Binding of two fluorescent cAMP analogues to type I and II regulatory subunits of cAMP-dependent protein kinases

Estimation of cAMP binding in hippocampus CA1 field by a fluorescent probe

The hippocampus is an allocortex structure involved in many complex processes, from memory formation to spatial navigation. It starts developing during prenatal life but acquires its adult functional properties around the peripubertal age, in both humans and mice. Such prolonged maturation is accompanied by structural changes in microcircuitry and functional changes involving biochemical and electrophysiological events. Moreover, hippocampus undergoes plasticity phenomena throughout life. In murine rodents, the most relevant maturation steps in Cornu Ammonis 1 (CA1) hippocampal subfield occur during the third-fourth weeks of life. During this period, also the expression and localization of cAMP-dependent protein kinases (PKA) refines: many regulatory (R1A) PKA clusters appear, bound to the cytoskeleton. Here the binding characteristics of R1A are determined in CA1 by using confocal microscopy. Apparently, two binding sites are present with no evidence of cooperativity. Equilibrium dissociation constant is estimated around 22.9 nM. This value is lower from that estimated for R1A in soluble form, suggesting a different binding site conformation or accessibility in the tissue. The method described here may be useful to track the developmental changes in binding activity, which affects cAMP availability at selected intracellular microzones. Possible relations with functional consequences are discussed.

Protein Kinase A Catalytic and Regulatory Subunits Interact Differently in Various Areas of Mouse Brain

Protein kinase A (PKA) are tetramers of two catalytic and two regulatory subunits, docked at precise intracellular sites to provide localized phosphorylating activity, triggered by cAMP binding to regulatory subunits and subsequent dissociation of catalytic subunits. It is unclear whether in the brain PKA dissociated subunits may also be found. PKA catalytic subunit was examined in various mouse brain areas using immunofluorescence, equilibrium binding and western blot, to reveal its location in comparison to regulatory subunits type RI and RII. In the cerebral cortex, catalytic subunits colocalized with clusters of RI, yet not all RI clusters were bound to catalytic subunits. In stria terminalis, catalytic subunits were in proximity to RI but separated from them. Catalytic subunits clusters were also present in the corpus striatum, where RII clusters were detected, whereas RI clusters were absent. Upon cAMP addition, the distribution of regulatory subunits did not change, while catalytic subunits were completely released from regulatory subunits. Unpredictably, catalytic subunits were not solubilized; instead, they re-targeted to other binding sites within the tissue, suggesting local macromolecular reorganization. Hence, the interactions between catalytic and regulatory subunits of protein kinase A consistently vary in different brain areas, supporting the idea of multiple interaction patterns.

A new sensitive and subunit-selective molecular tool for investigating protein kinase A in the brain

Despite cellular complexity, a limited number of small molecules act as intracellular second messengers. Protein kinase A (PKA) is the main transducer of the information carried by cyclic adenosine monophosphate (cAMP). Recently, cellular imaging has achieved major technical advancements, although the search for more specific and sensitive low-molecular-weight probes to explore subcellular events involving second messengers is still in progress. The convergent synthesis of a novel, fluorescent small molecule comprising the cAMP structure and a rhodamine-based fluorescent residue, connected through a flexible linker, is described here. The interaction motif of this compound with PKA was investigated in silico using a blind docking approach, comparing its theoretical binding energy with the one calculated for cAMP. Moreover, the predicted pharmacokinetic properties were also computed and discussed. The new probe was tested on three areas of the mouse central nervous system (parietal cerebral cortex, hippocampus, and cerebellar cortex) with different fixation methods demonstrating remarkable selectivity towards the PKA RIα subunit. The probe showed overall better performances when compared to other commercially available fluorescent cAMP analogues, acting at lower concentrations, and providing stable labeling.

Protein Kinase A Distribution in Meningioma

Deregulation of intracellular signal transduction pathways is a hallmark of cancer cells, clearly differentiating them from healthy cells. Differential intracellular distribution of the cAMP-dependent protein kinases (PKA) was previously detected in cell cultures and in vivo in glioblastoma and medulloblastoma. Our goal is to extend this observation to meningioma, to explore possible differences among tumors of different origins and prospective outcomes. The distribution of regulatory and catalytic subunits of PKA has been examined in tissue specimens obtained during surgery from meningioma patients. PKA RI subunit appeared more evenly distributed throughout the cytoplasm, but it was clearly detectable only in some tumors. RII was present in discrete spots, presumably at high local concentration; these aggregates could also be visualized under equilibrium binding conditions with fluorescent 8-substituted cAMP analogues, at variance with normal brain tissue and other brain tumors. The PKA catalytic subunit showed exactly overlapping pattern to RII and in fixed sections could be visualized by fluorescent cAMP analogues. Gene expression analysis showed that the PKA catalytic subunit revealed a significant correlation pattern with genes involved in meningioma. Hence, meningioma patients show a distinctive distribution pattern of PKA regulatory and catalytic subunits, different from glioblastoma, medulloblastoma, and healthy brain tissue. These observations raise the possibility of exploiting the PKA intracellular pathway as a diagnostic tool and possible therapeutic interventions.

