The PDE-Opathies: Diverse Phenotypes Produced by a Functionally Related Multigene Family.

The phosphodiesterase (PDE)-opathies, an expanding set of disorders caused by germline mutations in cyclic nucleotide PDEs, present an intriguing paradox. The enzymes encoded by the PDE family all hydrolyze cAMP and/or cGMP, but mutations in different family members produce very divergent phenotypes. Three interacting factors have been shown recently to contribute to this phenotypic diversity: (i) the 21 genes encode over 80 different isoforms, using alternative mRNA splicing and related mechanisms; (ii) the various isoforms have different regulatory mechanisms, mediated by their unique amino-terminal regulatory domains; (iii) the isoforms differ widely in their pattern of tissue expression. These mechanisms explain why many PDE-opathies are gain-of-function mutations and how they exemplify uniqueness and redundancy within a multigene family.

Expression and localization of phosphodiesterase 2A in the submandibular gland of mice.

OBJECTIVES: Phosphodiesterases comprise a superfamily of enzymes that hydrolyze and inactivate cyclic AMP (cAMP) and/or cyclic GMP (cGMP), thereby regulating cellular signaling mechanisms. We herein investigated the production of phosphodiesterase 2A (PDE2A) in the mouse submandibular gland. DESIGN: The expression and localization of the mRNA and protein of PDE2A were examined in the submandibular gland of male and female mice using the reverse transcription-polymerase chain reaction, in situ hybridization, Western blotting, and immunohistochemistry. RESULTS: Among the different species of phosphodiesterases examined in the mouse submandibular gland, PDE2A, which hydrolyzes cAMP and cGMP, exhibited a marked sexual difference; it was more abundantly expressed in females. The mRNA and protein signals for PDE2A were intense in all acinar and duct portions, including the striated duct, in females, whereas in males, these signals were markedly weaker in the granular convoluted duct, the counterpart of the female striated duct, than in acini and other duct portions. Furthermore, the signals for protein kinases A and G1, which are intracellular effectors of cAMP and cGMP, respectively, were markedly weaker in the male granular convoluted duct. CONCLUSIONS: These results suggest that cyclic nucleotide-dependent signaling mechanisms function poorly in granular convoluted duct cells in the mouse submandibular gland.

First report of in vitro selection of RNA aptamers targeted to recombinant Loxosceles laeta spider toxins.

BACKGROUND: Loxoscelism is the envenomation caused by the bite of Loxosceles spp. spiders. It entails severe necrotizing skin lesions, sometimes accompanied by systemic reactions and even death. There are no diagnostic means and treatment is mostly palliative. The main toxin, found in several isoforms in the venom, is sphingomyelinase D (SMD), a phospholipase that has been used to generate antibodies intended for medical applications. Nucleic acid aptamers are a promising alternative to antibodies. Aptamers may be isolated from a combinatorial mixture of oligonucleotides by iterative selection of those that bind to the target. In this work, two Loxosceles laeta SMD isoforms, Ll1 and Ll2, were produced in bacteria and used as targets with the aim of identifying RNA aptamers that inhibit sphingomyelinase activity. RESULTS: Six RNA aptamers capable of eliciting partial but statistically significant inhibitions of the sphingomyelinase activity of recombinant SMD-Ll1 and SMD-Ll2 were obtained: four aptamers exert ~17% inhibition of SMD-Ll1, while two aptamers result in ~25% inhibition of SMD-Ll2 and ~18% cross inhibition of SMD-Ll1. CONCLUSIONS: This work is the first attempt to obtain aptamers with therapeutic and diagnostic potential for loxoscelism and provides an initial platform to undertake the development of novel anti Loxosceles venom agents.

