Purification of S-adenosyl-L-homocysteine hydrolase from Dictyostelium discoideum: reversible inactivation by cAMP and 2'-deoxyadenosine

NAD+ promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1

Nicotinamide adenine dinucleotide (NAD) is the redox cofactor of many enzymes, including the vast aldehyde dehydrogenase (ALDH) superfamily. Although the function of NAD(H) in hydride transfer is established, its influence on protein structure is less understood. Herein, we show that NAD+ -binding promotes assembly of the ALDH7A1 tetramer. Multiangle light scattering, small-angle X-ray scattering, and sedimentation velocity all show a pronounced shift of the dimer-tetramer equilibrium toward the tetramer when NAD+ is present. Furthermore, electron microscopy shows that cofactor binding enhances tetramer formation even at the low enzyme concentration used in activity assays, suggesting the tetramer is the active species. Altogether, our results suggest that the catalytically active oligomer of ALDH7A1 is assembled on demand in response to cofactor availability.

Dynamic dissociating homo-oligomers and the control of protein function

Homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. Such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. This review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of these equilibria to allosteric regulation by the non-covalent binding of ligands. A dynamic quaternary structure equilibria is described where the dissociated state can have alternate conformations that cannot reassociate to the original multimer; the alternate conformations dictate assembly to functionally distinct alternate multimers of finite stoichiometry. The functional distinction between different assemblies provides a mechanism for allostery. The requirement for dissociation distinguishes this morpheein model of allosteric regulation from the classical MWC concerted and KNF sequential models. These models are described alongside earlier dissociating allosteric models. The identification of proteins that exist as an equilibrium of diverse native quaternary structure assemblies has the potential to define new targets for allosteric modulation with significant consequences for further understanding and/or controlling protein structure and function. Thus, a rationale for identifying proteins that may use the morpheein model of allostery is presented and a selection of proteins for which published data suggests this mechanism may be operative are listed.

S-adenosylhomocysteine hydrolase is localized at the front of chemotaxing cells, suggesting a role for transmethylation during migration

Chemotaxis of bacteria requires regulated methylation of chemoreceptors. However, despite considerable effort in the 1980s, transmethylation has never been established as a component of eukaryotic cell chemotaxis. S-adenosylhomocysteine (SAH), the product formed when the methyl group of the universal donor S-adenosylmethionine (SAM) is transferred to an acceptor molecule, is a potent inhibitor of all transmethylation reactions. In eukaryotic cells, this inhibition is relieved by hydrolysis of SAH to adenosine and homocysteine catalyzed by SAH hydrolase (SAHH). We now report that SAHH, which is diffuse in the cytoplasm of nonmotile Dictyostelium amoebae and human neutrophils, concentrates with F-actin in pseudopods at the front of motile, chemotaxing cells, but is not present in filopodia or at the very leading edge. Tubercidin, an inhibitor of SAHH, inhibits both chemotaxis and chemotaxis-dependent cell streaming of Dictyostelium, and chemotaxis of neutrophils at concentrations that have little effect on cell viability. Tubercidin does not inhibit starvation-induced expression of the cAMP receptor, cAR1, or G protein-mediated stimulation of adenylyl cyclase activity and actin polymerization in Dictyostelium. Tubercidin has no effect on either capping of Con A receptors or phagocytosis in Dictyostelium. These results add SAHH to the list of proteins that redistribute in response to chemotactic signals in Dictyostelium and neutrophils and strongly suggest a role for transmethylation in chemotaxis of eukaryotic cells.

Inhibition of S-adenosyl-L-homocysteine hydrolase by adrenaline in isolated guinea-pig papillary muscles

Purified S-adenosyl-L-homocysteine hydrolase from Dictyostelium discoideum or rabbit erythrocytes is inactivated when incubated with cAMP. The aim of this study was to investigate whether adrenaline, which increases cytosolic cAMP and calcium concentrations, is able to modify in situ the activity of S-adenosyl-L-homocysteine hydrolase in the heart. The enzyme was assayed in a crude extract obtained from superfused guinea-pig papillary muscles with the different tested substances. Adrenaline was found to inhibit S-adenosyl-L-homocysteine hydrolase in papillary muscles in a concentration-dependent fashion. This inhibition was associated with an increase in the concentration of S-adenosyl-L-homocysteine (326%), and a decrease of adenosine (40%). beta-Adrenoceptors are involved in the effect of adrenaline, since isoproterenol, a beta-adrenergic agonist, inhibited the enzyme, whereas the beta-adrenergic blocker, propranolol, prevented this inhibition. Participation of calcium in the inhibitory effect of adrenaline was suggested because the calcium channel blocker, verapamil, suppressed this inhibition, and high calcium in the perfusion medium inhibited the enzyme. In vitro experiments with calcium were performed in a semi-purified fraction of the enzyme, resulting in a concentration-dependent inhibition of the enzyme. Calcium concentration, which inhibited the enzyme 50%, was in the millimolar range for control and in the micromolar range for the obtained enzyme from adrenaline-treated muscles, indicating a different sensitivity to calcium inhibition. We conclude that adrenaline inhibits S-adenosyl-L-homocysteine hydrolase in situ, probably by a calcium-modulated mechanism.

