Deduced amino acid sequence of Escherichia coli adenosine deaminase reveals evolutionarily conserved amino acid residues: implications for catalytic function

Evolving spectrum of adenosine deaminase (ADA) deficiency: Assessing genotype pathogenicity according to expressed ADA activity of 46 variants

BACKGROUND

Deficiency of adenosine deaminase (ADA or ADA1) has broad clinical and genetic heterogeneity. Screening techniques can identify asymptomatic infants whose phenotype and prognosis are indeterminate, and who may carry ADA variants of unknown significance.

OBJECTIVE

We systematically assessed the pathogenic potential of rare ADA missense variants to better define the relationship of genotype to red blood cell (RBC) total deoxyadenosine nucleotide (dAXP) content and to phenotype.

METHODS

We expressed 46 ADA missense variants in the ADA-deficient SØ3834 strain of Escherichia coli and defined genotype categories (GCs) ranked I to IV by increasing expressed ADA activity. We assessed relationships among GC rank, RBC dAXP, and phenotype in 58 reference patients with 50 different genotypes. We used our GC ranking system to benchmark AlphaMissense for predicting variant pathogenicity, and we used a minigene assay to identify exonic splicing variants in ADA exon 9.

RESULTS

The 46 missense variants expressed ∼0.001% to ∼70% of wild-type ADA activity (40% had <0.05% of wild-type ADA activity and 50% expressed >1%). RBC dAXP ranged from undetectable to >75% of total adenine nucleotides and correlated well with phenotype. Both RBC dAXP and clinical severity were inversely related to total ADA activity expressed by both inherited variants. Our GC scoring system performed better than AlphaMissense in assessing variant pathogenicity, particularly for less deleterious variants.

CONCLUSION

For ADA deficiency, pathogenicity is a continuum and conditional, depending on the total ADA activity contributed by both inherited variants as indicated by GC rank. However, in patients with indeterminate phenotype identified by screening, RBC dAXP measured at diagnosis may have greater prognostic value than GC rank.

Understanding the mode of inhibition and molecular interaction of taxifolin with human adenosine deaminase

Adenosine deaminase is a zinc⁺² dependent key enzyme of purine metabolism which irreversibly converts adenosine to inosine and form ammonia. Overexpression of adenosine deaminase has been linked to a variety of pathophysiological conditions such as atherosclerosis, hypertension, and diabetes. In the case of a cell-mediated immune response, ADA is thought to be a marker, particularly in type II diabetes. Deoxycoformycin is the most potent ADA inhibitor that has been discovered so far, but it has several drawbacks, including being toxic and having poor pharmacokinetics. Taxifolin, a flavonoid derived from plants, was discovered to be a potent inhibitor of the human ADA (hADA) enzyme in the current study. Taxifolin bound at the active site of human ADA and showed fifty percent inhibition at a concentration of 400 µM against the enzyme. To better understand the interactions between taxifolin and human ADA, docking and molecular dynamic simulations were performed. In-silico studies using autodock revealed that taxifolin bound in the active site of human ADA with a binding energy of -7.4 kcal mol ^-1 and a theoretical Ki of 3.7 uM. Comparative analysis indicated that taxifolin and deoxycoformycin share a common binding space in the active site of human ADA and inhibit its catalytic activity similarly. The work emphasises the need of employing taxifolin as a lead chemical in order to produce a more precise and effective inhibitor of the human ADA enzyme with therapeutic potential.Communicated by Ramaswamy H. Sarma.

Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets

BACKGROUND

Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets.

METHODS

Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets.

RESULTS

Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.

Adenosine deaminase - A target for new piperazine derivatives

The level of adenosine deaminase (ADA) activity increases in pathological effusions. Therefore, the concentration of its substrate, anti-inflammatory adenosine, decreases, thereby aggravating inflammation. Hence, the quest for ADA inhibiting compounds is an actual problem in medicine and pharmacology. This work describes the inhibition of bovine ADA by new synthesized piperazine compounds. 15 compounds were screened; IC50 values for 5 more potent ones of them were between 3.4 and 98.6 μg/ml. The inhibition of activity of intracellular and ecto- forms of ADA by the most effective "compound 1" was of competitive nature. For these two forms of enzyme, the inhibition constants, Ki (1.5 and 115 μM) and IC50 values (6.5 and 480 μM), respectively, differed by nearly two orders. The constant of bimolecular interaction KSV between "compound 1" and the tryptophan residues in ADA was estimated in fluorescence quenching study as of 0.145 ± 0.027 μM. Finally, the molecular interactions between "compound 1" and the bovine enzyme ADA were highlighted through molecular docking studies.

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

Many genes in bacterial genomes are of unknown function, often referred to as y-genes. Recently, the analytic methods have divided bacterial transcriptomes into independently modulated sets of genes (iModulons). Functionally annotated iModulons that contain y-genes lead to testable hypotheses to elucidate y-gene function. The inversely correlated expression of a putative transporter gene, ydhC, relative to purine biosynthetic genes, has led to the hypothesis that it encodes a purine-related transporter and revealed a LysR-family regulator, YdhB, with a predicted 23-bp palindromic binding motif. RNA-Seq analysis of a ydhB knockout mutant confirmed the YdhB-dependent activation of ydhC in the presence of adenosine. The deletion of either the ydhC or the ydhB gene led to a substantially decreased growth rate for E. coli in minimal medium with adenosine, inosine, or guanosine as the nitrogen source. Taken together, we provide clear evidence that YdhB activates the expression of the ydhC gene that encodes a purine transporter in E. coli. We propose that the genes ydhB and ydhC be re-named as punR and punC, respectively.

Rodionova et al. find that the putative transporter gene, ydhC and its regulator ydhB are involved in purine transportation and that the expression of the ydhC gene is activated by the YdhB in E. coli. The authors suggest renaming the regulator PunR and the transporter PunC, respectively.

Detection of N6-Methyladenine in Eukaryotes

DNA N⁶-methyladenine (6mA) is a chemical modification at the N⁶-positon of adenine. In the last decades, 6mA had been found in genome from numerous prokaryotic species, but only existed in a few lower eukaryotes. In prokaryotes, 6mA plays an important role in restriction-modification, DNA replication, and DNA mismatch repair. Because of the too low abundance of 6mA, it was long-stalled whether 6mA existed in multicellular eukaryotes and playing any functions, particularly in mammals. In recent years, partially benefitting from the advances in analytical methods, 6mA was found in the genomes from Drosophila melanogaster, Chlamydomonas algae, Caenorhabditis elegans, zebrafish, Xenopus laevis and mouse embryonic stem cells and even in the human genome. The 6mA was dynamic changed in early embryonic development of fly and zebrafish and much more enriched in gene body of transposons in fly, repetitive regions in zebrafish, around the transcription start sites in Chlamydomonas, and widespread distribution in C. elegans, indicating 6mA probably playing different functions in different species. Meanwhile, 6mA methylases and demethylases were found in fly, worm, and Chlamydomonas. In this chapter, we will briefly review the distribution, regulation, and function of 6mA in eukaryotes and focus on the advances of 6mA analysis methods, especially LC-MS/MS, immunoprecipitation, next-generation sequencing, and single-molecule real-time sequencing technology.

