Essential role for protein kinase D family kinases in the regulation of class II histone deacetylases in B lymphocytes

We have taken a knockout approach to interrogate the function of protein kinase D (PKD) serine/threonine kinases in lymphocytes. DT40 B cells express two PKD family members, PKD1 and PKD3, which are both rapidly activated by the B-cell antigen receptor (BCR). DT40 cells with single or dual deletions of PKD1 and/or PKD3 were viable, allowing the role of individual PKD isoforms in BCR signal transduction to be assessed. One proposed downstream target for PKD1 in lymphocytes is the class II histone deacetylases (HDACs). Regulation of chromatin accessibility via class II histone deacetylases is an important mechanism controlling gene expression patterns, but the molecules that control this key process in B cells are not known. Herein, we show that phosphorylation and nuclear export of the class II histone deacetylases HDAC5 and HDAC7 are rapidly induced following ligation of the BCR or after treatment with phorbol esters (a diacylglycerol mimetic). Loss of either PKD1 or PKD3 had no impact on HDAC phosphorylation, but loss of both PKD1 and PKD3 abrogated antigen receptor-induced class II HDAC5/7 phosphorylation and nuclear export. These studies reveal an essential and redundant role for PKD enzymes in controlling class II HDACs in B lymphocytes and suggest that PKD serine kinases are a critical link between the BCR and epigenetic control of chromatin.     

A novel protein kinase C target site in protein kinase D is phosphorylated in response to signals for cardiac hypertrophy

Protein kinase D (PKD) regulates cardiac myocyte growth and contractility through phosphorylation of proteins such as class IIa histone deacetylases (HDACs) and troponin I (TnI). In response to agonists that activate G-protein-coupled receptors (GPCRs), PKD is phosphorylated by protein kinase C (PKC) on two serine residues (Ser-738 and Ser-742 in human PKD1) within an activation loop of the catalytic domain, resulting in stimulation of PKD activity. Here, we identify a novel PKC target site located adjacent to the auto-inhibitory pleckstrin homology (PH) domain in PKD. This site (Ser-412 in human PKD1) is conserved in each of the three PKD family members and is efficiently phosphorylated by multiple PKC isozymes in vitro. Employing a novel anti-phospho-Ser-412-specific antibody, we demonstrate that this site in PKD is rapidly phosphorylated in primary cardiac myocytes exposed to hypertrophic agonists, including norepinephrine (NE) and endothelin-1 (ET-1). Differential sensitivity of this event to pharmacological inhibitors of PKC, and data from in vitro enzymatic assays, suggest a predominant role for PKCδ in the control of PKD Ser-412 phosphorylation. Together, these data suggest a novel, signal-dependent mechanism for controlling PKD function in cardiac myocytes.     

Regulation of the Nuclear–Cytoplasmic Traffic of Class IIa Histone Deacethylases in Rat Soleus Muscle at the Early Stage of Gravitational Unloading

The negative regulation of expression of genes involved in various metabolic pathways in a skeletal muscle is the main function of histone deacetylases 4 and 5 (HDAC4/HDAC5). HDAC4 and HDAC5 seem to be the targets of the AMP-activated protein kinase (AMPK). Earlier, an essential decrease in the level of Thr172-phosphorylated-AMPK in a rat soleus muscle at the first day of gravitational unloading was shown. Possibility of a protein kinase D (PKD) to phosphorylate histone deacetylases 4/5 has been shown, too. We supposed that under the conditions of gravitational unloading, alterations in AMPK phosphorylation level can affect regulation of nuclear-cytoplasmic traffic of class II histone deacetylases and of various skeletal muscle genes expression. To verify the hypothesis, we used administration of an AMPK activator, AICAR, before and during a day-long hindlimb suspension. It was shown that at an early stage of gravitational unloading, HDAC4 is not a PKD target, and its nuclear import is realized due to decrease in AMPK activity. We were the first to show reciprocal relations between AMPK and PKD in a skeletal muscle at early gravitational unloading.     