First report of in vitro selection of RNA aptamers targeted to recombinant Loxosceles laeta spider toxins

BACKGROUND: Loxoscelism is the envenomation caused by the bite of Loxosceles spp. spiders. It entails severe necrotizing skin lesions, sometimes accompanied by systemic reactions and even death. There are no diagnostic means and treatment is mostly palliative. The main toxin, found in several isoforms in the venom, is sphingomyelinase D (SMD), a phospholipase that has been used to generate antibodies intended for medical applications. Nucleic acid aptamers are a promising alternative to antibodies. Aptamers may be isolated from a combinatorial mixture of oligonucleotides by iterative selection of those that bind to the target. In this work, two Loxosceles laeta SMD isoforms, Ll1 and Ll2, were produced in bacteria and used as targets with the aim of identifying RNA aptamers that inhibit sphingomyelinase activity. RESULTS: Six RNA aptamers capable of eliciting partial but statistically significant inhibitions of the sphingomyelinase activity of recombinant SMD-Ll1 and SMD-Ll2 were obtained: four aptamers exert ~17% inhibition of SMD-Ll1, while two aptamers result in ~25% inhibition of SMD-Ll2 and ~18% cross inhibition of SMD-Ll1. CONCLUSIONS: This work is the first attempt to obtain aptamers with therapeutic and diagnostic potential for loxoscelism and provides an initial platform to undertake the development of novel anti Loxoscelesvenom agents.

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.

Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21,900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins.

Phosphodiesterase inhibitors as a new generation of antiprotozoan drugs: exploiting the benefit of enzymes that are highly conserved between host and parasite.

Protozoan infections remain a major unsolved medical problem in many parts of our world. A major obstacle to their treatment is the blatant lack of medication that is affordable, effective, safe and easy to administer. For some of these diseases, including human sleeping sickness, very few compounds are available, many of them old and all of them fraught with toxic side effects. We explore a new concept for developing new-generation antiprotozoan drugs that are based on phosphodiesterase (PDE) inhibitors. Such inhibitors are already used extensively in human pharmacology. Given the high degree of structural similarity between the human and the protozoan PDEs, the vast expertise available in the human field can now be applied to developing disease-specific PDE inhibitors as new antiprotozoan drugs.

Phosphodiesterase inhibitors: factors that influence potency, selectivity, and action.

Cyclic nucleotide phosphodiesterases (PDEs) are promising targets for pharmacological intervention. The presence of multiple PDE genes, diversity of the isoforms produced from each gene, selective tissue and cellular expression of the isoforms, compartmentation within cells, and an array of conformations of PDE proteins are some of the properties that challenge the development of drugs that target these enzymes. Nevertheless, many of the characteristics of PDEs are also viewed as unique opportunities to increase specificity and selectivity when designing novel compounds for certain therapeutic indications. This chapter provides a summary of the major concepts related to the design and use of PDE inhibitors. The overall structure and properties of the catalytic domain and conformations of PDEs are summarized in light of the most recent X-ray crystal structures. The distinctive properties of catalytic domains of different families as well as the technical challenges associated with probing PDE properties and their interactions with small molecules are discussed. The effect of posttranslational modifications and protein-protein interactions are additional factors to be considered when designing PDE inhibitors. PDE inhibitor interaction with other proteins needs to be taken into account and is also discussed.

Differential function of phosphodiesterase families in the brain: gaining insights through the use of genetically modified animals.

Phosphodiesterases (PDEs) are the only known enzymes to degrade cAMP and cGMP, intracellular signaling molecules key to numerous cellular functions. There are 11 PDE families identified to date, and each is expressed in a unique pattern across brain regions. Here, we review genetic mouse models in which PDEs are either directly manipulated (e.g., genetically deleted) or are changed in a compensatory manner due to the manipulation of another target. We believe these genetic mouse models have contributed to our understanding of how the PDE1, PDE4, and PDE10 families contribute uniquely to overall brain function.

Phosphodiesterases in the central nervous system.

