Protein kinases in amphibian ectoderm induced for neural differentiation

Summary Ectoderm explants from early gastrula stages of Xenopus laevis were induced with a neutralizing factor. The factor was isolated from Xenopus gastrulae and partially purified by chromatography on DEAE cellulose. The ectoderm was cultured for different periods of time and then homogenized. Protein kinase activity was determined in the homogenates from induced and control explants with histone H 1 or C-terminal peptide derived from histone H 1 as substrates. The C-terminal peptide is a more specific substrate for protein kinase C, whereas histoneH 1 is a substrate for cAMP/cGMP-dependent protein kinases as well protein kinase C. With both substrates the enzyme activity increases after induction. With the C-terminal peptide as the substrate the protein kinase activity is lower, but its relative increase after induction higher. This suggests that besides cAMP/cGMP dependent protein kinases protein kinase C or related enzymes are involved in the neural induction and differentiation processes. This corresponds to previous experiments which have shown that treatment of ectoderm with phorbol myristate acetate, an activator of protein kinase C and protein kinase C related enzymes, initiates neural differentiation. Endogeneous substrates, which are more intensively phosphorylated after induction are proteins with apparent molecular weights 21 kDa and 31 kDa. Addition of protein kinase C to the induced and control homogenates abolishes the difference in the phosphorylation rate of these proteins.     

Protein kinases in elicitor signal transduction in plant cells

Plants have the ability to respond to pathogen invasion by specific defense reactions. Components of mammalian signal transduction chains have been identified in plants, and several lines of evidence have implicated such components in elicitor signal transmission in defense responses. In particular, it has been assumed that elicitor signals are transduced via a protein kinase cascade, although the identity of the protein kinases and the function of the phosphorylated proteins remain to be determined. The purpose of this review is to discuss the roles of protein kinases in elicitor signal transduction pathways in plant cells based on recent progress in this field.     

Calcified structures and calcification in protists

Summary The diversity of calcified structures found in protists, the mechanisms utilized to form these structures, and the role these structures play in the taxonomy and systematics of the protists are presented. The two most frequently studied orders of protists which produce calcified structures, the coccolithophorids and foraminifera, are featured. However, consideration is given to the less known and least studied organisms.     

Evolution of thesrc-related protein tyrosine kinases

A phylogenetic analysis ofsrc-related protein tyrosine kinases (PTKs) showed that one group of these genes is quite ancient in the animals, its divergence predating the divergence of the diploblast and triploblast phyla. Three other major groupings of genes were found to predate the divergence of protostome and deuterostome phyla. Most knownsrc-related PTKs of mammals were found to belong to five well-differentiated families: srcA, srcB, abl, csk, and tec. One srcA gene (fyn) has an alternatively spliced seventh exon which shows a different pattern of relationship from the remainder of the gene; this suggests that this exon may have been derived by a recombinational event with another gene, perhaps one related tofgr. The recently published claim that mammalian members of this family expressed in the nervous system evolve more slowly at nonsynonymous nucleotide sites than do those expressed in the immune system was not supported by an analysis of 13 pairs of human and mouse orthologues. Rather, T-cell-specificsrc-related PTKs were found to have higher rates of nonsynonymous substitution than were those having broader expression. This effect was particularly marked in the peptide binding site of the SH2 domain. While the SH2 binding site was highly conserved among paralogous mammalian members of the srcA and srcB subfamilies, no such effect was seen in the comparison of paralogous members of the csk and tec subfamilies. This suggests that, while the peptide binding function of SH2 is conserved within both srcA and srcB subfamilies, paralogous members of the csk and tec subfamilies have diverged functionally with respect to peptide recognition by SH2.     

Siliceous structures and silicification in flagellated protists

Summary Flagellated protists produce a diverse range of siliceous structures, such as internal and external skeletons, scales, spines, bristles, cell walls, cyst walls, and loricae. The different groups of silica-depositing flagellates, i.e., chrysophytes/synurophytes, choanoflagellates, dinoflagellates, ebriids, silicoflagellates, thaumatomastigids, and the genusPetasaria are reviewed. Brief mention is also given to those algal groups in which silicification is uncommon and rare (i.e., chlorophytes, euglenophytes, haptophytes/prymnesiophytes, xanthophytes/tribophytes), but in which silicified structures nevertheless occur in few flagellate genera. Special attention is given to aspects of morphology and development of the different siliceous structures as well as on aspects of systematics and taxonomy.     

