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At least 19 recordsLinked to original sources
PubMed2006

Functional analysis of protein kinase networks in living cells: beyond "knock-outs" and "knock-downs".

The identification of over 500 protein kinases encoded by the human genome sequence offers one measure of the importance of protein kinase networks in cell biology. High throughput technologies for inactivating genes are producing an awe-inspiring amount of data on the cellular and organismal effects of reducing the levels of individual protein kinases. Despite these technical advances, our understanding of kinase networks remains imprecise. Major challenges include correctly assigning kinases to particular networks, understanding how they are regulated, and identifying the relevant in vivo substrates. Genetic methods provide a way of addressing these questions, but their application requires understanding the nuances of how different types of mutations can affect protein kinases. The goal of this article is to provide a brief introductory primer into these issues using examples from yeast MAPK cascades and to motivate future systematic genetic analysis focusing on individual residues of protein kinases.

Genetic Techniques↗
PubMed2005

Structural and dynamical analyses of the kinase network derived from the transpath database.

We analyze the structural design and the dynamical properties of a protein kinase network derived from the Transpath database. We consider structural properties, such as feedback cycles, pathway lengths, fraction of shortest pathways and crosstalk. Dynamic characteristics of the network are analyzed by using nonlinear differential equations with a special focus on kinase amplitudes and signal propagation times. Comparison with random networks shows that the cellular kinase network exhibits special features which might be a result of natural selection. In particular, the Transpath network contains no cycles, and input kinases and output kinases are generally connected by shortest signalling routes. Moreover, it displays a characteristic spectrum of cross-talk between different pathways.

Algorithms↗
PubMed2006

Identification of functional domains within the septation initiation network kinase, Cdc7.

The septation initiation network (SIN) serves to coordinate cytokinesis with mitotic exit in the fission yeast Schizosaccharomyces pombe. SIN components Spg1 and Cdc7 together play a central role in regulating the onset of septation and cytokinesis. Spg1, a Ras-like GTPase, localizes to the spindle pole bodies (SPBs) throughout the cell cycle. It is converted to its GTP-bound (active) state during mitosis, only to become inactivated at one SPB during anaphase and at both SPBs as cells exit mitosis. Cdc7 functions as an effector kinase for Spg1, binding to Spg1 in its GTP-bound state, and therefore is present at both SPBs during mitosis and asymmetrically at only one during anaphase. Interestingly, the kinase activity of Cdc7 does not vary across the cell cycle, suggesting the possibility that Cdc7 kinase activity is independent of Spg1 binding. Consistent with this, we found that Cdc7 associates with Spg1 only during mitosis. To learn more about the essential role of Cdc7 kinase in the SIN and its regulation, we undertook a structure/function analysis and identified independent functional domains within Cdc7. We found that a region adjacent to the kinase domain is responsible for Spg1 association and identified an overlapping but distinct SPB localization domain. In addition Cdc7 associates with itself and exists as a dimer in vivo.

Binding Sites↗
PubMed2003

Protein kinase network in the regulation of phosphorylation and dephosphorylation of smooth muscle myosin light chain.

The contraction of smooth muscle is regulated primarily by intracellular Ca2+ signal. It is well established that the elevation of the cytosolic Ca2+ level activates myosin light chain kinase, which phosphorylates 20 kDa regulatory myosin light chain and activates myosin ATPase. The simultaneous measurement of cytosolic Ca2+ concentration and force development revealed that the alteration of the Ca2+-sensitivity of the contractile apparatus as well as the Ca2+ signal plays a critical role in the regulation of smooth muscle contraction. The fluctuation of an extent of myosin phosphorylation for a given change in Ca2+ concentration is considered to contribute to the major mechanisms regulating the Ca2+-sensitivity. The level of myosin phosphorylation is determined by the balance between phosphorylation and dephosphorylation. The phosphorylation level for a given Ca2+ elevation is increased either by Ca2+-independent activation of phosphorylation process or inhibition of dephosphorylation. In the last decade, the isolation and cloning of myosin phosphatase facilitated the understanding of regulatory mechanism of dephosphorylation process at the molecular level. The inhibition of myosin phosphatase can be achieved by (1) alteration of hetrotrimeric structure, (2) phosphorylation of 110 kDa regulatory subunit MYPT1 at the specific site and (3) inhibitory protein CPI-17 upon its phosphorylation. Rho-kinase was first identified to phosphorylate MYPT1, and later many kinases were found to phosphorylate MYPT1 and inhibit dephosphorylation of myosin. Similarly, the phosphorylation of CPI-17 can be catalysed by multiple kinases. Moreover, the myosin light chain can be phosphorylated by not only authentic myosin light chain kinase in a Ca2+-dependent manner but also by multiple kinases in a Ca2+-independent manner, thus adding a novel mechanism to the regulation of the Ca2+-sensitivity by regulating the phosphorylation process. It is now clarified that the protein kinase network is involved in the regulation of myosin phosphorylation and dephosphorylation. However, the physiological role of each component remains to be determined. One approach to accomplish this purpose is to investigate the effects of the dominant negative mutants of the signalling molecule on the smooth muscle contraction. In this regards, a protein transduction technique utilizing the cell-penetrating peptides would provide a useful tool. In the preliminary study, we succeeded in introducing a fragment of MYPT1 into the arterial strips, and found enhancement of contraction.