Phosphodiesterases (PDEs) represent important cornerstones of cGMP signaling in various tissues. Since the discovery of PDE activity in 1962, it has become clear that the functional characteristics of PDEs and their role in cyclic nucleotide signaling are fairly complex. On the one hand, members of the PDE family responsible for the hydrolysis of cGMP affect cellular responses by shaping cGMP signals derived from the activation of soluble cytosolic and/or membrane bound particulate guanylyl cyclases. Conversely, PDEs may function as downstream effectors in the cGMP signaling cascade. To make things even more sophisticated, cGMP modulates the activity of several PDEs either directly, by binding to a regulatory domain, or indirectly, through phosphorylation, and the result can be either inhibition or stimulation of the enzyme, depending on the subtype. Furthermore, cross-talk between cGMP and cAMP signaling is achieved by cGMP-dependent modulation of PDEs hydrolyzing cAMP and vice versa. Mammals possess at least 21 PDE genes and often express a set of PDEs in a tissue- and differentiation-dependent manner. Given these premises, it is still a challenging task to elucidate the physiological function(s) of individual PDE genes. The present chapter focuses on the role of PDEs as regulators of neuronal functions. Useful information regarding this topic has been gained by studying (1) the expression pattern of PDEs in the CNS, (2) the association of PDEs with specific macromolecular signaling complexes and (3) the phenotypes associated with mutations or ablation of PDE genes in man, mice and fruit flies, respectively. PDEs degrading cGMP and/or being regulated by cGMP have been implicated in cognition and learning, Parkinson's disease, attention deficit hyperactivity disorder, psychosis and depression. Correspondingly, modulators of PDEs have become attractive tools for treatment of these disorders of CNS function.

2',3'-Cyclic nucleotide 3'-phosphodiesterase: a novel RNA-binding protein that inhibits protein synthesis.

2',3'-Cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins to be specifically expressed in differentiating oligodendrocytes (ODCs) in the central nervous system (CNS) and is implicated in myelin biogenesis. CNP possesses an in vitro enzymatic activity, whose in vivo relevance remains to be defined, because substrates with 2',3,-cyclic termini have not yet been identified. To characterize CNP function better, we previously determined the structure of the CNP catalytic domain by NMR. Interestingly, the structure is remarkably similar to the plant cyclic nucleotide phosphodiesterase (CPDase) from A. thaliana and the bacterial 2'-5' RNA ligase from T. thermophilus, which are known to play roles in RNA metabolism. Here we show that CNP is an RNA-binding protein. Furthermore, by using precipitation analyses, we demonstrate that CNP associates with poly(A)(+) mRNAs in vivo and suppresses translation in vitro in a dose-dependent manner. With SELEX, we isolated RNA aptamers that can suppress the inhibitory effect of CNP on translation. We also demonstrate that CNP1 can bridge an association between tubulin and RNA. These results suggest that CNP1 may regulate expression of mRNAs in ODCs of the CNS.

Expression mapping of ectonucleotide pyrophosphatase/phosphodiesterase 1-3 (E-NPP1-3) in different brain structures during rat development.

Ecto-nucleotide pyrophosphatases/phosphodiesterases (E-NPPs) are membrane-bound ecto-enzymes involved in the modulation of purinergic signaling. Important physiological roles related to brain development have been associated to purinergic neurotransmission. NPP1, two splice isoforms of NPP2, and NPP3 have already been identified in adult rat brain. However, there are no studies evaluating the mRNA expression of these NPP members during the brain development. The effort of the present study was to map NPP gene expression pattern in olfactory bulb, hippocampus, cerebral cortex, striatum, and cerebellum at crucial ages for rat development (7, 14, 21, 60, and 150 days old) by a semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) strategy. Our results demonstrated an increase in the relative expression of NPP1 throughout the aging in all structures analyzed, except in hippocampus, where the higher expression has been detected in 14 days old rats. Both NPP2 isoforms have shown a similar pattern of expression among all structures. The relative expression of NPP3 decreased during the aging mainly on cerebellum, hippocampus, and olfactory bulb. Altogether, the different patterns of NPP gene expression during rat brain development reinforce the idea that each enzyme may play a distinct role on modulating the purinergic signaling throughout aging.