Protein kinases in Toxoplasma gondii

Toxoplasma gondii is an obligatory intracellular pathogen that causes life threatening illness in immunodeficient individuals, miscarriage in pregnant woman, and blindness in newborn children. Similar to any other eukaryotic cell, protein kinases play critical and essential roles in the Toxoplasma life cycle. Accordingly, many studies have focused on identifying and defining the mechanism of function of these signalling proteins with a long-term goal to develop anti-Toxoplasma therapeutics. In this review, we briefly discuss classification and key components of the catalytic domain which are critical for functioning of kinases, with a focus on domains, families, and groups of kinases within Toxoplasma. More importantly, this article provides a comprehensive, current overview of research on kinase groups in Toxoplasma including the established eukaryotic AGC, CAMK, CK1, CMGC, STE, TKL families and the apicomplexan-specific FIKK, ROPK and WNG family of kinases. This work provides an overview and discusses current knowledge on Toxoplasma kinases including their localization, function, signalling network and role in acute and chronic pathogenesis, with a view towards the future in probing kinases as viable drug targets.     

Direct and indirect effects in microcosm communities of protists

Increased complexity in biological communities can increase the variety of interactions among species, but the relative strengths and long-term consequences of various direct and indirect interactions require further investigation. I studied interactions among four species of protists by monitoring their population dynamics when they were cultured either together or in seven different subset communities. Two protists were bacterivores (Chilomonas and Tetrahymena) and two were predators (Actinosphaerium and Euplotes). Actinosphaerium was omnivorous, and could eat both predatory Euplotes and bacterivores. Three indirect effects occurred among the four species of protists, including indirect facilitation of one predator by the other, apparent competition between bacterivores, and indirect facilitation of one bacterivore by the omnivorous predator. Community structure and invasibility depended on both direct and indirect effects; thus both can be mechanisms for assembly rules.     

Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules, aiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization.     

Protein kinases and protein phosphatases in prokaryotes: a genomic perspective

For many years, the regulation of protein structure and function by phosphorylation and dephosphorylation was considered a relatively recent invention that arose independently in each phylogenetic domain. Over time, however, incidents of apparent domain trespass involving the presence of 'eukaryotic' protein kinases or protein phosphatases in prokaryotic organisms were reported with increasing frequency. Today, genomics has provided the means to examine the phylogenetic distribution of 'eukaryotic' protein kinases and protein phosphatases in a comprehensive and systematic manner. The results of these genome searches challenge previous conceptions concerning the origins and evolution of this versatile regulatory mechanism.     

Alpha-kinases: analysis of the family and comparison with conventional protein kinases

Alpha-kinases are a recently discovered family of protein kinases that have no detectable sequence homology to conventional protein kinases (CPKs). They include elongation factor 2 kinase, Dictyostelium myosin heavy chain kinases and many other protein kinases from diverse organisms, as revealed by various genome sequencing projects. Mammals have six alpha-kinases, including two channel-kinases-novel signaling molecules that contain an alpha-kinase domain fused to an ion-channel. Analysis of all known alpha-kinase sequences reveals the presence of several highly conserved motifs. Despite the fact that alpha-kinases have no detectable sequence identity with CPKs, the recently determined three-dimensional structure of the channel-kinase TRPM7/ChaK1 kinase domain reveals that alpha-kinases have a fold very similar to CPKs. Using the structural alignment of channel-kinase TRPM7/ChaK1 with cyclic-AMP dependent kinase, the consensus motifs of alpha-kinases and CPKs were aligned and compared. Remarkably, the majority of structural elements, sequence motifs, and the position of key amino acid residues important for catalysis appear to be very similar in alpha-kinases and CPKs. Differences between alpha-kinases and CPKs, and their possible impact on substrate recognition are discussed.     