Aggregates of cAMP-dependent kinase isoforms characterize different areas in the developing central nervous system of the chicken, Gallus gallus

The intracellular second messenger adenosine 3',5'-cyclic monophosphate (cAMP) acts mainly through cAMP-dependent protein kinases (PKA). In mammals and reptiles, the PKA regulatory isoforms (RI and RII) are differentially distributed among the various brain areas and cell types, according to the age of the animal. Since PKA distribution may be an additional marker for homologous areas, PKA regulatory subunit types RI and RII were examined in the chicken brain, a species not yet investigated. Chicken brains were examined from prehatching to adult age, by means of immunohistochemistry and biochemical characterization. Most PKA regulatory subunits were segregated in discrete non-soluble clusters that contained either RI or RII. While RII aggregates were present also in non-neuronal cells, RI aggregates were detected only in neurons of some brain areas that are mainly related to the telencephalon. They appeared later than RII aggregates; their presence and location varied during development. RI aggregates were detected first in the olfactory bulb, around embryonic day 14; within 3 days they appeared in the hyperpallium and nidopallium, where the most intense labeling was observed in the perihatching period. Fainter RI aggregates persisted up to 3 years in the olfactory bulb and nidopallium caudale. Less intense RI aggregates were present for a shorter time, from 2 weeks to 3 months, in the septal nuclei, thalamic medial nuclei, periventricular hypothalamus, optic tectum periventricular area, brainstem reticular formation and spinal cord substantia gelatinosa. RI aggregates were not detected in many brain areas including the arcopallium, striatum and cranial nerve nuclei. RII distribution showed less variation during development. From embryonic day 12, some insoluble RII aggregates were detected in the brain; however, only minor modifications were observed in positive structures once they started to harbor insoluble RII aggregates. The present results suggest that the distribution of PKA aggregates may assist in characterizing phylogenetically homologous structures of the vertebrate central nervous system and may also unravel biochemical differences among areas considered homologous.

Protein kinase a in cancer

In the past, many chromosomal and genetic alterations have been examined as possible causes of cancer. However, some tumors do not display a clear molecular and/or genetic signature. Therefore, other cellular processes may be involved in carcinogenesis. Genetic alterations of proteins involved in signal transduction have been extensively studied, for example oncogenes, while modifications in intracellular compartmentalization of these molecules, or changes in the expression of unmodified genes have received less attention. Yet, epigenetic modulation of second messenger systems can deeply modify cellular functioning and in the end may cause instability of many processes, including cell mitosis. It is important to understand the functional meaning of modifications in second messenger intracellular pathways and unravel the role of downstream proteins in the initiation and growth of tumors. Within this framework, the cAMP system has been examined. cAMP is a second messenger involved in regulation of a variety of cellular functions. It acts mainly through its binding to cAMP-activated protein kinases (PKA), that were suggested to participate in the onset and progression of various tumors. PKA may represent a biomarker for tumor detection, identification and staging, and may be a potential target for pharmacological treatment of tumors.

Biochemical characterization and cellular imaging of a novel, membrane permeable fluorescent cAMP analog

BACKGROUND

A novel fluorescent cAMP analog (8-[Pharos-575]- adenosine-3', 5'-cyclic monophosphate) was characterized with respect to its spectral properties, its ability to bind to and activate three main isoenzymes of the cAMP-dependent protein kinase (PKA-Ialpha, PKA-IIalpha, PKA-IIbeta) in vitro, its stability towards phosphodiesterase and its ability to permeate into cultured eukaryotic cells using resonance energy transfer based indicators, and conventional fluorescence imaging.

RESULTS

The Pharos fluorophore is characterized by a Stokes shift of 42 nm with an absorption maximum at 575 nm and the emission peaking at 617 nm. The quantum yield is 30%. Incubation of the compound to RIIalpha and RIIbeta subunits increases the amplitude of excitation and absorption maxima significantly; no major change was observed with RIalpha. In vitro binding of the compound to RIalpha subunit and activation of the PKA-Ialpha holoenzyme was essentially equivalent to cAMP; RII subunits bound the fluorescent analog up to ten times less efficiently, resulting in about two times reduced apparent activation constants of the holoenzymes compared to cAMP. The cellular uptake of the fluorescent analog was investigated by cAMP indicators. It was estimated that about 7 muM of the fluorescent cAMP analog is available to the indicator after one hour of incubation and that about 600 muM of the compound had to be added to intact cells to half-maximally dissociate a PKA type IIalpha sensor.