Therapeutic Perspectives of Adenosine Deaminase Inhibition in Cardiovascular Diseases

Adenosine deaminase (ADA) is an enzyme of purine metabolism that irreversibly converts adenosine to inosine or 2'deoxyadenosine to 2'deoxyinosine. ADA is active both inside the cell and on the cell surface where it was found to interact with membrane proteins, such as CD26 and adenosine receptors, forming ecto-ADA (eADA). In addition to adenosine uptake, the activity of eADA is an essential mechanism that terminates adenosine signaling. This is particularly important in cardiovascular system, where adenosine protects against endothelial dysfunction, vascular inflammation, or thrombosis. Besides enzymatic function, ADA protein mediates cell-to-cell interactions involved in lymphocyte co-stimulation or endothelial activation. Furthermore, alteration in ADA activity was demonstrated in many cardiovascular pathologies such as atherosclerosis, myocardial ischemia-reperfusion injury, hypertension, thrombosis, or diabetes. Modulation of ADA activity could be an important therapeutic target. This work provides a systematic review of ADA activity and anchoring inhibitors as well as summarizes the perspectives of their therapeutic use in cardiovascular pathologies associated with increased activity of ADA.

Alternative conformation induced by substrate binding for Arabidopsis thalianaN6-methyl-AMP deaminase

Adenosine deaminase is involved in adenosine degradation and salvage pathway, and plays important physiological roles in purine metabolism. Recently, a novel type of adenosine deaminase-like protein has been identified, which displays deamination activity toward N⁶-methyl-adenosine monophosphate but not adenosine or AMP, and was consequently named N⁶-methyl-AMP deaminase (MAPDA). The underlying structural basis of MAPDA recognition and catalysis is poorly understood. Here, we present the crystal structures of MAPDA from Arabidopsis thaliana in the free and in the ligand-bound forms. The protein contains a conserved (β/α)₈ Tim-barrel domain and a typical zinc-binding site, but it also exhibits idiosyncratic local differences for two flexible helices important for substrate binding. The extensive interactions between the N⁶-methyl-AMP substrate or the inosine monophosphate product and the enzyme were identified, and subsequently evaluated by the deamination activity assays. Importantly, each structure reported here represents a different stage of the catalytic pathway and their structural differences suggested that the enzyme can exist in two distinct conformational states. The open state switches to the closed one upon the binding of ligands, brought about by the two critical helices. Our structural studies provide the first look of this important metabolic enzyme and shed lights on its catalytic pathway, which holds promise for the structure-based drug design for MAPDA-related diseases.

Inverted Regulation of Multidrug Efflux Pumps, Acid Resistance, and Porins in Benzoate-Evolved Escherichia coli K-12

Benzoic acid, a partial uncoupler of the proton motive force (PMF), selects for sensitivity to chloramphenicol and tetracycline during the experimental evolution of Escherichia coli K-12. Transcriptomes of E. coli isolates evolved with benzoate showed the reversal of benzoate-dependent regulation, including the downregulation of multidrug efflux pump genes, the gene for the Gad acid resistance regulon, the nitrate reductase genes narHJ, and the gene for the acid-consuming hydrogenase Hyd-3. However, the benzoate-evolved strains had increased expression of OmpF and other large-hole porins that admit fermentable substrates and antibiotics. Candidate genes identified from benzoate-evolved strains were tested for their roles in benzoate tolerance and in chloramphenicol sensitivity. Benzoate or salicylate tolerance was increased by deletion of the Gad activator ariR or of the acid fitness island from slp to the end of the gadX gene encoding Gad regulators and the multidrug pump genes mdtEF Benzoate tolerance was also increased by deletion of multidrug component gene emrA, RpoS posttranscriptional regulator gene cspC, adenosine deaminase gene add, hydrogenase gene hyc (Hyd-3), and the RNA chaperone/DNA-binding regulator gene hfq Chloramphenicol resistance was decreased by mutations in genes for global regulators, such as RNA polymerase alpha subunit gene rpoA, the Mar activator gene rob, and hfq Deletion of lipopolysaccharide biosynthetic kinase gene rfaY decreased the rate of growth in chloramphenicol. Isolates from experimental evolution with benzoate had many mutations affecting aromatic biosynthesis and catabolism, such as aroF (encoding tyrosine biosynthesis) and apt (encoding adenine phosphoribosyltransferase). Overall, benzoate or salicylate exposure selects for the loss of multidrug efflux pumps and of hydrogenases that generate a futile cycle of PMF and upregulates porins that admit fermentable nutrients and antibiotics.IMPORTANCE Benzoic acid is a common food preservative, and salicylic acid (2-hydroxybenzoic acid) is the active form of aspirin. At high concentrations, benzoic acid conducts a proton across the membrane, depleting the proton motive force. In the absence of antibiotics, benzoate exposure selects against proton-driven multidrug efflux pumps and upregulates porins that admit fermentable substrates but that also allow the entry of antibiotics. Thus, evolution with benzoate and related molecules, such as salicylates, requires a trade-off for antibiotic sensitivity, a trade-off that could help define a stable gut microbiome. Benzoate and salicylate are naturally occurring plant signal molecules that may modulate the microbiomes of plants and animal digestive tracts so as to favor fermenters and exclude drug-resistant pathogens.

Structure of Arabidopsis thaliana N6-methyl-AMP deaminase ADAL with bound GMP and IMP and implications for N6-methyl-AMP recognition and processing

Arabidopsis thaliana aminohydrolase (AtADAL) has been shown to be involved in the metabolism of N⁶-methyl-AMP, a proposed intermediate during m⁶A-modified RNA metabolism, which can be subsequently incorporated into newly synthesized RNA by Pol II. It has been proposed that AtADAL will prevent N⁶-methyl-AMP reuse and catabolize it to inosine monophosphate (IMP). Here, we have solved the crystal structures of AtADAL in the apo form and in complex with GMP and IMP in the presence of Zn²⁺. We have identified the substrate-binding pocket of AtADAL and compared it with that for adenosine deaminase (ADA), adenine deaminase (ADE) and AMP deaminase (AMPD) from multiple species. The comparisons reveal that plant ADAL1 may have the potential ability to catalyze different alkyl-group substituted substrates.

