Two-dimensional expression pattern analysis of protein kinases after separation by MicroRotofor/SDS–PAGE

A method for profiling the phosphorylation state of tyrosine protein kinases

Protein kinases are known to be implicated in various biological phenomena and diseases through their involvement in protein phosphorylation. Therefore, analysis of the activity of protein kinases by examination of their phosphorylation state is important to elucidate their mechanisms. However, a method for analyzing the phosphorylation state of entire protein kinases in cells is not established. In the present study, we developed a new profiling method to analyze the expression and phosphorylation state of protein kinases using a Multi-PK antibody and Phos-tag 2D-PAGE. When HL-60 cells were differentiated into macrophage-like cells induced by 12-O-tetradecanoylphorbol-13-acetate, we observed significant changes in the expression and phosphorylation state of immunoreactive spots by this method. These results show that tyrosine kinase expression levels and phosphorylation state are changed by differentiation. Taken together, the developed method will be a useful tool for analysis of intracellular tyrosine protein kinases.

Multi-PK antibodies: Powerful analytical tools to explore the protein kinase world

Diverse biological events are regulated through protein phosphorylation mediated by protein kinases. Some of these protein kinases are known to be involved in the pathogenesis of various diseases. Although 518 protein kinase genes were identified in the human genome, it remains unclear how many and what kind of protein kinases are expressed and activated in cells and tissues under varying situations. To investigate cellular signaling by protein kinases, we developed monoclonal antibodies, designated as Multi-PK antibodies, that can recognize multiple protein kinases in various biological species. These Multi-PK antibodies can be used to profile the kinases expressed in cells and tissues, identify the kinases of special interest, and analyze protein kinase expression and phosphorylation state. Here we introduce some applications of Multi-PK antibodies to identify and characterize the protein kinases involved in epigenetics, glucotoxicity in type 2 diabetes, and pathogenesis of ulcerative colitis. In this review, we focus on the recently developed technologies for kinomics studies using the powerful analytical tools of Multi-PK antibodies.

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Multi-PK antibodies recognize a wide variety of protein kinases.

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New analytical methods using Multi-PK antibodies for protein kinase studies are explained.

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Kinomics studies using Multi-PK antibodies are introduced.

Expression and phosphorylation state analysis of intracellular protein kinases using Multi-PK antibody and Phos-tag SDS-PAGE

Protein kinase expression and activity play important roles in diverse cellular functions through regulation of phosphorylation signaling. The most commonly used tools for detecting the protein kinase are protein kinase-specific antibodies, and phosphorylation site-specific antibodies were used for detecting activated protein kinase. Using these antibodies, only one kinase was analyzed at a time, however, a method for analyzing the expression and activation of a panel of protein kinases in cells is not established. Therefore, we developed a combined method using Multi-PK antibody and Phos-tag SDS-PAGE for profiling the expression and phosphorylation state of intracellular protein kinases. Using the new method, changes in the expression and phosphorylation state of various protein kinases were detected in cells treated with anticancer agent which inhibit multiple tyrosine kinase activities. Therefore, the new method is a useful technique for analysis of intracellular protein kinases.•

Multi-PK antibody recognizes a wide variety of protein kinases in various species.

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Using Phos-tag SDS-PAGE, phosphorylated proteins are visualized as slower migration bands compared with corresponding non-phosphorylated proteins.

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This combined method can be used for detecting changes in the expression and phosphorylation state of various intracellular protein kinases.

In-gel phosphatase assay using non-denaturing two-dimensional electrophoresis

We developed a method for detecting phosphatase activities in crude tissue extracts after separation of proteins by a novel non-denaturing two-dimensional electrophoresis. In the first dimension, protein samples were separated by a MicroRotofor, a liquid-phase isoelectric focusing, in the presence or absence of urea. In the second dimension, fractionated proteins by the MicroRotofor were resolved by a native polyacrylamide gel electrophoresis in the presence of 20 mM 2-mercaptoethanol. After electrophoresis, the polyacrylamide gel was directly immersed in a reaction mixture containing 4-methylumbelliferyl phosphate (MUP), a fluorogenic substrate, and phosphatase activities were detected as fluorescent bands. In this assay, a variety of phosphatase activities were clearly detected in gel when the tissue extracts were separated by the MicroRotofor in the presence of 1.5 M urea. Furthermore, after detecting phosphatase activities in polyacrylamide gel at neutral pH, its activities at acidic pH could be detected by immersing the gel in sodium citrate buffer (pH 3.0). Therefore, this method is a quite useful technique to analyze various phosphatases by sequential reactions with MUP under different conditions after sample separation by the two-dimensional electrophoresis.