The gene and pseudogenes of rat S-adenosyl-L-homocysteine hydrolase

Two rat liver genomic DNA libraries constructed in lambda DASH and lambda Charon 4A were screened for sequences with similarity to S-adenosyl-L-homocysteine (AdoHcy) hydrolase cDNA. Of 36 clones purified, two contained the AdoHcy hydrolase gene sequence and 34 contained pseudogene sequences. The AdoHcy hydrolase gene, which has been sequenced in its entirety, spans approximately 15 kb and consists of 10 exons. Primer extension and S1 experiments show that transcription is initiated from two major initiation sites located at positions -63 and -62 from the starting codon and from several minor sites. The promoter region is located in a CpG island, sequence TATTTAAA is present 23 bases upstream from the transcription start site, and an inverted CCAAT box is located 285 bp upstream from the transcription start site. Other potential transcription-factor binding sites including SP1, AP-2, GRE and Oct-1 sites were identified in the 5'-flanking region. Several different processed pseudogenes were found and analyzed.

Comparison of the inhibition of type A and type B S-adenosylhomocysteine hydrolase: effects of cofactor content on inhibition behavior and nucleoside binding

The enzyme S-adenosylhomocysteine hydrolase (E.C.3.3.1.1) occurs in two forms in bovine liver: Type A, which carries four moles of NAD+ per mole of enzyme tetramer, and Type B, which carries two moles of NAD+ per mole of tetramer. The inhibition of these two forms of the enzyme with 2',2'-difluoro-2'-deoxyadenosine has been investigated. The studies examined the binding stoichiometry and stability of the enzyme-inhibitor complexes formed from each type of the enzyme, the degree of NAD+ reduction and NAD+ release, and the possibility of covalent bond formation between the enzyme and the inhibitor. Significant differences in the behavior of the two forms of the enzyme were encountered which may have important implications for the design of S-adenosylhomocysteine hydrolase inhibitors as therapeutic agents.

S-adenosylhomocysteine hydrolase from the thermophilic archaeon Sulfolobus solfataricus: purification, physico-chemical and immunological properties

S-Adenosylhomocysteine hydrolase from Sulfolobus solfataricus, a thermoacidophilic archaeon optimally growing at 87 degrees C, has been purified to homogeneity. The specific activity of the homogeneous enzyme is 161 nmol of S-adenosylhomocysteine formed per min per mg of protein, and the overall yield, by immunoaffinity purification, is 51%. The enzyme has a molecular mass of 190 kDa, is composed of four identical subunits (subunit mass 47 kDa), and contains four molecules of tightly-bound NAD+ per tetramer of which about 40% is in the reduced form. Physico-chemical features, including amino-acid composition and secondary structure, are reported. The pure protein, used to raise specific rabbit antisera, shows immunological properties different from other S-adenosylhomocysteine-metabolizing enzymes. The enzyme is thermophilic with an optimum temperature of 75 degrees C, and shows an apparent melting temperature of 95 degrees C by measuring its residual activity after 10 min incubation at increasing temperatures.

9-(5',6'-dideoxy-beta-D-ribo-hex-5'-ynofuranosyl)adenine, a novel irreversible inhibitor of S-adenosylhomocysteine hydrolase

