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The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.

UNLABELLED: TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system (Wingender et al., Nucleic Acids Res., 28, 316-319, 2000). It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways like complexes, signaling molecules, and their states are stored together with information about their interaction in an object-oriented database. The database interface provides clickable maps and automatically generated pathway cascades as additional ways to explore the data. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, SWISS-PROT, EMBL, PubMed and others). AVAILABILITY: The database is available over (http://transpath.gbf.de) for interactive perusal. As an exchange format for the data, eXtensible Markup Language (XML) flatfiles and a Document Type Definition (DTD) are provided.

Algorithms↗

Cellular mechanisms of wingless/Wnt signal transduction.

Wg/Wnt signaling regulates cell proliferation and differentiation in species as divergent as nematodes, flies, frogs, and humans. Many components of this highly conserved process have been characterized and work from a number of laboratories is beginning to elucidate the mechanism by which this class of secreted growth factor triggers cellular decisions. The Wg/Wnt ligand apparently binds to Frizzled family receptor molecules to initiate a signal transduction cascade involving the novel cytosolic protein Dishevelled and the serine/threonine kinase Zeste-white 3/GSK3. Antagonism of Zw3 activity leads to stabilization of Armadillo/beta-catenin, which provides a transactivation domain when complexed with the HMG box transcription factor dTCF/LEF-1 and thereby activates expression of Wg/Wnt-responsive genes. The Wg/Wnt ligands pass through the secretory pathway and associate with extracellular matrix components; recent work shows that sulfated glycosaminoglycans are essential for proper transduction of the signal. Mutant forms of Wg in Drosophila reveal separable aspects of Wg function and suggest that proper transport of the protein across cells is essential for cell fate specification. Complex interactions with the Notch and EGF/Ras signaling pathways also play a role in cell fate decisions during different phases of Drosophila development. These many facets of Wg/Wnt signaling have been elucidated through studies in a variety of species, each with powerful and unique experimental approaches. The remarkable conservation of this pathway suggests that Wg/Wnt signal transduction represents a fundamental mechanism for the generation of diverse cell fates in animal embryos.

Amino Acid Sequence↗

Functional similarities among two-component sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction.

Signal-responsive components of transmembrane signal-transducing regulatory systems include methyl-accepting chemotaxis proteins and membrane-bound, two-component histidine kinases. Prokaryotes use these regulatory networks to channel environmental cues into adaptive responses. A typical network is highly discriminating, using a specific phosphoryl relay that connects particular signals to appropriate responses. Current understanding of transmembrane signal transduction includes periplasmic signal binding with the subsequent conformational changes being transduced, via transmembrane helix movements, into the sensory protein's cytoplasmic domain. These induced conformational changes bias the protein's regulatory function. Although the mutational analyses reviewed here identify a role for the linker region in transmembrane signal transduction, no specific mechanism of linker function has yet been described. We propose a speculative, mechanistic model for linker function based on interactions between two putative amphipathic helices. The model attempts to explain both mutant phenotypes and hybrid sensor data, while accounting for recognized features of amphipathic helices.

Amino Acid Sequence↗

[Recent progress in the molecular biology of receptors and intra-cellular signal transduction].

Extracellular signals are recognized by the receptors on the surface of cytoplasmic membrane and are transmitted through the complex array of intracellular signal transduction networks. Through recent advances in molecular and genetic analyses, we are beginning to understand the outline of the signaling machineries leading from receptors to targets at molecular level. This review intends to describe the general characteristics of receptors and components of intra-cellular signal transduction systems. Future prospects of the studies on signal transduction in medicine are also discussed.

Animals↗

Signal-transduction pathways that regulate smooth muscle function I. Signal transduction in phasic (esophageal) and tonic (gastroesophageal sphincter) smooth muscles.