PKL01, an Ndr kinase homologue in plant, shows tyrosine kinase activity

Protein phosphorylation by protein tyrosine (Tyr) kinases plays important roles in a variety of signalling pathways in cell growth, differentiation and oncogenesis in animals. Despite the absence of classical Tyr kinases in plants, a similar ratio of phosphotyrosine residues in phosphorylated proteins was found in Arabidopsis thaliana as in human. However, protein kinases responsible for tyrosine phosphorylation in plants except some dedicated dual-specificity kinases still remain unclear. In this study, we found that PKL01, a nuclear Dbf2-related (Ndr) kinase homologue in Lotus japonicus, was autophosphorylated at a tyrosine residue when it was expressed in Escherichia coli, but kinase-dead mutant of PKL01 was not. Tyrosine phophorylation site in PKL01 was identified as Tyr-56 by LC-MS/MS analysis. Recombinant PKL01, which had been dephosphorylated by an alkaline phosphatase, could be phosphorylated again at the Tyr residue when it was incubated with ATP. Furthermore, other Ndr kinases in plants and PKL01 phosphorylated on Tyr residues in the exogenous substrates such as poly(Glu, Tyr)(4:1) and casein. Therefore, the Ndr kinases in plants, which had been assumed as protein serine (Ser)/threonine (Thr) kinases, turned out to be dual-specificity kinases responsible for phosphorylation of Tyr residues and Ser/Thr residues in plant proteins.

α-synuclein phosphorylation and truncation are normal events in the adult human brain

α-synuclein is a key protein in Lewy body diseases (LBDs) and a major component of Lewy bodies and related aberrant cytoplasmic and neuritic inclusions. Regional differences in α-synuclein have been associated with selective neuronal vulnerability to Lewy pathology. Furthermore, phosphorylation at serine 129 (Ser129) and α-synuclein truncation have been considered crucial in the pathogenesis of Lewy inclusions. The present study shows consistent reduction in α-synuclein protein expression levels in the human substantia nigra and nucleus basalis of Meynert compared with other brain regions independently of age and pathology. Phosphorylated α-synuclein at Ser129 is naturally increased in these same regions, thus inversely related with the total amount of α-synuclein. In contrast, truncated α-synuclein is naturally observed in control and diseased brains and correlating with the total amount of α-synuclein. Several truncated variants have been identified where some of these variants are truncated at the C-terminal domain, whereas others are truncated at the N-terminal domain, and all are present in cases with and without Lewy pathology. Although accumulation of truncated α-synuclein variants and phosphorylated α-synuclein occurs in Lewy bodies, α-synuclein phosphorylation and truncation can be considered constitutive in control and diseased brains.

The frequency of 1,4-benzoquinone-lysine adducts in cytochrome c correlate with defects in apoptosome activation

Electrophile-mediated post-translational modifications (PTMs) are known to cause tissue toxicities and disease progression. These effects are mediated via site-specific modifications and structural disruptions associated with such modifications. 1,4-Benzoquinone (BQ) and its quinone-thioether metabolites are electrophiles that elicit their toxicity via protein arylation and the generation of reactive oxygen species. Site-specific BQ-lysine adducts are found on residues in cytochrome c that are necessary for protein-protein interactions, and these adducts contribute to interferences in its ability to facilitate apoptosome formation. To further characterize the structural and functional impact of these BQ-mediated PTMs, the original mixture of BQ-adducted cytochrome c was fractionated by liquid isoelectric focusing to provide various fractions of BQ-adducted cytochrome c species devoid of the native protein. The fractionation process separates samples based on their isoelectric point (pI), and because BQ adducts form predominantly on lysine residues, increased numbers of BQ adducts on cytochrome c correlate with a lower protein pI. Each fraction was analyzed for structural changes, and each was also assayed for the ability to support apoptosome-mediated activation of caspase-3. Circular dichroism revealed that several of the BQ-adducted cytochrome c species maintained a slightly more rigid structure in comparison to native cytochrome c. BQ-adducted cytochrome c also failed to activate caspase-3, with increasing numbers of BQ-lysine adducts corresponding to a greater inability to activate the apoptosome. In summary, the specific site of the BQ-lysine adducts, and the nature of the adduct, are important determinants of the subsequent structural changes to cytochrome c. In particular, adducts at sites necessary for protein-protein interactions interfere with the proapoptotic function of cytochrome c.