Role of the HPRG Component of Striated Muscle AMP Deaminase in the Stability and Cellular Behaviour of the Enzyme

Multiple muscle-specific isoforms of the Zn²⁺ metalloenzyme AMP deaminase (AMPD) have been identified based on their biochemical and genetic differences. Our previous observations suggested that the metal binding protein histidine-proline-rich glycoprotein (HPRG) participates in the assembly and maintenance of skeletal muscle AMP deaminase (AMPD1) by acting as a zinc chaperone. The evidence of a role of millimolar-strength phosphate in stabilizing the AMPD-HPRG complex of both AMPD1 and cardiac AMP deaminase (AMPD3) is suggestive of a physiological mutual dependence between the two subunit components with regard to the stability of the two isoforms of striated muscle AMPD. The observed influence of the HPRG content on the catalytic behavior of the two enzymes further strengthens this hypothesis. Based on the preferential localization of HPRG at the sarcomeric I-band and on the presence of a Zn²⁺ binding motif in the N-terminal regions of fast TnT and of the AMPD1 catalytic subunit, we advance the hypothesis that the Zn binding properties of HPRG could promote the association of AMPD1 to the thin filament.

Molecular Evidence of Adenosine Deaminase Linking Adenosine A2A Receptor and CD26 Proteins

Adenosine is an endogenous purine nucleoside that acts in all living systems as a homeostatic network regulator through many pathways, which are adenosine receptor (AR)-dependent and -independent. From a metabolic point of view, adenosine deaminase (ADA) is an essential protein in the regulation of the total intracellular and extracellular adenosine in a tissue. In addition to its cytosolic localization, ADA is also expressed as an ecto-enzyme on the surface of different cells. Dipeptidyl peptidase IV (CD26) and some ARs act as binding proteins for extracellular ADA in humans. Since CD26 and ARs interact with ADA at opposite sites, we have investigated if ADA can function as a cell-to-cell communication molecule by bridging the anchoring molecules CD26 and A2AR present on the surfaces of the interacting cells. By combining site-directed mutagenesis of ADA amino acids involved in binding to A2AR and a modification of the bioluminescence resonance energy transfer (BRET) technique that allows detection of interactions between two proteins expressed in different cell populations with low steric hindrance (NanoBRET), we show direct evidence of the specific formation of trimeric complexes CD26-ADA-A2AR involving two cells. By dynamic mass redistribution assays and ligand binding experiments, we also demonstrate that A2AR-NanoLuc fusion proteins are functional. The existence of this ternary complex is in good agreement with the hypothesis that ADA could bridge T-cells (expressing CD26) and dendritic cells (expressing A2AR). This is a new metabolic function for ecto-ADA that, being a single chain protein, it has been considered as an example of moonlighting protein, because it performs more than one functional role (as a catalyst, a costimulator, an allosteric modulator and a cell-to-cell connector) without partitioning these functions in different subunits.

Adenosine Deaminase (ADA)-Deficient Severe Combined Immune Deficiency (SCID): Molecular Pathogenesis and Clinical Manifestations

Deficiency of adenosine deaminase (ADA, EC3.5.4.4), a housekeeping enzyme of purine metabolism encoded by the Ada gene, is a cause of human severe combined immune deficiency (SCID). Numerous deleterious mutations occurring in the ADA gene have been found in patients with profound lymphopenia (T^- B^- NK^-), thus underscoring the importance of functional purine metabolism for the development of the immune defense. While untreated ADA SCID is a fatal disorder, there are multiple life-saving therapeutic modalities to restore ADA activity and reconstitute protective immunity, including enzyme replacement therapy (ERT), allogeneic hematopoietic stem cell transplantation (HSCT) and gene therapy (GT) with autologous gene-corrected hematopoietic stem cells (HSC). We review the pathogenic mechanisms and clinical manifestations of ADA SCID.

Adenosine Deaminases That Act on RNA (ADARs)

Inosine is one of the most common modifications found in human RNAs and the Adenosine Deaminases that act on RNA (ADARs) are the main enzymes responsible for its production. ADARs were first discovered in the 1980s and since then our understanding of ADARs has advanced tremendously. For instance, it is now known that defective ADAR function can cause human diseases. Furthermore, recently solved crystal structures of the human ADAR2 deaminase bound to RNA have provided insights regarding the catalytic and substrate recognition mechanisms. In this chapter, we describe the occurrence of inosine in human RNAs and the newest perspective on the ADAR family of enzymes, including their substrate recognition, catalytic mechanism, regulation as well as the consequences of A-to-I editing, and their relation to human diseases.

Nucleotides, Nucleosides, and Nucleobases

We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.

Bioproduction of ribavirin by green microbial biotransformation

•

Biotransformation of ribavirin was performed by E. coli ATCC 12407, reaching yields of 86%.

•

This mesophile microorganism was successfully stabilized in agarose and polyacrylamide.

•

Biocatalyst immobilized in agarose could be reused during 270 h without activity loss.

•

Packed-bed bioreactor prototype was able to produce 95 mg ribavirin.

Ribavirin is an antiviral compound widely used in Hepatitis C Virus therapy. Biotransformation of this nucleoside analogue using Escherichia coli ATCC 12407 as biocatalyst is herein reported. Reaction parameters such as microorganism amounts, substrate ratio and temperature were optimized reaching conversion yields of 86%. Biocatalyst stability was enhanced by immobilization in agarose matrix. This immobilized biocatalyst was able to be reused for more than 270 h and could be stored during more than 4 months without activity loss. Batch and packed-bed reactors based on a stabilized biocatalyst were assayed for bioprocess scale-up. A continuous sustainable bioprocess was evaluated using a prototype packed-bed reactor, which allowed to produce 95 mg of ribavirin.

Finally, in this work an efficient green bioprocess for ribavirin bioproduction using a stabilized biocatalyst was developed.

Temperature-driven differential gene expression by RNA thermosensors

Many prokaryotic genes are organized in operons. Genes organized in such transcription units are co-transcribed into a polycistronic mRNA. Despite being clustered in a single mRNA, individual genes can be subjected to differential regulation, which is mainly achieved at the level of translation depending on initiation and elongation. Efficiency of translation initiation is primarily determined by the structural accessibility of the ribosome binding site (RBS). Structured cis-regulatory elements like RNA thermometers (RNATs) can contribute to differential regulation of individual genes within a polycistronic mRNA. RNATs are riboregulators that mediate temperature-responsive regulation of a downstream gene by modulating the accessibility of its RBS. At low temperature, the RBS is trapped by intra-molecular base pairing prohibiting translation initiation. The secondary structure melts with increasing temperature thus liberating the RBS. Here, we present an overview of different RNAT types and specifically highlight recently discovered RNATs. The main focus of this review is on RNAT-based differential control of polycistronic operons. Finally, we discuss the influence of temperature on other riboregulators and the potential of RNATs in synthetic RNA biology. This article is part of a Special Issue entitled: Riboswitches.

