Nonparametric simulation of signal transduction networks with semi-synchronized update

Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational framework to describe the profile of the evolving process and the time course of the proportion of active form of molecules in the signal transduction networks. The model is also capable of incorporating perturbations. The model was validated on four signaling networks showing that it can effectively uncover the activity levels and trends of response during signal transduction process.     

Stochastic signal processing and transduction in chemotactic response of eukaryotic cells

Single-molecule imaging analysis of chemotactic response in eukaryotic cells has revealed a stochastic nature in the input signals and the signal transduction processes. This leads to a fundamental question about the signaling processes: how does the signaling system operate under stochastic fluctuations or noise? Here, we report a stochastic model of chemotactic signaling in which noise and signal propagation along the transmembrane signaling pathway by chemoattractant receptors can be analyzed quantitatively. The results obtained from this analysis reveal that the second-messenger-production reactions by the receptors generate noisy signals that contain intrinsic noise inherently generated at this reaction and extrinsic noise propagated from the ligand-receptor binding. Such intrinsic and extrinsic noise limits the directional sensing ability of chemotactic cells, which may explain the dependence of chemotactic accuracy on chemical gradients that has been observed experimentally. Our analysis also reveals regulatory mechanisms for signal improvement in the stochastically operating signaling system by analyzing how the SNR of chemotactic signals can be improved on or deteriorated by the stochastic properties of receptors and second-messenger molecules. Theoretical consideration of noisy signal transduction by chemotactic signaling systems can further be applied to signaling systems in general.     

花衰老相关的乙烯信号转导基因研究进展

乙烯在许多切花衰老过程中起着重要的调节作用,不同的植物乙烯信号转导组分在花衰老过程中有不同的转录调节特性。根据乙烯信号转导标准模式,通过调节乙烯信号转导基因表达能够调控花对乙烯的敏感性,深入研究乙烯信号转导机制;可能有多条途径可延缓切花衰老。综述了香石竹和月季等几种观赏植物在花衰老过程中乙烯受体和乙烯信号转导基因表达及特性。     

An integrated model of epidermal growth factor receptor trafficking and signal transduction

Endocytic trafficking of many types of receptors can have profound effects on subsequent signaling events. Quantitative models of these processes, however, have usually considered trafficking and signaling independently. Here, we present an integrated model of both the trafficking and signaling pathway of the epidermal growth factor receptor (EGFR) using a probability weighted-dynamic Monte Carlo simulation. Our model consists of hundreds of distinct endocytic compartments and approximately 13,000 reactions/events that occur over a broad spatio-temporal range. By using a realistic multicompartment model, we can investigate the distribution of the receptors among cellular compartments as well as their potential signal transduction characteristics. Our new model also allows the incorporation of physiochemical aspects of ligand-receptor interactions, such as pH-dependent binding in different endosomal compartments. To determine the utility of this approach, we simulated the differential activation of the EGFR by two of its ligands, epidermal growth factor (EGF) and transforming growth factor-alpha (TGF-alpha). Our simulations predict that when EGFR is activated with TGF-alpha, receptor activation is biased toward the cell surface whereas EGF produces a signaling bias toward the endosomal compartment. Experiments confirm these predictions from our model and simulations. Our model accurately predicts the kinetics and extent of receptor downregulation induced by either EGF or TGF-alpha. Our results suggest that receptor trafficking controls the compartmental bias of signal transduction, rather than simply modulating signal magnitude. Our model provides a new approach to evaluating the complex effect of receptor trafficking on signal transduction. Importantly, the stochastic and compartmental nature of the simulation allows these models to be directly tested by high-throughput approaches, such as quantitative image analysis.     

Timing is everything the role of kinetics in G protein activation

The binding of a drug to a G-protein coupled receptor initiates a complex series of dynamic events that ultimately leads to a cellular response. In addition to the concentrations of receptor, drug and G-protein, important determinants of the cellular response are the rates at which these species interact. However, most models for G-protein coupled receptor signaling are equilibrium models that neglect the role of reaction kinetics. A kinetic ternary-complex model of signaling through G-protein coupled receptors is presented. We demonstrate that this kinetic model can make significantly different predictions than an equilibrium ternary complex model, which provides a different perspective on multiple aspects of the signal transduction cascade, such as agonist efficacy, the effect of precoupled receptors, and the role of RGS proteins. Incorporation of the reaction kinetics is critical for a complete understanding of signal transduction and will ultimately impact the fields of drug discovery and drug design.     

Additive effects of PDGF receptor beta signaling pathways in vascular smooth muscle cell development

The platelet-derived growth factor beta receptor (PDGFRbeta) is known to activate many molecules involved in signal transduction and has been a paradigm for receptor tyrosine kinase signaling for many years. We have sought to determine the role of individual signaling components downstream of this receptor in vivo by analyzing an allelic series of tyrosine-phenylalanine mutations that prevent binding of specific signal transduction components. Here we show that the incidence of vascular smooth muscle cells/pericytes (v/p), a PDGFRbeta-dependent cell type, can be correlated to the amount of receptor expressed and the number of activated signal transduction pathways. A decrease in either receptor expression levels or disruption of multiple downstream signaling pathways lead to a significant reduction in v/p. Conversely, loss of RasGAP binding leads to an increase in this same cell population, implicating a potential role for this effector in attenuating the PDGFRbeta signal. The combined in vivo and biochemical data suggest that the summation of pathways associated with the PDGFRbeta signal transduction determines the expansion of developing v/p cells.     