Expression of the protein kinase D (PKD) family during mouse embryogenesis

The serine/threonine protein kinase D (PKD) family comprises of three members, PKD1 (PKCmu), PKD2 and PKD3 (PKCnu). Like the related C-type protein kinases (PKCs), PKDs are activated by diacylglycerol (DAG). PKDs have been implicated in numerous intracellular signaling pathways including vesicular transport, cell proliferation, survival, migration and immune responses. While experimental data on this recently discovered kinase family are starting to accumulate family member specific information is still sparse and only small effort has been taken to functionally differentiate the three PKDs. To address this issue we followed the expression patterns of PKD1, 2 and 3 during the development of the mouse embryo. Using specific probe sets for RT-PCR and in situ hybridization, we demonstrate shared and differential expression domains for the three PKD family members in both neuronal and non-neuronal tissues.     

Protein kinases C and D mediate agonist-dependent cardiac hypertrophy through nuclear export of histone deacetylase 5

A variety of stress signals stimulate cardiac myocytes to undergo hypertrophy. Persistent cardiac hypertrophy is associated with elevated risk for the development of heart failure. Recently, we showed that class II histone deacetylases (HDACs) suppress cardiac hypertrophy and that stress signals neutralize this repressive function by triggering phosphorylation- and CRM1-dependent nuclear export of these chromatin-modifying enzymes. However, the identities of cardiac HDAC kinases have remained unclear. Here, we demonstrate that signaling by protein kinase C (PKC) is sufficient and, in some cases, necessary to drive nuclear export of class II HDAC5 in cardiomyocytes. Inhibition of PKC prevents nucleocytoplasmic shuttling of HDAC5 in response to a subset of hypertrophic agonists. Moreover, a nonphosphorylatable HDAC5 mutant is refractory to PKC signaling and blocks cardiomyocyte hypertrophy mediated by pharmacological activators of PKC. We also demonstrate that protein kinase D (PKD), a downstream effector of PKC, directly phosphorylates HDAC5 and stimulates its nuclear export. These findings reveal a novel function for the PKC/PKD axis in coupling extracellular cues to chromatin modifications that control cellular growth, and they suggest potential utility for small-molecule inhibitors of this pathway in the treatment of pathological cardiac gene expression.     

A novel kinase inhibitor establishes a predominant role for protein kinase D as a cardiac class IIa histone deacetylase kinase

Class IIa histone deacetylases (HDACs) repress genes involved in pathological cardiac hypertrophy. The anti-hypertrophic action of class IIa HDACs is overcome by signals that promote their phosphorylation-dependent nuclear export. Several kinases have been shown to phosphorylate class IIa HDACs, including calcium/calmodulin-dependent protein kinase (CaMK), protein kinase D (PKD) and G protein-coupled receptor kinase (GRK). However, the identity of the kinase(s) responsible for phosphorylating class IIa HDACs during cardiac hypertrophy has remained controversial. We describe a novel and selective small molecule inhibitor of PKD, bipyridyl PKD inhibitor (BPKDi). BPKDi blocks signal-dependent phosphorylation and nuclear export of class IIa HDACs in cardiomyocytes and concomitantly suppresses hypertrophy of these cells. These studies define PKD as a principal cardiac class IIa HDAC kinase.     

A comparative analysis of binding sites between human PKD1 and PKC1 based on homology modelling,molecular dynamics simulation and docking studies

Human protein kinase C1 (PKC1) and protein kinase D1 (PKD1) are two closely related enzymes, which have emerged as key regulators of many important cellular processes. In this study, 3D models of human PKC1 and PKD1 were constructed based on homology modelling and molecular dynamics simulations. A novel 2,6-naphthyridine is a potent and selective inhibitor for human PKD1 and not for PKC1, which was docked into them and positioned in their active sites with different orientations. By comparison of active site architectures between human PKC1 and PKD1, the possible reasons affecting their inhibitor binding were proposed. In addition, some residues are identified as critical residues for inhibitor binding.     

PKD is recruited to sites of actin remodelling at the leading edge and negatively regulates cell migration

Protein kinase D (PKD) has been implicated in the regulation of cell shape, adhesion, and migration. At the leading edge of migrating cells active PKD co-localizes with F-actin, Arp3 and cortactin. Platelet derived growth factor (PDGF) activates PKD and recruits the kinase to the leading edge, suggesting a role for PKD in actin remodelling. In support of this, PKD directly interacts with F-actin and phosphorylates cortactin in vitro. Interference with PKD function by overexpression of a dominant negative PKD or by PKD-specific siRNA enhanced cell migration, whereas cells overexpressing PKD wild type displayed reduced migratory potential. Taken together, these data reveal a negative regulatory function of PKD in cell migration.     