Calcium/calmodulin-dependent protein kinase IV involvement in the pathophysiology of glucotoxicity in rat pancreatic β-cells

Glucotoxicity is a critical component of the pathophysiology of type 2 diabetes mellitus; however, the molecular mechanisms of glucotoxicity are still not fully understood. We have attempted to determine the protein kinases involved in glucotoxicity in pancreatic β-cells by the use of a new technique. Using Multi-PK antibodies, which are capable of detecting a wide variety of protein kinases, we analyzed the protein kinase that correlated with insulin synthesis in INS-1 cells under glucotoxic conditions. When expression patterns of protein kinases in INS-1 cells were analyzed by Western blotting with Multi-PK antibodies, a kinase of 63 kd was significantly reduced concomitant with the decrease of insulin secretion under glucotoxic conditions. To identify the 63-kd kinase, we used a unique 2-dimensional gel electrophoretic technique and MicroRotofor (Bio-Rad Laboratories, Tokyo, Japan) electrophoresis. From the molecular size of a native kinase/cyanogen bromide fragment and pI value, the 63-kd protein kinase was deduced to be CaMKIV. This was confirmed by Western blotting analysis using anti-CaMKIV antibodies. The decreased CaMKIV levels under glucotoxic conditions recovered to original levels after changing the medium to a normal glucose concentration. Recombinant CaMKIV was degraded in a Ca²+-dependent manner by incubation with cell lysates from INS-1 cells under glucotoxic conditions, and degradation was protected by calpain inhibitor. Furthermore, CaMKIV was reduced in the pancreatic islets of diabetic Otsuka Long-Evans Tokushima fatty rats, whereas that of nondiabetic Long-Evans Tokushima Otsuka rats was not. This study suggests that the abnormal regulation of CaMKIV is a component of β-cell dysfunction caused by high glucose.

Identification of an endogenous substrate of zebrafish doublecortin-like protein kinase using a highly active truncation mutant

Doublecortin-like protein kinase (DCLK), a Ser/Thr protein kinase predominantly expressed in brain and eyes, is believed to play crucial roles in neuronal functions. However, the regulatory mechanisms for DCLK activation and its physiological targets are still unknown. In the present study, we found that a deletion mutant consisting of the catalytic domain of zebrafish DCLK, zDCLK(377-677), exhibited the highest activity among various mutants. Since fully active zDCLK(377-677) showed essentially the same substrate specificity as wild-type zDCLK, we used it to search for physiological substrates of zDCLK. When a zebrafish brain extract was resolved by isoelectric focusing and then phosphorylated by zDCLK(377-677), a highly basic protein with a molecular mass of approximately 90 kDa was detected. This protein was identified as synapsin II by mass spectrometric analysis. Synapsin II was found to interact with the catalytic domain of zDCLK and was phosphorylated at Ser-9 and Ser-58. When synaptosomes were isolated from zebrafish brain, both synapsin II and zDCLK were found to coexist in this preparation. Furthermore, synapsin II in the synaptosomes was efficiently phosphorylated by zDCLK. These results suggest that zDCLK mediates its neuronal functions through phosphorylation of physiological substrates such as synapsin II.

Cyclin-dependent kinase-like 5 binds and phosphorylates DNA methyltransferase 1

DNA methyltransferase 1 (Dnmt1) is an enzyme that recognizes and methylates hemimethylated CpG after DNA replication to maintain methylation patterns. Although the N-terminal region of Dnmt1 is known to interact with various proteins, such as methyl-CpG-binding protein 2 (MeCP2), the associations of protein kinases with this region have not been reported. In the present study, we found that a 110-kDa protein kinase in mouse brain could bind to the N-terminal domain of Dnmt1. This 110-kDa kinase was identified as cyclin-dependent kinase-like 5 (CDKL5) by LC-MS/MS analysis. CDKL5 and Dnmt1 were found to colocalize in nuclei and appeared to interact with each other. Catalytically active CDKL5, CDKL5(1-352), phosphorylated the N-terminal region of Dnmt1 in the presence of DNA. Considering that defects in the MeCP2 or CDKL5 genes cause Rett syndrome, we propose that the interaction between Dnmt1 and CDKL5 may contribute to the pathogenic processes of Rett syndrome.