Protein kinases and multidrug resistance

The role of protein kinases in the multidrug resistance phenotype of cancer cell lines is discussed with an emphasis on protein kinase C and protein kinase A. Evidence that P-glycoprotein is phosphorylated by these kinases is summarised and the relationship between P-glycoprotein phosphorylation and the multidrug-resistant phenotype discussed. Results showing that protein kinase C, particularly the alpha subspecies, is overexpressed in many MDR cell lines are described: this common but by no means universal finding seems to be drug- and cell line-dependent and in only in a few cases is there a direct correlation between protein kinase C activity and multidrug resistance. From co-immunoprecipitation results it is suggested that P-glycoprotein is a specific protein kinase C receptor, as well as being a substrate. Revertant experiments provide conflicting results as to a direct relationship between expression of P-glycoprotein and protein kinase C. Evidence that protein kinase A influences P-glycoprotein expression at the gene level is well documented and the mechanisms by which this occurs are becoming clarified. Results on the relationship between protein kinase C and multidrug resistance using many inhibitors and phorbol esters are difficult to interpret because such compounds bind to P-glycoprotein. In spite of huge effort, a direct involvement of protein kinase C in regulating multidrug resistance has not yet been firmly established. However, evidence that PKC regulates a Pgp-independent mechanism of drug resistance is accumulating. This revised version was published online in August 2006 with corrections to the Cover Date.     

Protein kinases predominately expressed in human ES cell lines during differentiation

Capacity of human embryonic stem cells (ESC) for unlimited proliferation and differentiation make them an attractive object in fundamental science and medicine. Little is known about the mechanisms that direct cells to particular differentiation or sustain them in an undifferentiated state. Activation of these mechanisms is determined by gene expression mediated by cascades of signal transduction. Protein kinases are essential components of signal pathways. The study of protein kinases expression in ESC and embryoid bodies facilitates a better understanding of the processes underlying the differentiation stages. We isolated cDNA libraries with fragments of catalytic domains of protein kinases expressed in human ESC and embryoid bodies (EB) of hESM01 and hESM02 cell lines. Using Northern hybridization, we revealed a high level of protein kinases MAK-V in human ESC. Expressions of MAK-V, A-RAF-1, MAPK3, IGF1R, NEK3, and NEK7 in ESC and EB in hESM01 and hESM02 cell lines were compared by the semiquantitative method RT-PCR.     

Protein tyrosine kinases in neutrophil activation and recruitment

Migration of leukocytes into tissue is a key element of innate and adaptive immunity. The first contact of leukocytes with endothelial cells is mediated by engagement of selectins with their counter-receptors which results in leukocyte rolling. During rolling, leukocytes collect different inflammatory signals that activate intracellular signaling pathways. Integration of these signals induces leukocyte activation, firm arrest, post-adhesion strengthening, intravascular crawling, and transmigration. In neutrophils, like in T-cells and platelets, both G-protein-coupled receptor-dependent and -independent activation pathways exist that lead to integrin activation. Accumulating evidence suggests that different protein tyrosine kinases play key roles in signal transduction pathways regulating neutrophil activation and recruitment to inflammatory sites. This review focuses on the role of protein tyrosine kinases of the Src, Syk, and Tec families for neutrophil activation and recruitment.     