Identification of a new class of adenosine deaminase from Helicobacter pylori with homologs among diverse taxa

Early studies of Helicobacter pylori's nutritional requirements alluded to a complete purine salvage network in this organism. Recently, this hypothesis was confirmed in two strains of H. pylori, whose purine requirements were satisfied by any single purine base or nucleoside. Most of the purine conversion enzymes in H. pylori have been studied using mutant analysis; however, the gene encoding adenosine deaminase (ADD) in H. pylori remained unidentified. Through stepwise protein purification followed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF), we discovered that H. pylori ADD is encoded by hp0267, an apparently essential gene. Hp0267 shares no sequence homology with previously characterized ADDs, yet both are members of the amidohydrolase superfamily. Hp0267 is grouped within cog0402, while other ADDs studied to date are found in cog1816. The hp0267 locus was previously misannotated as encoding a chlorohydrolase. Using purified recombinant Hp0267, we determined the enzyme's pH optimum, temperature optimum, substrate specificity, and estimated kinetic constants. In contrast to other known ADDs, Hp0267 contains Fe(II) as the relevant metal ligand. Furthermore, Hp0267 exhibits very low deaminase activity on 2'-deoxyadenosine, a substrate that is readily hydrolyzed by cog1816 ADDs. Our preliminary comparative genomic analysis suggests that Hp0267 represents a second enzyme class of adenosine deaminase whose phyletic distribution among prokaryotes is broad.

The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors

The enzyme adenosine deaminase (ADA) is a multifunctional protein that can both degrade adenosine and bind extracellularly to adenosine receptors, acting as an allosteric modulator regulating the hormonal effects of adenosine. The molecular regions of ADA responsible for the latter are unknown. In this work, alanine scanning mutagenesis of various ADA amino acid stretches, selected through in silico docking experiments, allowed us to identify regions of the enzyme responsible for modulating both its catalytic activity and its ability to modulate agonist binding to A and A adenosine receptors (AR and AR). The combination of computational and in vitro experiments show that the structural gate to the catalytic site; i.e., the α-1 helix containing residues L58-I72 and the loop containing residues A184-I188 of ADA, were important to maintain both the catalytic efficiency of the enzyme and its action as an allosteric modulator of the adenosine receptors. These data are consistent with a predicted supramolecular assembly, in which ADA bridges AR and CD26 and are in line with the notion that the interaction of ADA with adenosine receptors has an important role in the immunosynapse. We propose that it is the ADA open form, but not the closed one, that is responsible for the functional interaction with A₁R and A₂AR.

Adenosine deaminase-like protein 1 (ADAL1): characterization and substrate specificity in the hydrolysis of N(6)- or O(6)-substituted purine or 2-aminopurine nucleoside monophosphates

Human N(6)-methyl-AMP/dAMP aminohydrolase has been shown to be involved in metabolism of pharmacologically important N(6)-substituted purine nucleosides and 5'-monophosphate prodrugs thereof. This enzyme was cloned and expressed in E. coli, and mass spectroscopic analysis followed by amino acid sequence analyses indicated that the protein was adenosine deaminase-like protein isoform 1 (ADAL1). An extensive structure-activity relationship study showed that ADAL1 was able to catalyze removal of different alkyl groups not only from N(6)-substituted purine or 2-aminopurine nucleoside monophosphates but also from O(6)-substituted compounds. The ADAL1 activity was susceptible to modifications in the phosphate moiety but not to changes in the sugar moiety. Overall, our data indicated that ADAL1 specifically acts at the 6-position of purine and 2-aminopurine nucleoside monophosphates. Our results may help designing of new therapeutic nucleoside/nucleotide prodrugs with desired metabolic profiles. Furthermore, amino acid sequence analysis in conjunction with crystallographic data and metal analysis suggested that ADAL1 contains a catalytic zinc ion. Finally, a potential physiological role of ADAL1 is discussed.

Accumulation of gene-targeted Bacillus subtilis mutations that enhance fermentative inosine production

In order to test a possible approach to enhance fermentative inosine production by Bacillus subtilis, seven gene-targeted mutations were introduced in the laboratory standard strain168 in a stepwise fashion. The mutations were employed in order to prevent inosine 5'-monophosphate (IMP) from being consumed for AMP and GMP synthesis, to minimize inosine degradation, and to expand the intracellular IMP pool. First, the genes for adenylosuccinate synthase (purA) and IMP dehydrogenase (guaB) were inactivated. Second, two genes for purine nucleoside phosphorylase, punA and deoD, were inactivated. Third, to enhance purine nucleotide biosynthesis, the pur operon repressor PurR and the 5'-UTR of the operon, containing the guanine riboswitch, were disrupted. Finally, the -10 sequence of the pur promoter was optimized to elevate its transcription level. The resulting mutant was capable of producing 6 g/L inosine from 30 g/L glucose in culture broth without the detectable by-production of hypoxanthine. This indicates the validity of this approach for the breeding of the next generation of B. subtilis strains for industrial nucleoside production.

Isolation and characterization of a novel adenosine deaminase inhibitor, IADA-7, from Bacillus sp. J-89

Adenosine deaminase (ADA), an enzyme involved in purine metabolism, catalyzes the hydrolytic breakdown of adenosine into inosine and free ammonia. ADA regulation has been targeted as a potential therapeutic agent for viral infections and lymphoproliferative disorders. In this study, we isolated a novel ADA inhibitor from a culture of Bacillus sp. J-89, and evaluated its anti-proliferative activity on human cancer cell lines. The ADA inhibitor was deduced as a 2-N-methyl-2,4-diazacycloheptanone by analyses of UV, IR, EI-MASS, (1)H-NMR, (13)C-(1)H NMR, and (13)C-NMR spectroscopy, and was designated IADA-7. IADA-7 was shown to inhibit purified mammalian and Actinomyces ADA. IADA-7 also inhibited the proliferation of both Jurkat T cells (IC(50) = 15 microg/mL) and J 82 (human transitional-cell carcinoma, bladder) cells (IC(50) = 25 microg/mL). In Jurkat T cells, apoptosis with 15 microg/mL IADA-7 for 24 and 48 hours was 9 and 13%, respectively. These results suggest that IADA-7 can inhibit ADA activity in multiple species and that it may represent a good candidate as an anti-cancer therapeutic agent due to its demonstrated anti-proliferative activity on cancer cells.