Histone deacetylases in Trypanosoma brucei: two are essential and another is required for normal cell cycle progression

Reversible protein acetylation is established as a modification of major regulatory significance. In particular, histone acetylation regulates access to genetic information in eukaryotes. For example, class I and class II histone deacetylases are regulatory components of corepressor complexes involved in cell cycle progression and differentiation. Here, we have investigated the function of such enzymes in Trypanosoma brucei, mono-flagellated parasitic protozoa that branched very early from the eukaryotic lineage. Four T. brucei genes encoding histone deacetylase orthologues have been identified, cloned and characterized. The predicted deacetylases, DAC1-4 are approximately 43, 61, 75 and 64 kDa respectively. They share significant similarity with mammalian and yeast class I (DAC1 and DAC2) and class II (DAC3 and DAC4) histone deacetylases, and all except DAC2 have the critical residues predicted to be required for deacetylase activity. In gene targeting experiments, DAC1 and DAC3 appear to be essential whereas DAC2 and DAC4 are not required for viability. Of the two mutant cell types, the dac4 mutant displays a delay in the G2/M phase of the cell cycle. Our results provide genetic validation of DAC1 and DAC3 as potential chemotherapy targets and demonstrate that T. brucei expresses at least three probable histone deacetylases with distinct function.     

Characterization of a novel protein kinase D: Caenorhabditis elegans DKF-1 is activated by translocation-phosphorylation and regulates movement and growth in vivo

Protein kinase D (PKD) isoforms are protein kinase C (PKC) effectors in diacylglycerol (DAG)-regulated signaling pathways. Key physiological processes are placed under DAG control by the distinctive substrate specificity and intracellular distribution of PKDs. Comprehension of the roles of PKDs in homeostasis and signal transduction requires further knowledge of regulatory interplay among PKD and PKC isoforms, analysis of PKC-independent PKD activation, and characterization of functions controlled by PKDs in vivo. Caenorhabditis elegans and mammals share conserved signaling mechanisms, molecules, and pathways Thus, characterization of the C. elegans PKDs could yield insights into regulation and functions that apply to all eukaryotic PKDs. C. elegans DKF-1 (D kinase family-1) contains tandem DAG binding (C1) modules, a PH (pleckstrin homology) domain, and a Ser/Thr protein kinase segment, which are homologous with domains in classical PKDs. DKF-1 and PKDs have similar substrate specificities. Phorbol 12-myristate 13-acetate (PMA) switches on DKF-1 catalytic activity in situ by promoting phosphorylation of a single amino acid Thr(588) in the activation loop. DKF-1 phosphorylation and activation are unaffected when PKC activity is eliminated by inhibitors. Both phosphorylation and kinase activity of DKF-1 are extinguished by substituting Ala for Thr(588) or Gln for Lys(455) ("kinase dead") or incubating with protein phosphatase 2C. Thus, DKF-1 is a PMA-activated, PKC-independent D kinase. In vivo, dkf-1 gene promoter activity is evident in neurons. Both dkf-1 gene disruption (null phenotype) and RNA interference-mediated depletion of DKF-1 protein cause lower body paralysis. Targeted DKF-1 expression corrected this locomotory defect in dkf-1 null animals. Supraphysiological expression of DKF-1 limited C. elegans growth to approximately 60% of normal length.     