Protein kinases expressed by interstitial cells of Cajal

Interstitial cells of Cajal (ICC) are involved in the generation of electrical rhythmicity of intestinal muscle and in the transduction of neural inputs in the gut. Although the expression of receptors for neurotransmitters and hormones and some second messengers have been investigated in ICC, the protein kinases present in these cells have not been well documented. This study has demonstrated the immunohistochemical localisation of PKA, PKC and PKC in ICC that were identified by the known ICC marker, c-Kit, in the guinea-pig gut. Other PKCs, PKC , , , , , and , and Ca²⁺-calmodulin-dependent protein kinase II were not localised in ICC. Double labelling studies were conducted on longitudinal muscle–myenteric plexus and external muscle–myenteric plexus preparations of the oesophagus, stomach (fundus, corpus and antrum), duodenum, distal ileum, caecum, proximal and distal colon, and rectum. The three protein kinases were detected in c-Kit-immunoreactive ICC at the level of the myenteric plexus (IC-MY), in the muscle (IC-IM) and at the level of the deep muscular plexus (IC-DMP) in the small intestine. PKA was found in over 90% of IC-IM in all regions examined, and in over 90% of IC-MY in the gastric body and antrum and throughout the small and large intestines. PKC was in the majority of ICC in the gastric body and antrum and in the small intestine, but was largely absent from ICC in the oesophagus, proximal stomach and large intestine. PKC occurred in the majority of ICC in all regions except the rectum. The intensity of staining was greatest for PKA, with PKC giving comparatively weak labelling of ICC. PKA was also detected in myenteric neurons, smooth muscle, macrophages and fibroblast-like cells. PKC labelling occurred in large, multipolar neurons throughout the small and large intestine, as well as in lymph vessels and in capillaries. It is concluded that PKA, PKC and PKC are all present in ICC, with the differences in their localisations suggesting specific roles for each in ICC function.     

Reconciliation of evolution and nomenclature among the higher taxa of protists*

Existing taxonomic schemes for the protists at the highest levels are confusing owing to insensitivity to evolutionary data, lack of stability, evolutionary misleading terminology and multiple, contradictory systems. We propose a system which circumvents these problems by recognizing the largest monophyletic groups possible, and creating a nomenclature for these by appending the suffix ‘protista’ onto an already recognizable prefix: for example, euglenoprotista, cilioprotista, chytridioprotista. This system provides a high degree of stability while also allowing for the further clustering of these groups and inclusion of their descendant groups, such as the plants, as more evolutionary data become available.     

Depolarisation-Dependent Protein Phosphorylation and Dephosphorylation in Rat Cortical Synaptosomes Is Modulated by Calcium

The effect of calcium on protein phosphorylation was investigated using intact synaptosomes isolated from rat cerebral cortex and prelabelled with 32Pi. For nondepolarised synaptosomes a group of calcium-sensitive phosphoproteins were maximally labelled in the presence of 0.1 mM calcium. The phosphorylation of these proteins was slightly decreased in the presence of strontium and absent in the presence of barium, consistent with the decreased ability of these cations to activate calcium-stimulated protein kinases. Addition of calcium alone to synaptosomes prelabelled in its absence increased phosphorylation of a number of proteins. On depolarisation in the presence of calcium certain of the calcium-sensitive phosphoproteins were further increased in labelling above nondepolarised levels. These increases were maximal and most sustained after prelabelling at 0.1 mM calcium. On prolonged depolarisation at this calcium concentration a slow decrease in labelling was observed for most phosphoproteins, whereas a greater rate and extent of decrease occurred at higher calcium concentrations. At 2.5 mM calcium a rapid and then a subsequent slow dephosphorylation was observed, indicating two distinct phases of dephosphorylation. Of all the phosphoproteins normally stimulated by depolarisation, only phosphoprotein 59 did not exhibit the rapid phase of dephosphorylation at high calcium concentrations. Replacing calcium with strontium markedly decreased the extent of change observed on depolarisation whereas barium decreased phosphorylation changes even further. Taken together these data suggest that an influx of calcium into synaptosomes initially activates protein phosphorylation, but as the levels of intrasynaptosomal calcium rise protein dephosphorylation predominates. Other phosphoproteins were dephosphorylated immediately on depolarisation in the presence of calcium. The fine control of protein phosphorylation levels exerted by calcium supports the idea that the synaptosomal phosphoproteins could play a role in modulating events such as neurotransmitter release in the nerve terminal.     

Molecular evolution of calmodulin-like domain protein kinases (CDPKs) in plants and protists

Many genes for calmodulin-like domain protein kinases (CDPKs) have been identified in plants and Alveolate protists. To study the molecular evolution of the CDPK gene family, we performed a phylogenetic analysis of CDPK genomic sequences. Analysis of introns supports the phylogenetic analysis; CDPK genes with similar intron/exon structure are grouped together on the phylogenetic tree. Conserved introns support a monophyletic origin for plant CDPKs, CDPK-related kinases, and phosphoenolpyruvate carboxylase kinases. Plant CDPKs divide into two major branches. Plant CDPK genes on one branch share common intron positions with protist CDPK genes. The introns shared between protist and plant CDPKs presumably originated before the divergence of plants from Alveolates. Additionally, the calmodulin-like domains of protist CDPKs have intron positions in common with animal and fungal calmodulin genes. These results, together with the presence of a highly conserved phase zero intron located precisely at the beginning of the calmodulin-like domain, suggest that the ancestral CDPK gene could have originated from the fusion of protein kinase and calmodulin genes facilitated by recombination of ancient introns. Received: 11 July 2000 / Accepted: 18 April 2001     