Human adenosine deaminase as an allosteric modulator of human A(1) adenosine receptor: abolishment of negative cooperativity for [H](R)-pia binding to the caudate nucleus

It has been shown that adenosine deaminase (ADA; EC 3.5.4.4) behaves as an ecto-enzyme anchored to membrane proteins, among them A(1) adenosine receptors (A(1)Rs). Bovine ADA interacts with A(1)Rs from many species and regulates agonists binding to receptors in an activity-independent form. However, it was not known whether human ADA exerted any effect on the agonist binding to human A(1)Rs, because of both technical difficulties in obtaining pure human ADA and tissues containing human A(1)Rs. In this study, human ADA was purified to homogeneity. Taking in consideration that A(1)Rs form homodimers and taking advantage of a new procedure to fit binding data to receptors dimers, which allows to calculate ligand dissociation constants and the degree of cooperativity between the two subunits in the dimer, here it is demonstrated that human ADA markedly enhances the agonist and antagonist affinity and abolishes the negative cooperativity on agonist binding to human striatal A(1)Rs. ADA also increases the ability of the agonist to decrease the forskolin-induced cAMP levels. The results show that human ADA, apart from reducing the adenosine concentration and thus preventing A(1)R desensitization, binds to A(1)R behaving as an allosteric effector that markedly enhances agonist affinity and increases receptor functionality. The physiological role of the interaction is to make receptors more sensitive to adenosine. This powerful regulation has important implications for the physiology and pharmacology of neuronal A(1)Rs.

Molecular characterization and expression patterns of AMP deaminase1 (AMPD1) in porcine skeletal muscle

AMPD1 is the muscle-specific form of the AMPD multigene families in mammals and plays an important role in the purine nucleotide cycle and energy metabolism in skeletal muscle. In this study, we cloned and characterized AMPD1 from Sus scrofa muscle. The promoter of porcine AMPD1 contained several putative muscle-specific transcription factor binding sites (E box, myogenin, MEF2, Spl-CTF/NF-l), one RORalpha2 binding motif and NF-kappaB site. The deduced amino acid sequence of porcine AMPD1 contains an AMP deaminase signature sequence (SLSTDDP). RT-PCR analyses showed that AMPD1 was expressed specifically in skeletal muscle. Expression of AMPD1 was up-regulated during the muscle development and was higher in Yorkshire than in Meishan pigs. AMPD1 gene was expressed at higher levels in longissimus dorsi and bicepsfemoris muscles compared with soleus and masseter muscles in both Yorkshire and Meishan pigs. Moreover, we found that a single nucleotide polymorphism (SNP, T/C(426)) in exon12 of the AMPD1 gene was significantly associated with loin muscle area trait (p<0.01), loin muscle height (p<0.01) and average backfat thickness (p<0.05). This result suggests that the AMPD1 gene might be a candidate gene of meat production trait and provides useful information for further studies on its roles in porcine skeletal muscle.

Sequence similarity searching using the BLAST family of programs

Database sequence similarity searching is carried out thousands of times each day by researchers worldwide and has become a very valuable tool. Over the years, a number of algorithms have been implemented to facilitate database searching. The BLAST (Basic Local Alignment Research Tool) family of sequence similarity search programs allows searches to be done quickly and easily, but with sensitive, yet rigorous statistical expectations. In this unit, which is a completely new version of its predecessor of the same title, the user learns how to access the databases, determine the correct searching strategies, and apply examples of BLAST searches to his or her own data.

The extracellular adenosine deaminase growth factor, ADGF/CECR1, plays a role in Xenopus embryogenesis via the adenosine/P1 receptor

Adenosine deaminase-related growth factors (ADGF), also known as CECR1 in vertebrates, are a novel family of growth factors with sequence similarity to classical cellular adenosine deaminase. Although genes for ADGF/CECR1 have been identified in both invertebrates as well as vertebrates, their in vivo functions in vertebrates remain unknown. We isolated cDNA clones for two cerc 1s from Xenopus laevis. Both recombinant Xenopus CECR1s exhibited adenosine deaminase and growth factor activity, and the adenosine deaminase activity was found to be indispensable for growth factor activity. The Xenopus cerc 1s are expressed in the somites, pronephros, eyes, cement gland, neural tube, and neural floor plate of the embryos. Knock-down of these two genes using morpholino oligonucleotides caused a reduction in the body size and abnormalities of the body axis in the Xenopus embryos, accompanied by selective changes in the expression of developmental marker genes. Injection of adenosine, agonists for adenosine/P1 receptors, or adenosine deaminase inhibitor into late gastrula archenteron embryos resulted in developmental defects similar to those caused by morpholino oligonucleotide injection. These results show, for the first time, the involvement of CECR1s via the adenosine/P1 receptors in vertebrate embryogenesis via regulation of extracellular adenosine concentrations.

Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1)

Embryonic factor 1 (FAC1) is one of the earliest expressed plant genes and encodes an AMP deaminase (AMPD), which is also an identified herbicide target. This report identifies an N-terminal transmembrane domain in Arabidopsis FAC1, explores subcellular fractionation, and presents a 3.3-A globular catalytic domain x-ray crystal structure with a bound herbicide-based transition state inhibitor that provides the first glimpse of a complete AMPD active site. FAC1 contains an (alpha/beta)(8)-barrel characterized by loops in place of strands 5 and 6 that places it in a small subset of the amidohydrolase superfamily with imperfect folds. Unlike tetrameric animal orthologs, FAC1 is a dimer and each subunit contains an exposed Walker A motif that may be involved in the dramatic combined K(m) (25-80-fold lower) and V(max) (5-6-fold higher) activation by ATP. Normal mode analysis predicts a hinge motion that flattens basic surfaces on each monomer that flank the dimer interface, which suggests a reversible association between the FAC1 globular catalytic domain and intracellular membranes, with N-terminal transmembrane and disordered linker regions serving as the anchor and attachment to the globular catalytic domain, respectively.

Anti-inflammatory activity of non-nucleoside adenosine deaminase inhibitor FR234938

Adenosine has anti-inflammatory activity. Adenosine deaminase (EC 3.5.4.4) metabolizes extracellular adenosine, resulting in an exacerbation of inflammation. Consequently, it was hypothesized that adenosine deaminase inhibitors produce anti-inflammatory activity by increasing extracellular adenosine concentration. This group recently developed a non-nucleoside adenosine deaminase inhibitor, FR234938, by using rational structure-based drug design. FR234938 inhibits recombinant human adenosine deaminase enzyme competitively. FR234938 inhibits interleukin (IL)-6-dependent immunoglobulin (Ig) M production by SKW6.4 cells, in the presence of adenosine. Inhibitory effect of FR234938/adenosine combination is blocked by an A2a adenosine receptor antagonist. FR234938 also inhibits anti-type II collagen delayed type hypersensitivity (DTH) in a dose-dependent manner, both in the presence and absence of recombinant human adenosine deaminase. Moreover, FR234938 inhibits tumor necrosis factor (TNF)-alpha and IL-10 production in a lipopolysaccharide (LPS)-induced cytokine production model in mice. These results indicate that FR234938 has potential anti-inflammatory activity. Non-nucleoside adenosine deaminase inhibitor FR234938 has good potential as a new type of anti-rheumatic and anti-inflammatory drug, by modulating host-defense concentrations of adenosine.