Adenosine Triphosphatases↗
PubMed1995

Ras-dependent and -independent pathways target the mitogen-activated protein kinase network in macrophages.

Mitogen-activated protein kinases (MAPKs) are activated upon a variety of extracellular stimuli in different cells. In macrophages, colony-stimulating factor 1 (CSF-1) stimulates proliferation, while bacterial lipopolysaccharide (LPS) inhibits cell growth and causes differentiation and activation. Both CSF-1 and LPS rapidly activate the MAPK network and induce the phosphorylation of two distinct ternary complex factors (TCFs), TCF/Elk and TCF/SAP. CSF-1, but not LPS, stimulated the formation of p21ras. GTP complexes. Expression of a dominant negative ras mutant reduced, but did not abolish, CSF-1-mediated stimulation of MEK and MAPK. In contrast, activation of the MEK kinase Raf-1 was Ras independent. Treatment with the phosphatidylcholine-specific phospholipase C inhibitor D609 suppressed LPS-mediated, but not CSF-1-mediated, activation of Raf-1, MEK, and MAPK. Similarly, down-regulation or inhibition of protein kinase C blocked MEK and MAPK induction by LPS but not that by CSF-1. Phorbol 12-myristate 13-acetate pretreatment led to the sustained activation of the Raf-1 kinase but not that of MEK and MAPK. Thus, activated Raf-1 alone does not support MEK/MAPK activation in macrophages. Phosphorylation of TCF/Elk but not that of TCF/SAP was blocked by all treatments that interfered with MAPK activation, implying that TCF/SAP was targeted by a MAPK-independent pathway. Therefore, CSF-1 and LPS target the MAPK network by two alternative pathways, both of which induce Raf-1 activation. The mitogenic pathway depends on Ras activity, while the differentiation signal relies on protein kinase C and phosphatidylcholine-specific phospholipase C activation.

Amino Acid Sequence↗
PubMed2006

Signaling through MAP kinase networks in plants.

Protein phosphorylation is the most important mechanism for controlling many fundamental cellular processes in all living organisms including plants. A specific class of serine/threonine protein kinases, the mitogen-activated protein kinases (MAP kinases) play a central role in the transduction of various extra- and intracellular signals and are conserved throughout eukaryotes. These generally function via a cascade of networks, where MAP kinase (MAPK) is phosphorylated and activated by MAPK kinase (MAPKK), which itself is activated by MAPKK kinase (MAPKKK). Signaling through MAP kinase cascade can lead to cellular responses including cell division, differentiation as well as response to various stresses. In plants, MAP kinases are represented by multigene families and are organized into a complex network for efficient transmission of specific stimuli. Putative plant MAP kinase cascades have been postulated based on experimental analysis of in vitro interactions between specific MAP kinase components. These cascades have been tested in planta following expression of epitope-tagged kinases in protoplasts. It is known that signaling for cell division and stress responses in plants are mediated through MAP kinases and even auxin, ABA and possibly ethylene and cytokinin also utilize a MAP kinase pathway. Most of the biotic (pathogens and pathogen-derived elicitors) including wounding and abiotic stresses (salinity, cold, drought, and oxidative) can induce defense responses in plants through MAP kinase pathways. In this article we have covered the historical background, biochemical assay, activation/inactivation, and targets of MAP kinases with emphasis on plant MAP kinases and the responses regulated by them. The cross-talk between plant MAP kinases is also discussed to bring out the complexity within this three-component module.