Polyamine uptake in cultured astrocytes: characterization and modulation by protein kinases

The properties and regulation of the polyamine transport system in brain are still poorly understood. The present study shows, for the first time, the existence of a polyamine transport system in cerebellar astrocytes and suggests that polyamine uptake is mediated by a single and saturable high-affinity transport system for putrescine, spermine, and spermidine (K:(m) = 3.2, 1.2, and 1.8 microM:, respectively). Although substitution of NaCl by choline chloride produced a decrease in the putrescine, spermine, and spermidine uptake, it seems that polyamine transport in cerebellar astrocytes is not mediated by an Na(+) cotransport as in the presence of Na(+) and cholinium, polyamine uptake was much lower than when measured in a sucrose-based medium. On the other hand, ouabain, gramicidin (a Na(+) ionophore), and ionomycin (a Ca(2+) ionophore) produced a strong inhibition of polyamine uptake, suggesting that membrane potential could have an important role in the functioning of the astroglial polyamine uptake system. Moreover, protein kinase C inhibition produced an enhancement of polyamine uptake, whereas stimulation of protein kinase C with phorbol esters inhibited polyamine uptake. Alternatively, the tyrosine kinase inhibitor genistein caused a marked reduction in the uptake. No effects on polyamine uptake were observed with inhibitors and activators of cyclic AMP-dependent protein kinase or when Ca(2+)/calmodulin-dependent protein kinase II was inhibited with KN-62. These results suggest that the polyamine uptake system in cerebellar astrocytes could be modulated by protein kinase C and tyrosine kinase activities.     

Protein flexibility in ligand docking and virtual screening to protein kinases

The main complicating factor in structure-based drug design is receptor rearrangement upon ligand binding (induced fit). It is the induced fit that complicates cross-docking of ligands from different ligand-receptor complexes. Previous studies have shown the necessity to include protein flexibility in ligand docking and virtual screening. Very few docking methods have been developed to predict the induced fit reliably and, at the same time, to improve on discriminating between binders and non-binders in the virtual screening process.We present an algorithm called the ICM-flexible receptor docking algorithm (IFREDA) to account for protein flexibility in virtual screening. By docking flexible ligands to a flexible receptor, IFREDA generates a discrete set of receptor conformations, which are then used to perform flexible ligand-rigid receptor docking and scoring. This is followed by a merging and shrinking step, where the results of the multiple virtual screenings are condensed to improve the enrichment factor. In the IFREDA approach, both side-chain rearrangements and essential backbone movements are taken into consideration, thus sampling adequately the conformational space of the receptor, even in cases of large loop movements.As a preliminary step, to show the importance of incorporating protein flexibility in ligand docking and virtual screening, and to validate the merging and shrinking procedure, we compiled an extensive small-scale virtual screening benchmark of 33 crystal structures of four different protein kinases sub-families (cAPK, CDK-2, P38 and LCK), where we obtained an enrichment factor fold-increase of 1.85±0.65 using two or three multiple experimental conformations. IFREDA was used in eight protein kinase complexes and was able to find the correct ligand conformation and discriminate the correct conformations from the “misdocked” conformations solely on the basis of energy calculation. Five of the generated structures were used in the small-scale virtual screening stage and, by merging and shrinking the results with those of the original structure, we show an enrichment factor fold increase of 1.89±0.60, comparable to that obtained using multiple experimental conformations.Our cross-docking tests on the protein kinase benchmark underscore the necessity of incorporating protein flexibility in both ligand docking and virtual screening. The methodology presented here will be extremely useful in cases where few or no experimental structures of complexes are available, while some binders are known.