The acetylenic analogue of adenosine 9-(5',6'-dideoxy-beta-D-ribo-hex-5'-ynofuranosyl)adenine has been synthesized, and its behavior as an inhibitor of bovine S-adenosylhomocysteine hydrolase has been examined. Incubation of the enzyme with excess inhibitor caused a time-dependent, irreversible inactivation of the enzyme that was accompanied by the reduction of two equivalents of NAD+ to NADH and the loss of the two remaining equivalents of NAD+. With use of radiolabeled inhibitor, it was established that 4 equiv of the acetylenic analog bind irreversibly to the enzyme and that 4 equiv were required to inactivate the enzyme completely. The inactivated enzyme could not be reactivated by incubation with NAD+. Denaturation studies revealed that 2 equiv of the inhibitor are bound more tightly to the enzyme than the remainder, suggesting the formation of a covalent linkage between the oxidized inhibitor and the enzyme. The putative covalent linkage was found to be acid sensitive but stable to mild base. The linkage could not be stabilized by treatment of the enzyme-inhibitor complex with either borohydride or cyanoborohydride. A Kl of 173 nM was measured for the inhibitor, making it one of the more potent inhibitors that have been reported. The enzyme used in these studies was isolated by modification of an affinity chromatography method reported by Narayanan and Borchardt [(1988) Biochim. Biophys. Acta 965, 22-28]. The affinity chromatography unexpectedly led to the isolation of two forms of the enzyme. The major form contained 4.0 mol of nucleotide cofactor/mol of enzyme tetramer, while the minor form carried only 2.0 mol/tetramer.

Rat liver S-adenosylhomocysteinase. Spectrophotometric study of coenzyme binding

Rat liver S-adenosylhomocysteinase, a homotetramer, was resolved by treatment with acid ammonium sulfate into apoenzyme and NAD. The apoenzyme thus prepared retained a tetrameric structure but differed in the mobility on nondenaturing polyacrylamide gel electrophoresis. The inactive apoenzyme was reactivated upon incubation with NAD. The restoration of activity paralleled with the tight binding of NAD to apoenzyme, and full activity was obtained when 4 mol of NAD were bound per mol of apoenzyme. The kinetics of reconstitution were apparently biphasic and suggest the existence of two conformers in a slow equilibrium, one of which binds the coenzyme rapidly while the other does so very slowly, if at all. In addition to NAD, apoadenosylhomocysteinase tightly bound nicotinamide hypoxanthine dinucleotide, 3-acetylpyridine adenine dinucleotide and nicotinic acid-adenine dinucleotide. NADP was not bound. Catalytic activity was found only with the enzyme reconstituted with NAD or nicotinamide hypoxanthine dinucleotide. The spectral change observed on interaction of apoadenosylhomocysteinase with NAD was similar to those seen with adenine nucleotides, and was largely approximated by the addition of dioxane to aqueous solutions of adenine nucleotides. By comparison of the difference spectra, it is suggested that the adenine portion of the coenzyme is bound in the hydrophobic pocket of the protein, and that the binding is accompanied by perturbation of tryptophan residue of the protein.

ATP formation from deoxyadenosine in human erythrocytes: evidence for a hitherto unidentified route involving adenine and S-adenosylhomocysteine hydrolase

A novel route of ATP formation has been identified using erythrocytes from patients deficient in four different enzymes associated with ATP formation. It entails prior adenine production from deoxyadenosine (or adenosine) in a reaction involving S-adenosylhomocysteine hydrolase. The postulated route has been demonstrated in human erythrocytes which, unlike other human cells, cannot form ATP from IMP. It is based on studies by others using purified S-adenosylhomocysteine hydrolase preparations in vitro. The results provide the first confirmation that this reaction occurs in intact human cells in vitro and thus most probably in vivo. This adenine production is normally masked in intact cells by further metabolism to ATP. Clinical significance for such a route is suggested by the fact that some adenosine analogues with potent oncostatic and antiviral properties also release adenine (or analogues) in vitro.

Cloning of a cDNA for the S-adenosyl-L-homocysteine hydrolase from Dictyostelium discoideum

We screened a cDNA library of the primitive eukaryote Dictyostelium discoideum constructed in the expression vector lambda gt11 with a specific antiserum directed against S-adenosyl-L-homocysteine hydrolase (AdoHcy hydrolase) and isolated cDNA clones coding for fusion proteins with beta-galactosidase. The identity of the largest of these clones was further assessed by analysis of hybrid-selected in vitro translation products. Using the cDNA as a probe, we showed that only one gene coding for AdoHcy hydrolase is present per genome and that a single transcript of 1.6 kb could be detected at various stages of differentiation. The nucleotide sequence of the cDNA was determined. It corresponds to the carboxyterminal half of the protein whose primary structure is highly homologous to the AdoHcy hydrolase from rat liver. The significance of this strong conservation of AdoHcy hydrolase in the course of evolution is discussed.