Arabidopsis↗
PubMed2004

Integration and channeling of calcium signaling through the CBL calcium sensor/CIPK protein kinase network.

Plant development and reproduction depend on a precise recognition of environmental conditions and the integration of this information with endogenous metabolic and developmental cues. Calcium ions have been firmly established as ubiquitous second messengers functioning in these processes. Calcium signal deciphering and signal-response coupling often involve calcium-binding proteins as responders or relays in this information flow. Here we review the calcineurin B-like protein (CBL) calcium sensor/CBL-interacting protein kinase (CIPK) network as a newly emerging signaling system mediating a complex array of environmental stimuli. We focus particularly on the mechanisms generating signaling specificity. Moreover, we emphasize the functional implications that are emerging from the analyses of CBL and CIPK loss-of-function mutants.

Calcium↗
PubMed2002

A CDK-activating kinase network is required in cell cycle control and transcription in fission yeast.

Cyclin-dependent kinases (CDKs) involved in cell cycle control require activation by phosphorylation, but CDK-activating kinase (CAK) has diverged between metazoans and budding yeast. Fission yeast has two CAKs: the essential Mcs6 complex, homologous to the metazoan CDK7 complex implicated in cell cycle control and transcription; and Csk1, a nonessential ortholog of budding yeast Cak1. Both can activate the major CDK, Cdc2, but Csk1 can also activate Mcs6, so it was unclear whether the pathway is a linear cascade or a network. Here, we show that a mutation, mcs6-13, which selectively abrogates CDK activation, blocks both G1/S and G2/M transitions, but only when csk1(+) is absent. In contrast, gradual depletion or rapid inactivation of Mcs6 in csk1(+) cells causes cell separation defects or growth arrest, respectively, accompanied by decreased phosphorylation of RNA polymerase II (RNAP II), but not of Cdc2. Finally, neither cell cycle arrest nor CAK failure is recapitulated by a second mutation in mcs6-13 that prevents Mcs6 activation by Csk1, indicating that Csk1 activates Cdc2 directly in vivo. Thus, Mcs6 acts in concert with Csk1 to activate Cdc2 and independently to support transcription and facilitate cell separation. Csk1 likewise has multiple physiologic targets, including Mcs6 and Cdc2.

CDC2 Protein Kinase↗
PubMed2005

Hyposmolarity-induced ErbB4 phosphorylation and its influence on the non-receptor tyrosine kinase network response in cultured cerebellar granule neurons.

Exposure of cultured cerebellar granule neurons (24 h serum-starved) during 3 min to 30% hyposmotic medium activated the tyrosine kinase receptor ErbB4 in the absence of its ligand. Hyposmolarity also activated the non-receptor tyrosine kinases, Src, focal adhesion kinase (FAK), extracellular signal-regulated protein kinase (ERK)1/2, and the tyrosine kinase target phosphatidyl-inositol-3-kinase (PI3K). The hyposmotic-induced activation of these kinases required the prior phosphorylation of ErbB4 as shown by the effect of ErbB4 blockade with AG213 reducing by 85-95% the phosphorylation of FAK and ERK1/2, by 74% and 36% that of PI3K and Src, respectively. These results suggest a key role of ErbB4 as a signal integrator of events associated with hyposmolarity. PI3K seems to be an important connecting element in the signaling network evoked by the hyposmolarity/ErbB4 activation as: (i) the p85 regulatory subunit of PI3K co-immunoprecipitates with ErbB4 and with FAK; (ii) PI3K blockade with wortmannin reduced the hyposmotic activation of FAK (90%) and ERK1/2 (84-91%). Inhibition of Src with PP2 reduced ErbB4 phosphorylation and inhibited the subsequent cytosolic kinase activation with the same potency as ErbB4 blockade. These results point to Src and ErbB4 and as early targets of the hyposmotic stimulus and osmosignaling. The functional significance for cell volume regulation of the ErbB4-Src-PI3K signaling cascade is indicated by the 48-66% decrease of the hyposmotic taurine efflux observed by inhibition of these kinases.