Structural comparison analysis of 2H phosphodiesterase family proteins.

2',3'-Cyclic-nucleotide 3'-phosphodiesterase (CNP) is found mainly in the central nervous system of vertebrates and catalyzes the hydrolysis of 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Recently, Several 2H phosphodiesterase super family protein structures have been determined by X-ray crystallography and NMR spectroscopy. Here we report the structure-function relationship studies of two hydrophobic residues in CNP family proteins.

Cyclic nucleotide signaling mechanisms in trypanosomes: possible targets for therapeutic agents.

Trypanosome infections cause several major human diseases, including sleeping sickness and Chagas disease, which affect millions of people in Africa and South America, respectively. Although adenosine 3',5'-monophosphate (cAMP) signaling and regulation have been widely studied in mammalian systems, and these pathways provide targets for the treatment of numerous pathologies, a molecular understanding of cAMP signaling in trypanosomes remains incomplete. Recent studies in these parasites, however, have revealed diverse families of adenylyl cyclase and phosphodiesterase that regulate cAMP concentrations. Importantly, these enzymes differ pharmacologically and biochemically from their mammalian counterparts. In this review, we discuss recent developments, emerging ideas, and gaps in knowledge in this area of research, highlighting aspects of enzymes in the cAMP signaling pathway that may be good targets for antitrypanosomal drug therapy.

The molecular basis for different recognition of substrates by phosphodiesterase families 4 and 10.

Phosphodiesterases (PDEs) are key enzymes that control the cellular concentrations of the second messengers cAMP and cGMP. The mechanism for selective recognition of substrates cAMP and cGMP by individual PDE families remains a puzzle. To understand the mechanism for substrate recognition by PDE enzymes, the crystal structure of the catalytic domain of an inactive D201N mutant of PDE4D2 in complex with substrate cAMP has been determined at 1.56 A resolution. The structure shows that Gln369 forms only one hydrogen bond with the adenine of cAMP. This finding provides experimental evidence against the hypothesis of two hydrogen bonds between the invariant glutamine and the substrate cAMP in PDE4, and thus suggests that the widely circulated "glutamine switch" model is unlikely the mechanism for substrate recognition by PDEs. A structure comparison between PDE4D2-cAMP and PDE10A2-cAMP reveals an anti configuration of cAMP in PDE4D2 but syn in PDE10A2, in addition to different contact patterns of cAMP in these two structures. These observations imply that individual PDE families have their characteristic mechanisms for substrate recognition.

Biochemistry and physiology of cyclic nucleotide phosphodiesterases: essential components in cyclic nucleotide signaling.

Although cyclic nucleotide phosphodiesterases (PDEs) were described soon after the discovery of cAMP, their complexity and functions in signaling is only recently beginning to become fully realized. We now know that at least 100 different PDE proteins degrade cAMP and cGMP in eukaryotes. A complex PDE gene organization and a large number of PDE splicing variants serve to fine-tune cyclic nucleotide signals and contribute to specificity in signaling. Here we review some of the major concepts related to our understanding of PDE function and regulation including: (a) the structure of catalytic and regulatory domains and arrangement in holoenzymes; (b) PDE integration into signaling complexes; (c) the nature and function of negative and positive feedback circuits that have been conserved in PDEs from prokaryotes to human; (d) the emerging association of mutant PDE alleles with inherited diseases; and (e) the role of PDEs in generating subcellular signaling compartments.

Overview of PDEs and their regulation.