CONCLUSION

The novel analog combines good membrane permeability- comparable to 8-Br-cAMP - with superior spectral properties of a modern, red-shifted fluorophore. GFP-tagged regulatory subunits of PKA and the analog co-localized. Furthermore, it is a potent, PDE-resistant activator of PKA-I and -II, suitable for in vitro applications and spatial distribution evaluations in living cells.

High-throughput screening of holoprotein conformational stability by dynamic ligand exchange-affinity capillary electrophoresis

Dynamic ligand exchange-affinity capillary electrophoresis (DLE-ACE) is introduced as a convenient platform for assessing the conformational stability and relative affinity of a holoprotein to different ligands without off-line sample pretreatment, since ligand exchange and protein unfolding processes are integrated in-capillary during electromigration.

Distribution of insoluble cAMP-dependent kinase type RI and RII in the lizard and turtle central nervous system

cAMP is a universal second messenger. In eucaryotes it acts mainly via protein kinases composed of regulatory (R) and catalytic subunits; their subcellular distribution may differ according to the cell type. In rodent brain, peculiar detergent-insoluble RIalpha aggregates were previously described in neurons of areas related to the limbic system, while RIIbeta is more evenly distributed also in non-nervous cells. It is unclear whether the regional distribution of regulatory subunits is typical of mammalian brain. Western blots and immunohistochemistry showed that in lizard brains a large fraction of the cAMP-dependent protein kinase regulatory isoforms is insoluble, as in mammals. Insoluble RIalpha and RII regulatory isoforms were not evenly distributed but organized in clearly separated aggregates. Numerous RII aggregates were present in almost all brain regions and were found also in non-nervous cells. As shown by immunohistochemistry and equilibrium binding of fluorescently tagged cAMP, RIalpha aggregates were restricted to neurons of some brain regions: telencephalon, particularly medial cortical areas, dorsal ventricular ridge, olfactory pathways, medial hypothalamus and cerebellar granular layer were intensely labelled. A very weak RIalpha labelling was detected in the brainstem reticular formation, in the periaqueductal gray and in the spinal cord dorsal horn. A similar distribution of RIalpha aggregates was also found in turtle brains. Their distribution is reminiscent of that observed in mammals, although with some differences in relative intensity and persistence. The supramolecular organization of the RIalpha isoform may help in establishing homologies and differences between brain areas involved in visceroemotional control.

Biomolecular interaction analysis in functional proteomics

To understand the function of highly complex eukaryotic tissues like the human brain, in depth knowledge about cellular protein networks is required. Biomolecular interaction analysis (BIA), as a part of functional proteomics, aims to quantify interaction patterns within a protein network in detail. We used the cAMP dependent protein kinase (PKA) as a model system for the binding analysis between small natural ligands, cAMP and cAMP analogues, with their physiological interaction partner, the regulatory subunit of PKA. BIA comprises a variety of methods based on physics, biochemistry and molecular biology. Here we compared side by side real time SPR (surface plasmon resonance, Biacore), a bead based assay (AlphaScreen), a fluorescence based method (Fluorescence polarisation) and ITC (isothermal titration calorimetry). These in vitro methods were complemented by an in cell reporter assay, BRET(2) (bioluminescence resonance energy transfer), allowing to test the effects of cAMP analogues in living cells.

Regional variations in the localization of insoluble kinase A regulatory isoforms during rodent brain development

In eukaryothes, the second messenger cAMP regulates many cellular functions by binding to the regulatory subunits of cAMP-dependent protein kinases, and releasing the catalytic subunits. In the mammalian brain all four regulatory isoforms (RIalpha and beta, RIIalpha and beta) are present. Apparently, they are simple inhibitors of the catalytic subunits. It is still unclear why four isoforms are needed, but possibly they can target kinase activity at precise intracellular locations. Therefore, we examined the distribution of the insoluble regulatory isoforms in rat and mouse brains during prenatal (from embryonic day 8) and postnatal development up to senescence (13 months), via immunohistochemistry. RIIalpha labelling is always restricted to the ventricular ependyma. Punctated RIIbeta labelling is observed in the embryo from early stages of development, and is mainly localized in the cortical plate. After birth, punctate RIIbeta labelling is present throughout almost the whole brain, often observed in proximity of neurofilaments. It shows different characteristics and relationships to the other isoforms: for example in the CA1 hippocampal field, RIIbeta is substituted by RIalpha 2 weeks after birth, while in CA2 it persists for life. In other regions, as in the reticular formation, RIIbeta and RIalpha aggregates are found in the same cell, although clearly segregated. The different regulatory isoforms show distinct patterns of distribution that change consistently during development. A careful characterization of second messenger systems may be as useful as the study of neurotransmitters to understand neuronal properties and their modifications during development, so as to relate biochemical to functional properties.