Contraction of esophageal (Eso) and lower esophageal sphincter (LES) circular muscle depends on distinct signal-transduction pathways. ACh-induced contraction of Eso muscle is linked to phosphatidylcholine metabolism, production of diacylglycerol and arachidonic acid (AA), and activation of the Ca(2+)-insensitive PKCepsilon. Although PKCepsilon does not require Ca(2+) for activation, either influx of extracellular Ca(2+) or release of Ca(2+) from stores is needed to activate the phospholipases responsible for hydrolysis of membrane phospholipids and production of second messengers, which activate PKCepsilon. In contrast, the LES uses two distinct intracellular pathways: 1) a PKC-dependent pathway activated by low doses of agonists or during maintenance of spontaneous tone, and 2) a Ca(2+)-calmodulin-myosin light chain kinase (MLCK)-dependent pathway activated in response to maximally effective doses of agonists during the initial phase of contraction. The Ca(2+) levels, released by agonist-induced activity of phospholipase C, determine which contractile pathway is activated in the LES. The Ca(2+)-calmodulin-MLCK-dependent contractile pathway has been well characterized in a variety of smooth muscles. The steps linking activation of PKC to myosin light chain (MLC20) phosphorylation and contraction, however, have not been clearly defined for LES, Eso, or other smooth muscles. In addition, in LES circular muscle, a low-molecular weight pancreatic-like phospholipase A2 (group I PLA2) causes production of AA, which is metabolized to prostaglandins and thromboxanes. These AA metabolites act on receptors linked to heterotrimeric G proteins to induce activation of phospholipases and production of second messengers to maintain contraction of LES circular muscle. We have examined the signal-transduction pathways activated by PGF(2alpha) and by thromboxane analogs during the initial contractile phase and found that these pathways are the same as those activated by other agonists. In response to low doses of agonists or during maintenance of tone, presumably due to low levels of calcium release, a PKC-dependent pathway is activated, whereas at high doses of PGF(2alpha) and thromboxane analogs, in the initial phase of contraction, calmodulin is activated, PKC activity is reduced, and contraction is mediated, in part, through a Ca(2+)-calmodulin-MLCK-dependent pathway. The PKC-dependent signaling pathways activated by PGF(2alpha) and by thromboxanes during sustained LES contraction, however, remain to be examined, but preliminary data indicate that a distinct PKC-dependent pathway may be activated during maintenance of tonic contraction, which is different from the one activated during the initial contractile response. The initial contractile response to low levels of agonists depends on activation of G(q). Sustained contraction in response to PGF(2alpha) may involve activation of the monomeric G protein RhoA, because the contraction is inhibited by the RhoA-kinase antagonist Y27632. This shift in signal-transduction pathways between initial and sustained contraction has been recently reported in intestinal smooth muscle.

Animals↗

Signal transduction. Just another signalling pathway.

The recently identified JAK-STAT signal transduction pathway plays a major role in signalling the arrival of cytokines at the cell surface and can, in part, account for the pleiotropic and redundant effects of cytokines.

Animals↗

Two-component signal transduction systems, environmental signals, and virulence.

The relevance toward virulence of a variety of two-component signal transduction systems is reviewed for 16 pathogenic bacteria, together with the wide array of environmental signals or conditions that have been implicated in their regulation. A series of issues is raised, concerning the need to understand the environmental cues that determine their regulation in the infected host and in the environment outside the laboratory, which shall contribute toward the bridging of bacterial pathogenesis and microbial ecology.

Animals↗

The different facets of protein kinases C: old and new players in neuronal signal transduction pathways.

Signal transduction pathways are crucial for cell-to-cell communication. Various molecular cascades allow the translation of distinct stimuli, targeting the cell, into a language that the cell itself is able to understand, thus elaborating specific responses. Within this context, a strategic role is played by protein kinases which catalyze the phosphorylation of specific substrates. The serine/threonine protein kinase C (PKC) enzymes family (at least 10 isoforms) is implicated in the transduction of signals coupled to receptor-mediated hydrolysis of membrane phospholipids. Within this molecular pathway, protein-protein interactions play a critical role in directing the distinct activated PKCs towards selective subcellular compartments, in order to guarantee spatio-temporal and localized cellular responses. A space-specific modulation of biochemical events is particularly important during learning. Among the various mechanisms, the modulation of mRNA decay appears to be an efficient post-transcriptional way of controlling gene expression during learning, allowing changes to take place in selected neuronal regions, in particular at synaptic level. To this regard, recent studies have pointed out that PKC activation is also involved in a novel signalling cascade leading to the stabilization of specific mRNAs. This review will especially focus the attention on the implication of PKC in memory trace formation and how alterations within this molecular cascade may have consequences on physiological and pathological neuronal aging (i.e. Alzheimer's disease).

Animals↗

Brassinosteroid signal transduction--choices of signals and receptors.

Small signaling molecules that mediate cell-cell communication are essential for developmental regulation in multicellular organisms. Among them are the steroids and peptide hormones that regulate growth in both plants and animals. In plants, brassinosteroids (BRs) are perceived by the cell surface receptor kinase BRI1, which is distinct from the animal steroid receptors. Identification of components of the BR signaling pathway has revealed similarities to other animal and plant signal transduction pathways. Recent studies demonstrated that tomato BRI1 (tBRI1) perceives both BR and the peptide hormone systemin, raising new questions about the molecular mechanism and evolution of receptor-ligand specificity.

Brassinosteroids↗

Dual transduction signaling by a Xenopus muscarinic receptor: adenylyl cyclase inhibition and MAP kinase activation.