Contraction and relaxation of vascular smooth muscle and cardiac myocytes are key physiological events in the cardiovascular system. These events are regulated by second messengers, cAMP and cGMP, in response to extracellular stimulants. The strength of signal transduction is controlled by intracellular cyclic nucleotide concentrations, which are determined by a balance in production and degradation of cAMP and cGMP. Degradation of cyclic nucleotides is catalyzed by 3',5'-cyclic nucleotide phosphodiesterases (PDEs), and therefore regulation of PDEs hydrolytic activity is important for modulation of cellular functions. Mammalian PDEs are composed of 21 genes and are categorized into 11 families based on sequence homology, enzymatic properties, and sensitivity to inhibitors. PDE families contain many splice variants that mostly are unique in tissue-expression patterns, gene regulation, enzymatic regulation by phosphorylation and regulatory proteins, subcellular localization, and interaction with association proteins. Each unique variant is closely related to the regulation of a specific cellular signaling. Thus, multiple PDEs function as a particular modulator of each cardiovascular function and regulate physiological homeostasis.

Acyl carrier protein phosphodiesterase (AcpH) of Escherichia coli is a non-canonical member of the HD phosphatase/phosphodiesterase family.

The Escherichia coli AcpH acyl carrier protein phosphodiesterase (also called ACP hydrolyase) is the only enzyme known to cleave a phosphodiester-linked post-translational protein modification. AcpH hydrolyzes the link between 4'-phosphopanthetheine and the serine-36 side chain of acyl carrier protein (ACP). Although the existence of this enzyme activity has long been known, study of the enzyme was hampered by its recalcitrant properties and scarcity. We recently isolated the gene encoding AcpH and have produced the recombinant enzyme in quantity (Thomas, J., and Cronan, J. E., (2005) J. Biol. Chem. 280, 34675-34683), thus allowing the first studies of its reaction mechanism. AcpH requires Mn2+ for activity, and thus, we focused on the metal binding ligands in order to locate the active site. Bioinformatic investigations indicated that AcpH and its homologues were weakly related to a phosphodiesterase of known structure, the hydrolyase domain of the bifunctional bacterial protein, SpoT, suggesting that AcpH is a member of the HD family of phosphatases/ phosphodiesterases despite lacking the characteristic histidine of the motif. Indeed, we found that AcpH could be convincingly modeled on the SpoT structure with acceptable parameters, which allowed the identification of putative metal binding ligands. These were then tested by site-directed mutagenesis. Mutagenic removal of any of the putative ligands resulted in a severe or total loss of phosphodiesterase activity. In two cases, the H6Q and D24N proteins, the residual activities could be markedly stimulated by addition of high Mn2+ concentrations, thereby demonstrating a role for these residues in metal binding. We conclude that AcpH is a member of the HD protein family despite the lack of the signature histidine residue.

Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases.

Spider venom sphingomyelinases D catalyze the hydrolysis of sphingomyelin via an Mg(2+) ion-dependent acid-base catalytic mechanism which involves two histidines. In the crystal structure of the sulfate free enzyme determined at 1.85A resolution, the metal ion is tetrahedrally coordinated instead of the trigonal-bipyramidal coordination observed in the sulfate bound form. The observed hyperpolarized state of His47 requires a revision of the previously suggested catalytic mechanism. Molecular modeling indicates that the fundamental structural features important for catalysis are fully conserved in both classes of SMases D and that the Class II SMases D contain an additional intra-chain disulphide bridge (Cys53-Cys201). Structural analysis suggests that the highly homologous enzyme from Loxosceles bonetti is unable to hydrolyze sphingomyelin due to the 95Gly-->Asn and 134Pro-->Glu mutations that modify the local charge and hydrophobicity of the interfacial face. Structural and sequence comparisons confirm the evolutionary relationship between sphingomyelinases D and the glicerophosphodiester phosphoesterases which utilize a similar catalytic mechanism.

Phosphodiesterase 11: a brief review of structure, expression and function.

Phosphodiesterase 11 (PDE11) is the latest isoform of the phosphodiesterase family to be identified. Interest in PDE11 has increased recently because tadalafil, an oral phosphodiesterase 5 inhibitor, cross reacts with PDE11. The function of PDE11 remains largely unknown, but growing evidence points to a possible role in male reproduction. The published literature on PDE11 structure, function and expression is reviewed.