Adenosine Deaminase in Nucleoside Synthesis. A Review

Adenosine deaminase (ADA) is an enzyme in the purine salvage pathway that catalyzes the deamination of adenosine and deoxyadenosine to inosine and deoxyinosine, respectively. This deamination is an important factor in limiting the usefulness of adenosine analogues in chemotherapy. However, the biocatalysis by ADA is also a useful transformation in enzymatic synthesis. In this review, examples from both the principal investigator's laboratory and from the literature, which depict the synthetic usefulness of this enzyme in deamination, dehalogenation, demethoxylation reactions and in diastereoisomeric resolution, are presented. It is not the intent of this review to comprehensively list all of the biotransformations induced by adenosine deaminase, but rather to present representative examples to highlight the powerful synthetic utility of this enzyme. A review with 72 references.

Phylogenetic analysis reveals a novel protein family closely related to adenosine deaminase

Adenosine deaminase (ADA) is a well-characterized enzyme involved in the depletion of adenosine levels. A group of proteins with similarity to ADA, the adenosine deaminase-related growth factors (ADGF; known as CECR1 in vertebrates), has been described recently in various organisms. We have determined the phylogenetic relationships of various gene products with significant amino acid similarity to ADA using parsimony and Bayesian methods, and discovered a novel paralogue, termed ADA-like (ADAL). The ADGF proteins share a novel amino acid motif, "MPKG," within which the proline and lysine residues are also conserved in the ADAL and ADA subfamilies. The significance of this new domain is unknown, but it is located just upstream of two ADA catalytic residues, of which all eight are conserved among the ADGF and ADAL proteins. This conservation suggests that ADGF and ADAL may share the same catalytic function as ADA, which has been proven for some ADGF members. These analyses also revealed that some genes previously thought to be classic ADAs are instead ADAL or ADGFs. We here define the ADGF, ADAL, ADA, adenine deaminase (ADE), and AMP deaminase (AMPD) groups as subfamilies of the adenyl-deaminase family. The availability of genomic data for the members of this family allowed us to reconstruct the intron evolution within the phylogeny and strengthen the introns-late hypothesis of the synthetic introns theory. This study shows that ADA activity is clearly more complex than once thought, perhaps involving a delicately balanced pattern of temporal and spatial expression of a number of paralogous proteins.

The emerging role of adenosine deaminases in insects

Adenosine deaminases catalyze the deamination of adenosine and deoxyadenosine into their respective inosine nucleosides. Recent sequencing of the genomes of several model organisms and human reveal that Metazoa usually have more than one adenosine deaminase gene. A deficiency in the gene encoding the major enzyme is lethal in mouse and Drosophila and leads to severe combined deficiency (SCID) in human. In these organisms, enzyme deficiency causes increased adenosine/deoxyadenosine concentration in body fluids and some organs. Elevated levels of adenosine and deoxyadenosine are toxic to certain mammalian and insect cells, and it was shown for human and mouse that it is a primary cause of pathophysiological effects. Data suggest that the major role of adenosine deaminases in various taxa is the protection of tissues against increased levels of adenosine and deoxyadenosine. This review also discusses potential roles of adenosine deaminases in Drosophila metamorphosis and the employment of a Drosophila model to study the cell-specific toxicity of elevated nucleoside levels.

Adenosine deaminase 2 from chicken liver: purification, characterization, and N-terminal amino acid sequence

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.

Sub-families of alpha/beta barrel enzymes: a new adenine deaminase family

No gene coding for an adenine deaminase has been described in eukaryotes. However, physiological and genetical evidence indicates that adenine deaminases are present in the ascomycetes. We have cloned and characterised the genes coding for the adenine deaminases of Aspergillus nidulans, Saccharomyces cerevisiae and Schizosaccharomyces pombe. The A.nidulans gene was expressed in Escherichia coli and the purified enzyme shows adenine but not adenosine deaminase activity. The open reading frames coded by the three genes are very similar and obviously related to the bacterial and eukaryotic adenosine deaminases rather than to the bacterial adenine deaminases. The latter are related to allantoinases, ureases and dihydroorotases. The fungal adenine deaminases and the homologous adenosine deaminases differ in a number of residues, some of these being clearly involved in substrate specificity. Other prokaryotic enzymes in the database, while clearly related to the above, do not fit into either sub-class, and may even have a different specificity. These results imply that adenine deaminases have appeared twice in the course of evolution, from different ancestral enzymes constructed both around the alpha/beta barrel scaffold.

N-terminal extensions of the human AMPD2 polypeptide influence ATP regulation of isoform L

Human tissues and cells express three AMP deaminase (AMPD) isoforms containing divergent N-terminal domains, and each member of the multigene family encoding these enzymes produces alternative transcripts that confer additional N-terminal divergence through extensions and cassette-type substitutions. Available data suggest that divergent N-terminal domains can influence AMPD isoform behavior, but the functional significance for additional divergence within each enzyme is unknown. Three isoform L (AMPD2) variants, 1A/2, 1B/2, and 1B/3, contain N-terminal extensions of 47, 128, and 53 amino acids, respectively. This study has determined the kinetic and regulatory behaviors of these three isoform L enzymes in the presence of positive (ATP) and negative (phosphate) allosteric effectors. All display nearly identical kinetic parameters and regulatory responses in the presence of phosphate alone, or in combination with ATP. Regulation by ATP is biphasic and the three isoform L enzymes also exhibit similar activation profiles and maximum initial velocities at 2-3mM in the presence of 1mM phosphate, whereas higher concentrations of phosphate suppress this activation. However, maximum initial velocities are achieved at lower ATP concentrations (0.8-1.5mM) in the absence of phosphate and under these conditions 1B/2 is less active, 1B/3 is more active, and 1A/2 is similarly active when compared to 1mM phosphate over the range of ATP concentrations found in non-muscle cells (0.8-3.7mM). These combined results suggest that isoform L enzymes are designed to function under different metabolic conditions encountered in the non-striated muscle environments where they are expressed.