Using transient transfection of COS-7 and human embryonic kidney 293 cells, we studied the functional properties of a previously cloned muscarinic Xenopus receptor [Herrera et al. (1994): FEBS Lett 352:175-179] and its coupling to adenylyl cyclase (AC) and mitogen-activated protein kinase (MAPK) pathways. Expression of the Xenopus muscarinic receptor results in the inhibition of AC activity and activation of the MAPK pathway through a mechanism that involves a Pertussis-toxin-sensitive G-protein and the G beta gamma subunits. The signal transduction properties of this receptor are similar to the mammalian m2 and m4 muscarinic receptors. These results strongly support the idea that inhibition of AC and MAPK activation, signaled out from the muscarinic oocyte receptor, are involved in the oocyte maturation process.

Adenylate Cyclase Toxin↗

Approximations and their consequences for dynamic modelling of signal transduction pathways.

Signal transduction is the process by which the cell converts one kind of signal or stimulus into another. This involves a sequence of biochemical reactions, carried out by proteins. The dynamic response of complex cell signalling networks can be modelled and simulated in the framework of chemical kinetics. The mathematical formulation of chemical kinetics results in a system of coupled differential equations. Simplifications can arise through assumptions and approximations. The paper provides a critical discussion of frequently employed approximations in dynamic modelling of signal transduction pathways. We discuss the requirements for conservation laws, steady state approximations, and the neglect of components. We show how these approximations simplify the mathematical treatment of biochemical networks but we also demonstrate differences between the complete system and its approximations with respect to the transient and steady state behavior.

Feedback, Physiological↗

Signal transduction during antibody-dependent cellular cytotoxicity mediated by U937 cells.

Stimulation of the human promonocytic cell line U937 with antibody-coated chicken red blood cells (Ab-CRBC), leads to inositol phosphate (IP) release in the effector cells. Neomycin (5 x 10(-4) M) completely inhibits activation of phosphoinositide breakdown, while ADCC is suppressed in a dose-dependent manner. Bordetella pertussis toxin (PT) (0.5 micrograms/ml), entirely inhibits IP release, while ADCC activity is markedly suppressed. The PKC inhibitors H-7 and propranolol also suppress ADCC. HA-1004, which has far lower PKC inhibitory activity than H-7, has a minimal effect on ADCC. The calmodulin antagonists W-7 and TFP are strongly inhibitory. These results indicate that stimulation of U937 cells for ADCC is associated to an increase in IP levels, which may provide positive transduction signals for the activation of this lytic mechanism.

Antibody-Dependent Cell Cytotoxicity↗

Epigallocatechin-3-gallate inhibits basic fibroblast growth factor-induced intracellular signaling transduction pathway in rat aortic smooth muscle cells.

Daily green tea drinking showed preventive effects on the progression of atherosclerosis. Although epigallocatechin-3-gallate [EGCG] has anti-proliferative effects on various cells, relatively little is known about the molecular mechanisms of the anti-proliferative effects of EGCG. To determine whether the transduction signals and protooncogene expression were affected by EGCG, this study investigated the molecular mechanism of the anti-proliferative effects in basic fibroblast growth factor (bFGF)-stimulated rat aortic smooth muscle cells (RAoSMCs). EGCG inhibited the proliferative response stimulated by 10% fetal bovine serum dose dependently in RAoSMCs (median inhibitory concentration [IC50]: 28.4 x 10(-6) M ). EGCG also inhibited the migration of bFGF-stimulated RAoSMCs in a dose-dependent manner, showing that 21.8 x 10(-6) M of EGCG significantly inhibited the migration by 75 +/- 5% in comparison with bFGF-stimulated migration. In RAoSMCs, EGCG dramatically inhibited Ras activation and c-jun N-terminal kinase (JNK) activity without affecting protein kinase C expression. Induction of c-jun mRNA stimulated by bFGF was significantly reduced dose dependently up to 87.3 x 10(-6) M of EGCG. These results indicate that the anti-proliferative effect of EGCG on RAoSMCs is partly Ras/JNK mediated, independent of protein kinase C, and is attributable to the downregulation of c-jun expression.

Animals↗

[Signal transduction, pillar of the neurobiological integration of memory. An alternative view to the cholinergic hypothesis].