Noise generation, amplification and propagation in chemotactic signaling systems of living cells

Theoretical considerations of stochastic signal transduction in living cells have revealed the gain-fluctuation relation, which provides a theoretical framework to describe quantitatively how noise is generated, amplified and propagated along a signaling cascade in living cells. We chose the chemotactic signaling of bacteria and eukaryotic cells as a typical example of noisy signal transduction and applied the gain-fluctuation relation to these signaling systems in order to analyze the effects of noise on signal transduction. Comparing our theoretical analysis with the experimental results of chemotaxis in bacteria Escherichia coli and eukaryote Dictyostelium discoideum revealed that noise in signal transduction systems limits the cells' chemotactic ability and contributes to their behavioral variability. Based on the kinetic properties of signaling molecules in living cells, the gain-fluctuation relation can quantitatively explain stochastic cellular behaviors.     

Plant stress surveillance monitored by ABA and disease signaling interactions

Abiotic and biotic stresses are the major factors that negatively impact plant growth. In response to abiotic environmental stresses such as drought, plants generate resistance responses through abscisic acid (ABA) signal transduction. In addition to the major role of ABA in abiotic stress signaling, ABA signaling was reported to downregulate biotic stress signaling. Conversely recent findings provide evidence that initial activation of plant immune signaling inhibits subsequent ABA signal transduction. Stimulation of effector-triggered disease response can interfere with ABA signal transduction via modulation of internal calcium-dependent signaling pathways. This review overviews the interactions of abiotic and biotic stress signal transduction and the mechanism through which stress surveillance system operates to generate the most efficient resistant traits against various stress condition.     

Discovery of intramolecular signal transduction network based on a new protein dynamics model of energy dissipation

A novel approach to reveal intramolecular signal transduction network is proposed in this work. To this end, a new algorithm of network construction is developed, which is based on a new protein dynamics model of energy dissipation. A key feature of this approach is that direction information is specified after inferring protein residue-residue interaction network involved in the process of signal transduction. This enables fundamental analysis of the regulation hierarchy and identification of regulation hubs of the signaling network. A well-studied allosteric enzyme, E. coli aspartokinase III, is used as a model system to demonstrate the new method. Comparison with experimental results shows that the new approach is able to predict all the sites that have been experimentally proved to desensitize allosteric regulation of the enzyme. In addition, the signal transduction network shows a clear preference for specific structural regions, secondary structural types and residue conservation. Occurrence of super-hubs in the network indicates that allosteric regulation tends to gather residues with high connection ability to collectively facilitate the signaling process. Furthermore, a new parameter of propagation coefficient is defined to determine the propagation capability of residues within a signal transduction network. In conclusion, the new approach is useful for fundamental understanding of the process of intramolecular signal transduction and thus has significant impact on rational design of novel allosteric proteins.     

Additive Effects of PDGF Receptor β Signaling Pathways in Vascular Smooth Muscle Cell Development

The platelet-derived growth factor β receptor (PDGFRβ) is known to activate many molecules involved in signal transduction and has been a paradigm for receptor tyrosine kinase signaling for many years. We have sought to determine the role of individual signaling components downstream of this receptor in vivo by analyzing an allelic series of tyrosine–phenylalanine mutations that prevent binding of specific signal transduction components. Here we show that the incidence of vascular smooth muscle cells/pericytes (v/p), a PDGFRβ-dependent cell type, can be correlated to the amount of receptor expressed and the number of activated signal transduction pathways. A decrease in either receptor expression levels or disruption of multiple downstream signaling pathways lead to a significant reduction in v/p. Conversely, loss of RasGAP binding leads to an increase in this same cell population, implicating a potential role for this effector in attenuating the PDGFRβ signal. The combined in vivo and biochemical data suggest that the summation of pathways associated with the PDGFRβ signal transduction determines the expansion of developing v/p cells.     

赤霉素信号转导与植物的矮化

论述近年来在拟南芥、水稻等模式植物中赤霉素信号转导的研究进展。通过对赤霉素相关突变体的生理研究 ,鉴定出几个介入赤霉素信号转导过程的重要基因 ,并对这些基因的产物进行分析 ,根据相应的蛋白特征结构域 ,推导了它们可能具有的功能。利用双突变体 ,分析了这些基因的上下游关系 ,确定了在植物中 ,GA信号转导的几个途径。在此基础上提出了赤霉素信号转导的基本模式 :阻遏是GA信号转导过程中最基本的方式 ,GA信号通过去除阻遏作用来激活转导途径 ,从而调节GA相关的生长与发育。     