PKD3 Is the Predominant Protein Kinase D Isoform in Mouse Exocrine Pancreas and Promotes Hormone-induced Amylase Secretion

The protein kinase D (PKD) family of serine/threonine kinases, which can be activated by gastrointestinal hormones, consists of three distinct isoforms that modulate a variety of cellular processes including intracellular protein transport as well as constitutive and regulated secretion. Although isoform-specific functions have been identified in a variety of cell lines, the expression and function of PKD isoforms in normal, differentiated secretory tissues is unknown. Here, we demonstrate that PKD isoforms are differentially expressed in the exocrine and endocrine cells of the pancreas. Specifically, PKD3 is the predominant isoform expressed in exocrine cells of the mouse and human pancreas, whereas PKD1 and PKD2 are more abundantly expressed in the pancreatic islets. Within isolated mouse pancreatic acinar cells, PKD3 undergoes rapid membrane translocation, trans-activating phosphorylation, and kinase activation after gastrointestinal hormone or cholinergic stimulation. PKD phosphorylation in pancreatic acinar cells occurs viaaCa²⁺-independent, diacylglycerol- and protein kinase C-dependent mechanism. PKD phosphorylation can also be induced by physiologic concentrations of secretagogues and by in vivo stimulation of the pancreas. Furthermore, activation of PKD3 potentiates MEK/ERK/RSK (RSK, ribosomal S6 kinase) signaling and significantly enhances cholecystokinin-mediated pancreatic amylase secretion. These findings reveal a novel distinction between the exocrine and endocrine cells of the pancreas and further identify PKD3 as a signaling molecule that promotes hormone-stimulated amylase secretion.Protein kinase D (PKD),² a serine/threonine kinase family with a catalytic domain homologous to the Ca²⁺/calmodulin-dependent kinase domain and two cysteine-rich phorbol ester binding domains similar to those of protein kinase C (PKC), is a physiologically important downstream mediator of diacylglycerol (DAG) signal transduction (1, 2). The mammalian PKDs include three members, PKD1, PKD2, and PKD3, which demonstrate different expression patterns and functions depending on the cell type and external signal stimuli. PKDs are ubiquitously expressed, but levels of individual isoforms vary with developmental stage and cell type (3). PKD proteins are reported to localize in the cytosol, Golgi, nucleus, and vesicle structures (4-9). Activation of PKDs results in a dynamic translocation among subcellular compartments (10, 11). Expression of multiple isoforms in different cell types and in different subcellular localizations suggests that individual PKD isoforms may serve specific functions. The majority of findings demonstrating the diverse expression patterns and functions of PKD have been described using established cell lines (4-9, 12). However, little is known about PKD isoform expression and function in normal differentiated cells and tissues.Recent functional studies have shown that PKD isoforms differentially regulate exocytic protein trafficking and cargo specificity (9, 12-14). Furthermore, PKD isoforms are differentially activated by oxidative stress signaling via PKCδ-mediated tyrosine phosphorylation (15). In each of these studies, PKD3 was found to have a regulatory mechanism or cellular function distinct from that of PKD1 and PKD2. Unlike the other two isoforms, PKD3 lacks the N terminus hydrophobic domain or the C terminus PDZ binding motif and contains divergent PH (pleckstrin homology) and C1 domains, which are important for regulating its catalytic activity (12, 16, 17). Current knowledge of the physiologic function of PKD3 is limited. It has been demonstrated using kinase-inactive mutants that PKD3 activity is required for basolateral exocytosis in Madin-Darby canine kidney cells (13). PKD3 has also been implicated in the epigenetic control of chromatin by regulating class II histone deacetylases in B lymphocytes (18). Furthermore, PKD3 was found to be a specific regulator of glucose transport in skeletal muscle cells (19).The exocrine pancreas is highly specialized for the synthesis, storage, and exocrine secretion of digestive enzymes and bicarbonate-rich fluid (20). More than 90% of the newly synthesized proteins in the pancreas is targeted to the secretory pathway (21). In addition, the pancreas contains a variety of endocrine cells localized to the islets which secrete peptide hormones. Numerous steps in the secretory pathway are modulated by DAG signaling, which promotes secretion by maintaining Golgi function and/or activating DAG receptor kinases such as PKCs, which are regulators of exocytic proteins (1, 22-25). PKD is also critical for DAG-mediated secretion, as it is recruited by DAG to the trans-Golgi network, where it phosphorylates the lipid kinase phosphatidylinositol 4-kinase to initiate the process of vesicle fission (9, 26). Gastrointestinal (GI) hormones such as cholecystokinin (CCK), gastrin, neurotensin (NT), and bombesin (BBS)/gastrin-releasing peptide are potent regulatory peptides that modulate pancreatic function (27, 28). They are known to activate PKDs to promote cell proliferation and survival in gut epithelial cells (29-32); however, the role of PKDs in modulating the secretory actions of GI hormones is unknown.Although the PKD isoforms have been reported to be expressed in secretory tissues such as salivary glands, adrenal glands, intestinal mucosa, and the pituitary (3, 5, 33), the role of PKD in the process of regulated secretion remains poorly understood. Previously, we demonstrated that PKD1 mediates NT peptide secretion from a pancreas-derived neuroendocrine cell line, BON, and that PKD1 activation is regulated by PKC and Rho/Rho kinase pathways (4); PKD1 and PKD2 isoforms are highly expressed in this endocrine cell line with little to no PKD3 expression, thus suggesting that PKD1/2 may be the predominant isoforms for endocrine secretion. The distribution and role of PKD isoforms in the pancreas, an organ with both exocrine and endocrine functions, is not known. Interestingly, we demonstrate that in both human and mouse pancreas, PKD3 is the predominant PKD isoform expressed in the exocrine acini, whereas PKD1 and PKD2 are more highly expressed in endocrine islets. PKD3 is catalytically activated by GI hormone stimulation of the pancreas, and its activation is dependent on CCK1/2 receptor binding and on DAG/PKC activity. PKD3 overexpression in mouse pancreatic acinar cells significantly increased CCK-mediated pancreatic amylase secretion, suggesting that PKD3, in concert with other signaling molecules, contributes to stimulated amylase secretion. Our findings reveal a distinct expression pattern in the exocrine and endocrine cells of the mouse and human pancreas and identify PKD3 as a novel DAG-activated mediator of the exocrine secretory process in response to GI hormone signaling.     