Clustered distribution of cAMP-dependent protein kinase regulatory isoform RI alpha during the development of the rat brain

cAMP is a ubiquitous second messenger, which acts mainly through specific protein kinases that consist of two regulatory and two catalytic subunits. An unsolved problem in cAMP physiology is how it can regulate so many cellular functions through this simple enzymatic cascade. A tentative explanation is related to the different biochemical properties of the four regulatory subunit isoforms (RI alpha and RI beta, RII alpha and RII beta) and to their differential cell and tissue distribution. For example, detergent insoluble aggregates of RI alpha are present in some cholinergic neurons of the adult rat brain. Rat brains, from the embryonic stage to old age, were examined for the presence of highly concentrated clusters of RI alpha. They are present only in some neurons of restricted brain areas, for a limited time span. During development, labeled neurons appear in different brain areas after neuron migration, at a stage of advanced functional maturation. They have their greatest expression after birth but before sexual maturation, and then they slowly decline, persisting only in a few brain areas throughout life. The first appearance, time course, and eventual disappearance is different in the different brain areas: RI alpha clusters appear in brainstem, hypothalamus, and accessory olfactory bulb at a late embryonic stage; in the main olfactory bulb, hippocampus, and medial thalamic nuclei shortly after birth; and in the cortex as late as in the third and fourth postnatal week. During the rat's lifespan, the distribution of these peculiar RI alpha clusters undergo changes that may contribute to shape neuronal responses differentially to agents modifying cAMP levels.

Visualization of detergent insoluble cyclic AMP-dependent protein kinase RIalpha aggregates in the rat brain

Regulatory subunits of the cAMP dependent protein kinases are the most abundant receptor for cAMP in eukaryotic cells. Four isoforms of regulatory subunits (RIalpha and -beta, RIIalpha and -beta) have been distinguished. Distribution of the most abundant RII isoforms has been extensively studied in the brain, by immunohistochemistry and biochemical fractionation, while the least abundant RI isoforms have been neglected. In neurons most regulatory subunits are bound to the cytoskeleton. A protocol is presented that allows immunohistochemical and biochemical characterization of detergent-insoluble RI isoforms in the brain.

Aggregates of cAMP-dependent kinase RIalpha characterize a type of cholinergic neurons in the rat brain

Acetylcholine is synthesized by different types of neurons, showing a distinct biochemical phenotype. Aggregates of RIalpha regulatory subunit of cAMP-dependent protein kinases are visualized by immunohistochemistry only in some cholinergic neurons, since they tightly colocalize with two different markers, choline acetyltransferase (ChAT) and vesicular acetylcholine transporter (VAChT). These neurons are present mainly in brain areas related to the limbic system. None of the other regulatory subunits of cAMP dependent kinases colocalize with cholinergic markers.

cAMP-dependent protein kinase type RI is found in clusters in the rat detergent-insoluble neuronal fraction

Different types of cAMP dependent regulatory subunits have been characterized in the mammalian brain: RI alpha and beta, RII alpha and beta. The subcellular distribution of RI subunits has been examined in the rat brain. Partial amino acid sequencing of tryptic fragments from the Triton insoluble pellet of the rat brain shows that cAMP dependent regulatory subunits type RI alpha are found in this fraction. Immunohistochemistry shows that Triton-insoluble RI subunits are concentrated to form clusters and this distribution is distinct from RII subunits. Immunohistochemistry and fluorescent cAMP labeling show that the clusters bind fluorescent cAMP analogues. These results suggest that the high local concentration of RI subunits can modulate cAMP distribution among different cellular compartments.

Fluorescent-protein biosensors: new tools for drug discovery

Recent improvements in target discovery and high-throughput screening have increased the pressure at key points along the drug-discovery pipeline. High-content screening was developed to ease the bottlenecks formed at the target-validation and lead-optimization points, and a new generation of reagents that report on specific molecular processes in living cells (fluorescent-protein biosensors) have been important in its development. Creative designs of fluorescent-protein biosensors have emerged and been used to measure the molecular dynamics of macromolecules, metabolites and ions. Recent applications of fluorescent-protein biosensors to biological problems have provided a foundation for their use in biotechnology.