Expression, purification, and inhibition of in vitro proteolysis of human AMPD2 (isoform L) recombinant enzymes

AMP deaminase (AMPD) is a multigene family in higher eukaryotes whose three members encode tetrameric isoforms that catalyze the deamination of AMP to IMP. AMPD polypeptides share conserved C-terminal catalytic domains of approximately 550 amino acids, whereas divergent N-terminal domains of approximately 200-330 amino acids may confer isoform-specific properties to each enzyme. However, AMPD polypeptides are subject to limited N-terminal proteolysis during purification and subsequent storage at 4 degrees C. This presents a technical challenge to studies aimed at determining the structural and functional significance of these divergent sequences. This study describes the recombinant overexpression of three naturally occurring human AMPD2 proteins, 1A/2, 1B/2, and 1B/3, that differ by N-terminal extensions of 47-128 amino acids, resulting from the use of multiple promoters and alternative splicing events. A survey of protease inhibitors reveals that E-64 and leupeptin are able to maintain the subunit structure of each AMPD2 protein when they are included in extraction and storage buffers. Gel filtration chromatography of these three purified AMPD2 enzymes comprised of intact subunits reveals that each migrates faster than expected, resulting in observed molecular masses significantly greater than those predicted for native tetrameric structures. However, chemical crosslinking analysis indicates four subunits per AMPD2 molecule, confirming that these enzymes have a native tetrameric structure. These combined results suggest that AMPD2 N-terminal extensions may exist as extended structures in solution.

Purification, substrate range, and metal center of AtzC: the N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism

N-Isopropylammelide isopropylaminohydrolase, AtzC, the third enzyme in the atrazine degradation pathway in Pseudomonas sp. strain ADP, catalyzes the stoichiometric hydrolysis of N-isopropylammelide to cyanuric acid and isopropylamine. The atzC gene was cloned downstream of the tac promoter and expressed in Escherichia coli, where the expressed enzyme comprised 36% of the soluble protein. AtzC was purified to homogeneity by ammonium sulfate precipitation and phenyl column chromatography. It has a subunit size of 44,938 kDa and a holoenzyme molecular weight of 174,000. The K(m) and k(cat) values for AtzC with N-isopropylammelide were 406 micro M and 13.3 s(-1), respectively. AtzC hydrolyzed other N-substituted amino dihydroxy-s-triazines, and those with linear N-alkyl groups had higher k(cat) values than those with branched alkyl groups. Native AtzC contained 0.50 eq of Zn per subunit. The activity of metal-depleted AtzC was restored with Zn(II), Fe(II), Mn(II), Co(II), and Ni(II) salts. Cobalt-substituted AtzC had a visible absorbance band at 540 nm (Delta epsilon = 84 M(-1) cm(-1)) and exhibited an axial electron paramagnetic resonance (EPR) signal with the following effective values: g((x)) = 5.18, g((y)) = 3.93, and g((z)) = 2.24. Incubating cobalt-AtzC with the competitive inhibitor 5-azacytosine altered the effective EPR signal values to g((x)) = 5.11, g((y)) = 4.02, and g((z)) = 2.25 and increased the microwave power at half saturation at 10 K from 31 to 103 mW. Under the growth conditions examined, our data suggest that AtzC has a catalytically essential, five-coordinate Zn(II) metal center in the active site and specifically catalyzes the hydrolysis of intermediates generated during the metabolism of s-triazine herbicides.

Clustered charged amino acids of human adenosine deaminase comprise a functional epitope for binding the adenosine deaminase complexing protein CD26/dipeptidyl peptidase IV

Human adenosine deaminase (ADA) occurs as a 41-kDa soluble monomer in all cells. On epithelia and lymphoid cells of humans, but not mice, ADA also occurs bound to the membrane glycoprotein CD26/dipeptidyl peptidase IV. This "ecto-ADA" has been postulated to regulate extracellular Ado levels, and also the function of CD26 as a co-stimulator of activated T cells. The CD26-binding site of human ADA has been localized by homolog scanning to the peripheral alpha2-helix (amino acids 126-143). Among the 5 non-conserved residues within this segment, Arg-142 in human and Gln-142 in mouse ADA largely determined the capacity for stable binding to CD26 (Richard, E., Arredondo-Vega, F. X., Santisteban, I., Kelly, S. J., Patel, D. D., and Hershfield, M. S. (2000) J. Exp. Med. 192, 1223-1235). We have now mutagenized conserved alpha2-helix residues in human and mouse ADA and used surface plasmon resonance to evaluate binding kinetics to immobilized rabbit CD26. In addition to Arg-142, we found that Glu-139 and Asp-143 of human ADA are also important for CD26 binding. Mutating these residues to alanine increased dissociation rates 6-11-fold and the apparent dissociation constant K(D) for wild type human ADA from 17 to 112-160 nm, changing binding free energy by 1.1-1.3 kcal/mol. This cluster of 3 charged residues appears to be a "functional epitope" that accounts for about half of the difference between human and mouse ADA in free energy of binding to CD26.

A Product Inhibition Study on Adenosine Deaminase by Spectroscopy and Calorimetry

Kinetic and thermodynamic studies have been made on the effect of the inosine product on the activity of adenosine deaminase in a 50 mM sodium phosphate buffer, pH 7.5, at 27 degrees C using UV spectrophotometry and isothermal titration calorimetry (ITC). A competitive inhibition was observed for inosine as a product of the enzymatic reaction. A graphical-fitting method was used for determination of the binding constant and enthalpy of inhibitor binding by using isothermal titration microcalorimetry data. The dissociation-binding constant is equal to 140 microM by the microcalorimetry method, which agrees well with the value of 143 microM for the inhibition constant that was obtained from the spectroscopy method

Functional cloning, heterologous expression, and purification of two different N-deoxyribosyltransferases from Lactobacillus helveticus

Lactobacillus helveticus contains two types of N-deoxyribosyltransferases: DRTase I catalyzes the transfer of 2'-deoxyribose between purine bases exclusively whereas DRTase II is able to transfer the 2'-deoxyribose between two pyrimidine or between pyrimidine and purine bases. An Escherichia coli strain, auxotrophic for guanine and unable to use deoxyguanosine as source of guanine, was constructed to clone the corresponding genes. By screening a genomic bank for the production of guanine, the L. helveticus ptd and ntd genes coding for DRTase I and II, respectively, were isolated. Although the two genes have no sequence similarity, the two deduced polypeptides display 25.6% identity, with most of the residues involved in substrate binding and the active site nucleophile Glu-98 being conserved. Overexpression and purification of the two proteins shows that DRTase I is specific for purines with a preference for deoxyinosine (dI) > deoxyadenosine > deoxyguanosine as donor substrates whereas DRTase II has a strong preference for pyrimidines as donor substrates and purines as base acceptors. Purine analogues were substrates as acceptor bases for both enzymes. Comparison of DRTase I and DRTase II activities with dI as donor or hypoxanthine as acceptor and colocalization of the ptd and add genes suggest a specific role for DRTase I in the metabolism of dI.

