altered receptor physiology. However, reports on the influence of A-to-I RNA editing on insecticide sensitivity have been very limited. We used the Gal4–UAS system in Drosophila melanogaster to reduce the expression of dAdar in specific tissues and evaluated the toxicity of spinosad and imidacloprid. Ubiquitous reduction of dAdar increased spinosad sensitivity, while dAdar reduction in cholinergic neurons and muscle reduced spinosad sensitivity. Imidacloprid sensitivity was reduced by decreased dAdar expression in cholinergic neurons, muscle and glia. While reduction in editing of nAChR subunits may explain some of these changes in insecticide toxicity, it is likely that editing of genes other than nAChRs can affect toxicity of these insecticides.

The catalase activity of diiron adenine deaminase

Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mössbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 × 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.

Investigation of the Molecular Origins of Protein-arginine Methyltransferase I (PRMT1) Product Specificity Reveals a Role for Two Conserved Methionine Residues

Protein-arginine methyltransferases aid in the regulation of many biological processes by methylating specific arginyl groups within targeted proteins. The varied nature of the response to methylation is due in part to the diverse product specificity displayed by the protein-arginine methyltransferases. In addition to site location within a protein, biological response is also determined by the degree (mono-/dimethylation) and type of arginine dimethylation (asymmetric/symmetric). Here, we have identified two strictly conserved methionine residues in the PRMT1 active site that are not only important for activity but also control substrate specificity. Mutation of Met-155 or Met-48 results in a loss in activity and a change in distribution of mono- and dimethylated products. The altered substrate specificity of M155A and M48L mutants is also evidenced by automethylation. Investigation into the mechanistic basis of altered substrate recognition led us to consider each methyl transfer step separately. Single turnover experiments reveal that the rate of transfer of the second methyl group is much slower than transfer of the first methyl group in M48L, especially for arginine residues located in the center of the peptide substrate where turnover of the monomethylated species is negligible. Thus, altered product specificity in M48L originates from the differential effect of the mutation on the two rates. Characterization of the two active-site methionines provides the first insight into how the PRMT1 active site is engineered to control product specificity.

Adenosine deaminase from Streptomyces coelicolor: Recombinant expression, purification and characterization

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 −1at 30 °C. Since adenine is deaminated ∼10 3 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.

Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase,

Adenine deaminase (ADE) catalyzes the conversion of adenine to hypoxanthine and ammonia. The enzyme isolated from Escherichia coli using standard expression conditions was low for the deamination of adenine (k(cat) = 2.0 s(-1); k(cat)/K(m) = 2.5 × 10(3) M(-1) s(-1)). However, when iron was sequestered with a metal chelator and the growth medium was supplemented with Mn(2+) prior to induction, the purified enzyme was substantially more active for the deamination of adenine with k(cat) and k(cat)/K(m) values of 200 s(-1) and 5 × 10(5) M(-1) s(-1), respectively. The apoenzyme was prepared and reconstituted with Fe(2+), Zn(2+), or Mn(2+). In each case, two enzyme equivalents of metal were necessary for reconstitution of the deaminase activity. This work provides the first example of any member of the deaminase subfamily of the amidohydrolase superfamily to utilize a binuclear metal center for the catalysis of a deamination reaction. [Fe(II)/Fe(II)]-ADE was oxidized to [Fe(III)/Fe(III)]-ADE with ferricyanide with inactivation of the deaminase activity. Reducing [Fe(III)/Fe(III)]-ADE with dithionite restored the deaminase activity, and thus, the diferrous form of the enzyme is essential for catalytic activity. No evidence of spin coupling between metal ions was evident by electron paramagnetic resonance or Mössbauer spectroscopy. The three-dimensional structure of adenine deaminase from Agrobacterium tumefaciens (Atu4426) was determined by X-ray crystallography at 2.2 Å resolution, and adenine was modeled into the active site on the basis of homology to other members of the amidohydrolase superfamily. On the basis of the model of the adenine-ADE complex and subsequent mutagenesis experiments, the roles for each of the highly conserved residues were proposed. Solvent isotope effects, pH-rate profiles, and solvent viscosity were utilized to propose a chemical reaction mechanism and the identity of the rate-limiting steps.

Phenotypic Consequences of Purine Nucleotide Imbalance inSaccharomyces cerevisiae

Coordinating homeostasis of multiple metabolites is a major task for living organisms, and complex interconversion pathways contribute to achieving the proper balance of metabolites. AMP deaminase (AMPD) is such an interconversion enzyme that allows IMP synthesis from AMP. In this article, we show that, under specific conditions, lack of AMPD activity impairs growth. Under these conditions, we found that the intracellular guanylic nucleotide pool was severely affected. In vivo studies of two AMPD homologs, Yjl070p and Ybr284p, indicate that these proteins have no detectable AMP, adenosine, or adenine deaminase activity; we show that overexpression of YJL070c instead mimics a loss of AMPD function. Expression of the yeast transcriptome was monitored in a AMPD-deficient mutant in a strain overexpressing YJL070c and in cells treated with the immunosuppressive drug mycophenolic acid, three conditions that lead to severe depletion of the guanylic nucleotide pool. These three conditions resulted in the up- or downregulation of multiple transcripts, 244 of which are common to at least two conditions and 71 to all three conditions. These transcriptome results, combined with specific mutant analysis, point to threonine metabolism as exquisitely sensitive to the purine nucleotide balance.