Amino acid sequence of S-adenosyl-L-homocysteine hydrolase from Dictyostelium discoideum as deduced from the cDNA sequence

S-Adenosyl-L-homocysteine hydrolase has been cloned from a lambda gt11 cDNA library prepared from Dictyostelium discoideum that had been starved for 3 hours. The sequence of the cloned cDNA was determined and the deduced amino acid sequence was compared to the amino acid sequence of rat AdoHcy hydrolase. When the sequences from the two species were aligned, 74% of the amino acids were in identical positions. If conservative changes were taken into account the homology was 84%. Because differences have been reported in the binding characteristics of NAD+ to the D. discoideum and rat AdoHcy hydrolases, changes in the amino acids of the putative NAD+-binding site were of particular interest. Six changes were observed in this region but the changes appeared to be in regions that are not critical to the three dimensional folding of the NAD+-binding site.

Purification of bovine liver S-adenosylhomocysteine hydrolase by affinity chromatography on blue dextran-agarose

S-Adenosylhomocysteine (AdoHcy) hydrolase (adenosylhomocysteinase, EC 3.3.1.1) was purified from bovine liver by conventional protein purification procedures (differential centrifugation, ammonium sulfate fractionation and DEAE-cellulose chromatography) followed by affinity chromatography on blue dextran coupled to agarose. The enzyme was eluted from the blue dextran-agarose column with adenosine and the adenosine was removed by chromatography on Sephadex G-75. The affinity chromatography step resulted in a substantial increase in total AdoHcy hydrolase activity (about 600%) suggesting either removal of some inhibitory substance or a change in the structure of the protein producing a more catalytically efficient enzyme. The isolation procedure afforded over 3400-fold purification of the enzyme, which was shown to be homogeneous by polyacrylamide gel electrophoresis. Using high pressure liquid chromatography, the nucleotide content of the freshly purified enzyme was determined to be 2 mol of nicotinamide adenine nucleotide per mol of enzyme tetramer. The ratio of the reduced to the oxidized form of the nucleotide was correlated to the activity of the enzyme preparation.

S-adenosylmethionine, S-adenosylhomocysteine and S-adenosylhomocysteine hydrolase variations during differentiation of Dictyostelium discoideum

We have analyzed the level of substrate (AdoMet) and products (AdoHcy) of transmethylations throughout the developmental cycle of the primitive eukaryote Dictyostelium discoideum. The ratio AdoMet/AdoHcy varied dramatically during differentiation. The intracellular level of AdoHcy decreased sharply after the beginning of starvation reaching a value of 18% of that in vegative cells within 4 h. In contrast, there was a two-fold transient increase in AdoMet at the time of aggregation. However, these changes were not related to changes in AdoHcy hydrolase since constant levels of both the protein and the activity were found until 16 h of differentiation. In particular, there was no indication of an in vivo inactivation of the enzyme by cAMP at the time of aggregation. These results are discussed with respect to the previously postulated role of AdoHcy hydrolase in the regulation of the AdoMet/AdoHcy ratio in eukaryotic cells.

Covalent labelling of ligand binding sites of human placental S-adenosylhomocysteine hydrolase with 8-azido derivatives of adenosine and cyclic AMP

S-Adenosylhomocysteine hydrolase (AdoHcyase) has previously been identified as a cytoplasmic adenosine and cyclic AMP binding protein. In order to examine the relationship between the adenosine and cyclic AMP binding sites on this enzyme we have explored the use of 8-azido analogues of adenosine and cyclic AMP as photoaffinity reagents for covalently labelling AdoHcyase purified from human placenta. 8-Azidoadenosine (8-N3-Ado), like adenosine, inactivated AdoHcyase, and the rate of inactivation was greatly increased by periodate oxidation. In addition, 8-N3-Ado was found to participate in the first step in the catalytic mechanism for AdoHcyase, resulting in conversion of enzyme-bound NAD+ to NADH, although it was not a substrate for the full enzyme-catalysed reaction. Radioactively labelled 8-N3-Ado, its periodate-oxidized derivative and 8-azidoadenosine 3', 5'-phosphate (8-N3-cAMP) bound specifically to adenosine binding sites on AdoHcyase and, after irradiation, became covalently linked to the enzyme. Photoaffinity-labelled enzyme could be precipitated by monoclonal antibody to human AdoHcyase. Two observations suggested that cyclic AMP and adenosine bind to the same sites on AdoHcyase. First cyclic AMP and adenosine each blocked binding of both radioactively labelled 8-N3-Ado and 8-N3-cAMP, and second, digestion with V8 proteinase generated identical patterns of peptides from AdoHcyase that had been photolabelled with [32P]8-N3-cAMP and [3H]8-N3-Ado. Binding sites for cyclic AMP on AdoHcyase were found to differ functionally and structurally from cyclic AMP binding sites on the R1 regulatory subunit of cyclic AMP-dependent protein kinase.