Animals↗
PubMed2005

Human LATS1 is a mitotic exit network kinase.

The kinase LATS/WARTS is a tumor suppressor protein conserved in evolution, but its function at the molecular level is not well understood. We report here that human LATS1 interacts with MOB1A, a protein whose homologue in budding yeast associates with kinases involved in mitotic exit. This suggested that LATS1 may be a component of the previously uncharacterized mitotic exit network in higher eukaryotes. Indeed, moderate overexpression of human LATS1 in cells exposed to microtubule poisons facilitated mitotic exit, and this activity required MOB1A. Reciprocally, small interfering RNA-mediated suppression of LATS1 or MOB1A prolonged telophase, but had no effect on the length of the earlier phases of mitosis. A role of LATS1 in mitotic exit may explain its previously described abilities to induce G2 arrest and promote cytokinesis.

Adaptor Proteins, Signal Transducing↗
PubMed1993

Intracellular signalling mediated by protein-tyrosine kinases: networking through phospholipid metabolism.

In recent years, it has become apparent that receptor-mediated intracellular signals are not linear cascades beginning at the plasma membrane and terminating with the production of a needed metabolite or the induction of gene expression. Instead, complex networks of interactive intracellular signals are activated in response to extracellular stimuli. Many responses to extracellular stimuli are mediated by protein-tyrosine kinases (PTKs). Activating PTKs leads to the recruitment of a variety of intracellular signalling molecules that execute a complex set of instructions. The response to PTK activity is dependent upon which PTK is activated and the cellular context in which the PTK exists. Several signalling molecules recruited by PTKs are involved in the metabolism of phospholipids. In this Mini Review, intracellular signalling networks activated by PTKs are discussed with an emphasis on the potential for generating highly specific and sophisticated responses to PTK activity through phospholipid metabolism.

Animals↗
PubMed2003

Regulation and function of serine kinase networks in lymphocytes.

Recent technological developments have facilitated explorations of the sustained signalling pathways important for lymphocyte activation. One key response necessary for lymphocyte activation is the prolonged activation of the lipid kinase phosphatidylinositol-3 kinase (PI3K). It has also been shown that there is sustained activation of diverse serine/threonine kinases in activated lymphocytes.

Animals↗
PubMed2006

ErbB receptor tyrosine kinase network inhibition radiosensitizes carcinoma cells.

PURPOSE: The expression of epidermal growth factor receptor (EGFR)-CD533, a truncation mutant of the wild-type EGFR, radiosensitizes carcinoma and malignant glioma cell lines. This deletion mutant disrupts EGFR activation and downstream signaling through the formation of inhibitory dimerizations. In this study, the effects of EGFR-CD533 on other ErbB receptor tyrosine kinase (RTK) family members were quantified to better understand the mechanism of EGFR-CD533-mediated radiosensitization. METHODS AND MATERIALS: Breast carcinoma cell lines with different ErbB RTK expression profiles were transduced with EGFR or ErbB2 deletion mutants (EGFR-CD533 and ErbB2-CD572) using an adenoviral vector. ErbB RTK activation, mitogen activated protein kinase (MAPK) and phosphatidylinositol-3-kinase (PI3K)/p70S6K signaling, and clonogenic survival were determined for expression of each deletion mutant. RESULTS: EGFR-CD533 radiosensitizes carcinoma cells with either high EGFR expression (MDA-MB231) or low EGFR expression (T47D) through significant blockade of the ErbB RTK network. Analysis of clonogenic survival demonstrate significant enhancement of the alpha/beta ratios, as determined by the linear-quadratic model. Split-dose survival experiments confirm that EGFR-CD533 reduces the repair of cellular damage after ionizing radiation. CONCLUSION: Expression of EGFR-CD533 inhibits the ErbB RTK network and radiosensitizes carcinoma cells irrespective of the ErbB RTK expression patterns, and ErbB2-CD572 does not radiosensitize cells with low EGFR expression. These studies demonstrate that the mechanism of action for EGFR-CD533-mediated radiosensitization is inhibition of the ErbB RTK network, and is an advantage for radiosensitizing multiple malignant cell types.