Adenosine deaminase deficiency with mosaicism for a "second-site suppressor" of a splicing mutation: decline in revertant T lymphocytes during enzyme replacement therapy

Four patients from 3 Saudi Arabian families had delayed onset of immune deficiency due to homozygosity for a novel intronic mutation, g.31701T>A, in the last splice acceptor site of the adenosine deaminase (ADA) gene. Aberrant splicing mutated the last 4 ADA amino acids and added a 43-residue "tail" that rendered the protein unstable. Mutant complementary DNA (cDNA) expressed in Escherichia coli yielded 1% of the ADA activity obtained with wild-type cDNA. The oldest patient, 16 years old at diagnosis, had greater residual immune function and less elevated erythrocyte deoxyadenosine nucleotides than his 4-year-old affected sister. His T cells and Epstein-Barr virus (EBV) B cell line had 75% of normal ADA activity and ADA protein of normal size. DNA from these cells and his whole blood possessed 2 mutant ADA alleles. Both carried g.31701T>A, but one had acquired a deletion of the 11 adjacent base pair, g.31702-12, which suppressed aberrant splicing and excised an unusual purine-rich tract from the wild-type intron 11/exon 12 junction. During ADA replacement therapy, ADA activity in T cells and abundance of the "second-site" revertant allele decreased markedly. This finding raises an important issue relevant to stem cell gene therapy.

Direct influence of S9 liver homogenate on fluorescence signals: impact on practical applications in a bacterial genotoxicity assay

Assays based on the bacterial SOS-response offer the possibility of automatization of genotoxicity testing for screening of large compound libraries. While existing assays use colorimetric detection or luminescence read-out, we describe here the use of a fluorescence-based system to achieve high sensitivity of detection required for assay miniaturization. Three commonly used fluorophores--fluorescein, DDAO and resorufin--are evaluated. Experimental evidence is given that S9 liver homogenate contains a heat-labile, reversible fluorophore-binding activity and therefore, significantly reduces fluorescence intensities. We have worked out simple solutions to overcome the S9 related interference in order to be able to establish a robust bacterial genotoxicity assay.

Localization of N-terminal sequences in human AMP deaminase isoforms that influence contractile protein binding

The reversible association of AMP deaminase (AMPD, EC 3.5.4.6) with elements of the contractile apparatus is an identified mechanism of enzyme regulation in mammalian skeletal muscle. All three members of the human AMPD multigene family contain coding information for polypeptides with divergent N-terminal and conserved C-terminal domains. In this study, serial N-terminal deletion mutants of up to 111 (AMPD1), 214 (AMPD2), and 126 (AMPD3) residues have been constructed without significant alteration of catalytic function or protein solubility. The entire sets of active enzymes are used to extend our understanding of the contractile protein binding of AMPD. Analysis of the most truncated active enzymes demonstrates that all three isoforms can associate with skeletal muscle actomyosin and suggests that a primary binding domain is located within the C-terminal 635-640 residues of each polypeptide. However, discrete stretches of N-terminal sequence alter this behavior. Residues 54-83 in the AMPD1 polypeptide contribute to a high actomyosin binding capacity of both isoform M spliceoforms, although the exon 2- enzyme exhibits significantly greater association compared to its exon 2+ counterpart. Conversely, residues 129-183 in the AMPD2 polypeptide reduce actomyosin binding of isoform L. In addition, residues 1-48 in the AMPD3 polypeptide dramatically suppress contractile protein binding of isoform E, thus allowing this enzyme to participate in other intracellular interactions.

Mollusk-derived growth factor: cloning and developmental expression in the central nervous system and reproductive tract of Aplysia

We have isolated and characterized an atrial gland cDNA that corrects the previously reported sequence for Aplysia atrial gland granule-specific antigen (AGSA), a glycoprotein of unknown function. We designated the protein mollusk-derived growth factor (MDGF) to distinguish the revised sequence from AGSA and to emphasize its similarity to an insect-derived growth factor (IDGF). We describe MDGF mRNA expression that suggests a possible role during embryonic development and CNS injury repair.

Tryptophan environment in adenosine deaminase. I. Enzyme modification with N-bromosuccinimide in the presence of adenosine and EHNA analogues

Adenosine deaminase from bovine cerebral hemisphere (white and gray matter) and spleen was treated with N-bromosuccinimide, a reagent known to oxidize selectively tryptophan residues in proteins. Spectrally observable tryptophan modification was accompanied by enzyme inactivation. Tsow graphics revealed that two Trps are essential for the activity of enzyme from both tissues. Enzyme inhibitors and substrate analogues, derivatives of erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA) and adenosine, were able to protect Trp against modification, and this effect correlated in general with the enzyme activity protection. In the presence of adenosine deaza analogues (the noninhibitor tubercidin among them) only two Trps were modified in the fully inactivated enzyme. In the presence of EHNA and its deaza analogues, full inactivation of the enzyme was accompanied by the modification of four Trps. The obtained data confirm the previous hypothesis about the presence on the enzyme of different binding sites for adenosine and EHNA derivatives that are responsible for the different effects on the enzyme conformation elicited by the corresponding derivatives. Moreover, these data allow us to suggest that Trp residues, still unidentified by X-ray analysis, are essential for the functioning of the enzyme.

Investigation of various genotype characteristics for inosine accumulation in Escherichia coli W3110

For the derivation of an inosine-overproducing strain from the wild type microorganism, it is known that the addition of an adenine requirement, removal of purine nucleoside hydrolyzing activity, removal of the feedback inhibition, and repression of key enzymes in the purine nucleotides biosynthetic pathway are essential. Thus, the disruption of purA (adenine requirement), deoD (removal of purine nucleosides phosphorylase activity), purR (derepression of the regulation of purine nucleotides biosynthetic pathway), and the insensitivity of the feedback inhibition of phosphoribosylpyrophosphate (PRPP) amidotransferase by adenosine 5'-monophosphate (AMP) and guanosine 5'-monophosphate (GMP) were done in the Escherichia coli strain W3110, and then the inosine productivity was estimated. In the case of using a plasmid harboring the PRPP amidotransferase gene (purF) that encoded a desensitized PRPP amidotransferase, purF disrupted mutants were used as the host strains. It was found that the innovation of the four genotypes brought about a small amount of inosine accumulation. Furthermore, an adenine auxotrophic mutant of E. coli showed inappropriate adenine use because its growth could not respond efficiently to the concentration of adenine added. As the presence of adenosine deaminase is well known in E. coli and it is thought to be involved in adenine use, a mutant disrupted adenosine deaminase gene (add) was constructed and tested. The mutant, which is deficient in purF, purA, deoD, purR, and add genes, and harboring the desensitized purF as a plasmid, accumulated about 1 g of inosine per liter. Although we investigated the effects of purR disruption and purF gene improvement, unexpectedly an increase in the inosine productivity could not be found with this mutant.