Inactivation of S-adenosyl-L-homocysteine hydrolase by cAMP results from dissociation of enzyme-bound NAD+

S-Adenosyl-L-homocysteine hydrolase (EC 3.3.1.1) is inactivated by cAMP and also by 2'-deoxyadenosine, and in both cases, activity is restored by incubating the inactivated enzyme with NAD+. We have previously presented evidence that, despite these similarities, inactivation by these two ligands proceeds by different mechanisms. We have now used a fluorescence technique to quantitate enzyme-bound NAD+ and NADH on S-adenosyl-L-homocysteine hydrolase from Dictyostelium discoideum, and we have confirmed that cAMP and 2'-deoxyadenosine inactivate by different mechanisms. Whereas inactivation by 2'-deoxyadenosine is due to reduction of the enzyme-bound NAD+ to NADH, incubation of S-adenosyl-L-homocysteine hydrolase with cAMP results in dissociation of the enzyme-bound NAD+. The dissociation is reversible, and reactivation likely occurs by restoration of the initial NAD+ content. This reversible inactivation by cAMP may be a mechanism of controlling biological methylation reactions by adjusting intracellular concentrations of S-adenosyl-L-homocysteine through action of S-adenosyl-L-homocysteine hydrolase.

Inactivation of S-adenosylhomocysteine hydrolase by nucleosides

The irreversible inactivation of S-adenosylhomocysteine hydrolase purified from hamster and bovine liver by adenosine analogs substituted in the 5' and 2 positions has been investigated in detail. 5'-Cyano-5'-deoxyadenosine inactivates as potently as 9-beta-D-arabinofuranosyladenine (Ara-A). Substitution of the Ara-A at the 2 position by halogens or deleting N at the 3 position decreases its potency. Although weak, 2',3'-dideoxyadenosine can also inactivate the enzyme. The irreversible inactivation of the hydrolase in rat hepatocytes incubated with 2-chloroadenosine or 3-deaza-Ara-A could be demonstrated, concomitant with increases in 35S-labeled S-adenosylhomocysteine and S-adenosylmethionine in the hepatocytes.

[Mode of action of cyclic amp in prokaryotes and eukaryotes, CAP and cAMP-dependent protein kinases]

cAMP is an ubiquitous compound which is involved in the regulation of many biological processes. In bacteria such as E. coli, cAMP mediates the activation of catabolic operons via the CAP protein. The CAP-cAMP complex, whose tridimensional structure has recently been established, binds to the promoter regions of catabolic operons at a specific site, and activates their transcription by inducing RNA polymerase to bind and initiate transcription at the correct site. Various phenomenons including protein-protein interactions or CAP-induced DNA bending or kinking could be involved in the process of forming the open transcription complex. In eukaryotes, cAMP activates cAMP dependent protein kinases which covalently modify proteins by phosphorylation on serine or threonine residues. The catalytically inactive holoenzyme is generally a tetramer containing two regulatory subunits, each capable of binding two molecules of cAMP, and two catalytic subunits. In mammalian cells, two types of cAMP dependent protein kinases (I and II) can be distinguished on the basis of their regulatory subunits; their relative proportion varies from tissue to tissue. Binding of cAMP to the regulatory subunits induces the dissociation of the holoenzyme and releases the free and active catalytic subunits. Phosphorylation of proteins occurs at sequences containing two basic residues in the vicinity of the phosphorylated serine or threonine. A heat-stable protein, present in most eukaryotic cells, specifically interacts with the catalytic subunit and inhibits its activity. The amino-acid sequence of cAMP dependent protein kinases has recently been determined. It is interesting to note that the domains responsible for cAMP binding by the regulatory subunits of mammalian cAMP dependent protein kinases and CAP share important sequence homologies. The same phenomenon is observed concerning the domain responsible for ATP binding to the catalytic subunit of cAMP dependent protein kinases and that of tyrosine-specific protein kinases from oncoviruses. Other eukaryotic proteins such as S-adenosyl-L-homocysteine (SAH) hydrolase are also capable of binding cAMP. The latter is involved in the regulation of S-adenosyl-L-methionine dependent methylations, and its activity could be affected by cAMP. Besides its role as an effector of enzymatic activity via phosphorylation, such as in the regulation of glycogen metabolism, cAMP has recently been shown to activate the transcription of a number of eukaryotic genes. This process probably also involves protein phosphorylation, but its precise mechanism remains to be understood.