Breast Neoplasms↗
PubMed2003

Phenotypic and transcriptional plasticity directed by a yeast mitogen-activated protein kinase network.

The yeast pheromone/filamentous growth MAPK pathway mediates both mating and invasive-growth responses. The interface between this MAPK module and the transcriptional machinery consists of a network of two MAPKs, Fus3 and Kss1; two regulators, Rst1 and Rst2 (a.k.a. Dig1 and Dig2); and two transcription factors, Ste12 and Tec1. Of 16 possible combinations of gene deletions in FUS3, KSS1, RST1, and RST2 in the sigma1278 background, 10 display constitutive invasive growth. Rst1 was the primary negative regulator of invasive growth, while other components either attenuated or enhanced invasive growth, depending on the genetic context. Despite activation of the invasive response by lesions at the same level in the MAPK pathway, transcriptional profiles of different invasive mutant combinations did not exhibit a unified program of gene expression. The distal MAPK regulatory network is thus capable of generating phenotypically similar invasive-growth states (an attractor) from different molecular architectures (trajectories) that can functionally compensate for one another. This systems-level robustness may also account for the observed diversity of signals that trigger invasive growth.

Haploidy↗
PubMed1993

A divergence in the MAP kinase regulatory network defined by MEK kinase and Raf.

Mitogen-activated protein kinases (MAPKs) are rapidly phosphorylated and activated in response to various extracellular stimuli in many different cell types. Such regulation of MAPK results from sequential activation of a series of protein kinases. The kinases that phosphorylate MAPKs, the MAP kinase kinases (MEKs) are also activated by phosphorylation. MEKs are related in sequence to the yeast protein kinases Byr1 (from Schizosaccharomyces pombe) and Ste7 (from Saccharomyces cerevisiae), which function in the pheromone-induced signaling pathway that results in mating. Byr1 and Ste7 are in turn regulated by the protein kinases Byr2 and Ste11. The amino acid sequence of the mouse homolog of Byr2 and Ste11, denoted MEKK (MEK kinase), was elucidated from a complementary DNA sequence encoding a protein of 672 amino acid residues (73 kilodaltons). MEKK was expressed in all mouse tissues tested, and it phosphorylated and activated MEK. Phosphorylation and activation of MEK by MEKK was independent of Raf, a growth factor-regulated protein kinase that also phosphorylates MEK. Thus, MEKK and Raf converge at MEK in the protein kinase network mediating the activation of MAPKs by hormones, growth factors, and neurotransmitters.

Amino Acid Sequence↗
PubMed2025

Inference of differential kinase interaction networks with KINference.

MOTIVATION: Differential kinase interaction networks (DKINs) are networks containing kinase-substrate links that are differentially active between two conditions. Existing methods are either able to predict condition-agnostic kinase-substrate links or condition-specific differential kinase activity, but do not provide differential kinase-substrate links. Moreover, existing methods for predicting kinase-substrate links usually rely on curated biochemical knowledge. Thus, there is a lack of data-driven DKIN inference methods that are also applicable when prior knowledge is scarce. RESULTS: To address this need, we present KINference. KINference combines computation of a baseline KIN representing the space of all possible kinase-substrate links with filters applied to nodes and edges to identify differentially active subnetworks that are relevant in the context of a specific phosphoproteomics dataset. For the node filters, we rely on functional relevance and differential phosphorylation scores; for the edge filters, we make use of prize-collecting Steiner trees and correlations between phosphorylation sites of kinases and their target proteins. Tests on two phosphoproteomics datasets (kinase inhibition in breast cancer cells, SARS-CoV-2 infection in Calu-3 cells) show that the proposed filters produce significant results in terms of overlap with known interactions between kinases and phosphorylation sites. Furthermore, a case study on the SARS-CoV-2 infection data, suggests a potential host pathway linked to virus replication, showcasing the process of hypothesis generation utilizing DKINs computed by KINference. AVAILABILITY AND IMPLEMENTATION: KINference is available as an R package at https://github.com/bionetslab/KINference and https://doi.org/10.5281/zenodo.15411150. Scripts to reproduce the results are available at https://github.com/bionetslab/KINference-Evaluation-Scripts and https://doi.org/10.5281/zenodo.15424599.

Humans↗