Neurophysiological, biochemical and molecular processes described in the integration of memory are closely related with neurotransmitters such as glutamate and serotonin (SHT) and with the function of calcium and potassium ion channels more than with cholinergic activity. Infact, glutamate and 5-HT receptors are closely related with Long-Term potentiation (L TP) processes, the mechanism by which memory is preserved throughout time. That is, the activation of the 5-HTI receptor triggers a transduction signal that after influencing nuclear cell activity, provokes several presynaptic changes, which leads to the displacement of magnesium from the postsynaptic area depolarizing the neuron and leading to the activation of N-methyl-D-aspartate receptors (NMDA). As a whole, this process contributes to the support and perpetuation of LTP, which consists of the following processes: LTPI that depends on protein kinase activity; LTP2 linked to translation of genes; and LTP3 closely related to genes transcription. On the opposite side but in perfect balance, we find the mechanism of Long-Term depression (LTD), which is triggered instead when the Ca+ +flow decreases in the presynaptic neuron activating the inhibitor-1 enzyme that promotes the dephosphorylation of a calmodulin-dependent protein kinasell and as a result, the inhibition of autophosphorylation and consequently of LTP too. Despite the widespread dissemination of the cholinergic hypothesis in Alzheimer's disease, memory build up rather than involving acetylcholine essentially depends on the participation of other neurotransmitters such as 5-HT and glutamate, which have not been adequately considered in the treatment of this disease. However, beyond neurotransmission, it is the cellular mechanism of autophosphorylation of several protein kinases, the process susceptible of being activated or controlled by the action of distinct substances. In such a case, it would be possible to exert some influence on gene expression improving perhaps, some of the physiopathological deficits that characterize memory disruption.

Calmodulin↗

[The classes, structures, functions and signaling transduction of cytokine receptors].

There are many kinds of cytokine receptors that belong to different receptor families. Most cytokine receptors function as: (1) receptor tyrosine kinase and tyrosine-kinase-associated receptor; (2) receptor serine/threonine kinase; (3) G-protein linked receptor. Following binding with cytokines and activation, the receptors trigger different cascade of intracellular protein phosphorylation to transduction signals, thereby altering the cell's pattern of gene expression and leading to biological effects.

Animals↗

Expansion of signal transduction networks.

Signal transduction networks of different cell types show a large variety in their structural design. In this paper, basic structural properties of signal transduction networks are investigated. For this, such networks with the recently developed method of network expansion are analysed. This method allows for a structural analysis of networks by calculating signal expansion profiles when provided with certain compounds, for example growth factors, inactive kinases and so on (seed compounds), to initiate such an expansion. The presented results may put forth valuable hints on the evolution of signalling networks.

Algorithms↗

Preformed dimeric state of the sensor protein VirA is involved in plant--Agrobacterium signal transduction.

Plant signal molecules such as acetosyringone and certain monosaccharides induce the expression of Agrobacterium tumefaciens virulence (vir) genes, which are required for the processing, transfer, and possibly integration of a piece of the bacterial plasmid DNA (T-DNA) into the plant genome. Two fo the vir genes, virA and virG, belonging to the bacterial two-component regulatory system family, control the induction of vir genes by plant signals. virA encodes a membrane-bound sensor kinase protein and virG encodes a cytoplasmic regulator protein. Although it is well established from in vitro studies that the signal transduction process involves VirA autophosphorylation and subsequent phosphate transfer to VirG, the structural state of the VirA protein involved in signal transduction is not understood. In this communication, we describe an in vivo crosslinking approach which provides physical evidence that VirA exists as a homodimer in its native configuration. The dimerization of VirA neither requires nor is stimulated by the plant signal molecule acetosyringone. We also present genetic data which support the hypothesis that VirA exists as a homodimer which is the functional state transducing the plant signal in an intersubunit mechanism. To our knowledge, this report provides the first evidence that a bacterial membrane-bound sensor kinase exists and functions as a homodimer in vivo.

Agrobacterium tumefaciens↗

In silico tools for signal transduction research.

Signal transduction is a fundamental process that takes place in all living organisms and understanding how this event occurs at the cellular level is of vital importance to virtually all fields of biomedicine. There are several major steps involved in deciphering the signalling pathways: (a) Which molecules are involved in signalling? (b) Who talks to whom?, ie making sense of the molecular interactions in a context-dependent way. (c) Where are the signalling events taking place?, eg when a resting cell becomes activated. The challenge lies in reconstructing signalling modules and networks evoked in a particular response to a single input as well as correlating the signalling response to different cellular inputs. There is also the need for interpretation of cross-talk between signalling modules in response to single and multiple inputs. To follow up these questions there are many good databases that provide an information system on regulatory networks. This review aims to find some of the bioinformatics tools and websites available to conduct signal transduction research and to discuss the representation of databases available for the processes of signalling. The databases considered here can provide a well-structured overview on the subject and a basis for advanced bioinformatics analysis to interpret the function of genomic sequences or to analyse signalling networks within a cell. However, the knowledge of most signalling pathways is incomplete and for this reason the existing databases will provide insight, but very rarely a more complete picture.

Computational Biology↗