PKD is a kinase of Vps34 that mediates ROS-induced autophagy downstream of DAPk

Autophagy, a process in which cellular components are engulfed and degraded within double-membrane vesicles termed autophagosomes, has an important role in the response to oxidative damage. Here we identify a novel cascade of phosphorylation events, involving a network of protein and lipid kinases, as crucial components of the signaling pathways that regulate the induction of autophagy under oxidative stress. Our findings show that both the tumor-suppressor death-associated protein kinase (DAPk) and protein kinase D (PKD), which we previously showed to be phosphorylated and consequently activated by DAPk, mediate the induction of autophagy in response to oxidative damage. Furthermore, we map the position of PKD within the autophagic network to Vps34, a lipid kinase whose function is indispensable for autophagy, and demonstrate that PKD is found in the same molecular complex with Vps34. PKD phosphorylates Vps34, leading to activation of Vps34, phosphatydilinositol-3-phosphate (PI(3)P) formation, and autophagosome formation. Consistent with its identification as a novel inducer of the autophagic machinery, we show that PKD is recruited to LC3-positive autophagosomes, where it localizes specifically to the autophagosomal membranes. Taken together, our results describe PKD as a novel Vps34 kinase that functions as an effecter of autophagy under oxidative stress.     

Role of the Second Cysteine-rich Domain and Pro275 in Protein Kinase D2 Interaction with ADP-Ribosylation Factor 1, Trans-Golgi Network Recruitment,and Protein Transport

Protein kinase D (PKD) isoenzymes regulate the formation of transport carriers from the trans-Golgi network (TGN) that are en route to the plasma membrane. The PKD C1a domain is required for the localization of PKDs at the TGN. However, the precise mechanism of how PKDs are recruited to the TGN is still elusive. Here, we report that ADP-ribosylation factor (ARF1), a small GTPase of the Ras superfamily and a key regulator of secretory traffic, specifically interacts with PKD isoenzymes. ARF1, but not ARF6, binds directly to the second cysteine-rich domain (C1b) of PKD2, and precisely to Pro275 within this domain. Pro275 in PKD2 is not only crucial for the PKD2-ARF1 interaction but also for PKD2 recruitment to and PKD2 function at the TGN, namely, protein transport to the plasma membrane. Our data suggest a novel model in which ARF1 recruits PKD2 to the TGN by binding to Pro275 in its C1b domain followed by anchoring of PKD2 in the TGN membranes via binding of its C1a domain to diacylglycerol. Both processes are critical for PKD2-mediated protein transport.