细胞水平筛选鉴定激活核因子κB通路的新基因TMEM9B

核因子κB(NF-κB)是细胞内重要的转录因子,其介导的细胞信号转导通路在细胞凋亡中的作用是国内外研究的热点．为了筛选NF-κB通路相关新基因,建立了基于细胞水平的报告基因高通量筛选模型．利用双荧光素酶报告系统检测报告基因荧光素酶活性,通过对构建的439个人类未知功能基因的筛选,获得了一批激活NF-κB信号通路的功能基因,其中基因TMEM9B可以明显激活NF-κB通路．进一步实验显示TMEM9B激活NF-κB通路呈明显剂量依赖性,Western blot及EMSA实验证实,TMEM9B能够促进胞质内NF-κB的抑制分子IκBα的降解,并促使NF-κB由胞质向胞核转移,同时流式细胞术实验发现TMEM9B可引起293T和HeLa细胞的凋亡．总之,所建立的基于细胞水平的NF-κB通路筛选模型稳定高效,筛选并验证TMEM9B可明显激活NF-κB信号转导通路,并从而引起细胞凋亡．     

Stomatal movements and long-distance signaling in plants

As the nerve-mediated signaling in animals, long-distance signaling in plants is a prerequisite for plants to be able to perceive environmental stimuli and initiate adaptive responses. While intracellular signal transduction has been attracting considerable attentions, studies on long-distance signaling in plants has been relatively overlooked. Stomatal movements are well recognized as a model system for studies on cellular signal transduction. It has been demonstrated that the stomatal movements may be frequently tuned by long-distance signaling under various environmental stimuli. Stomatal movements can not only respond to persistent stress stimuli but also respond to shock stress stimuli. Stomatal responses to drought stress situations may be best characterized in terms of interwoven networks of chemical signaling pathways playing predominant roles in these adaptive processes. In cases of shock stress stimuli, stomatal movements can be more sensitively regulated through the long-distance signaling but with distinctive patterns not observed for drought or other persistent stresses. Here, the fundamental characteristics of stomatal movements and associated long-distance signaling are reviewed and the implications for plant responses to environmental stresses are discussed.Key words: stomatal movement, long-distance signaling, environmental stresses, abscisic aci, pH signaling, hydraulic signaling, cytokinins, acetylcholine, heat-shock, electric signal     

Eph-ephrin介导反向信号传递的研究进展

双向信号传递是细胞间通讯领域中新近阐明的机制,酪氨酸激酶受体-配体(Eph-ephrin)介导的双向信号传递是此机制中的一个重要代表.Eph酪氨酸激酶家族受体及其配体ephrin家族成员是在神经发育、血管新生等方面起重要作用的分子,通过Eph向细胞内传递的信号称为正向信号,通过其配体ephrin的信号称为反向信号.Ephrin家族又可根据分子结构分为2个亚家族,其中ephrinB为跨膜蛋白,可通过酪氨酸磷酸化依赖和PDZ结合结构域介导2种方式向胞内传递反向信号,活化FAK、JNK、Wnt等信号通路,ephrinA为糖基磷脂酰肌醇锚定蛋白,也具有反向信号传递功能.     

Kinetics in signal transduction pathways involving promiscuous oligomerizing receptors can be determined by receptor specificity: apoptosis induction by TRAIL

Here we show by computer modeling that kinetics and outcome of signal transduction in case of hetero-oligomerizing receptors of a promiscuous ligand largely depend on the relative amounts of its receptors. Promiscuous ligands can trigger the formation of nonproductive receptor complexes, which slows down the formation of active receptor complexes and thus can block signal transduction. Our model predicts that increasing the receptor specificity of the ligand without changing its binding parameters should result in faster receptor activation and enhanced signaling. We experimentally validated this hypothesis using the cytokine tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and its four membrane-bound receptors as an example. Bypassing ligand-induced receptor hetero-oligomerization by receptor-selective TRAIL variants enhanced the kinetics of receptor activation and augmented apoptosis. Our results suggest that control of signaling pathways by promiscuous ligands could result in apparent slow biological kinetics and blocking signal transmission. By modulating the relative amount of the different receptors for the ligand, signaling processes like apoptosis can be accelerated or decelerated and even inhibited. It also implies that more effective treatments using protein therapeutics could be achieved simply by altering specificity.     

The contrasting roles of primary cilia and cytonemes in Hh signaling

Hedgehog (Hh) is a paracrine signaling protein with major roles in development and disease. In vertebrates and invertebrates, Hh signal transduction is carried out almost entirely by evolutionarily conserved components, and in both, intercellular movement of Hh is mediated by cytonemes – specialized filopodia that serve as bridges that bring distant cells into contact. A significant difference is the role of the primary cilium, a slender, tubulin-based protuberance of many vertebrate cells. Although the primary cilium is essential for Hh signaling in cells that have one, most Drosophila cells lack a primary cilium. This perspective addresses the roles of primary cilia and cytonemes, and proposes that for Hh signaling, the role of primary cilia is to provide a specialized hydrophobic environment that hosts lipid-modified Hh and other components of Hh signal transduction after Hh has traveled from elsewhere in the cell. Implicit in this model is the idea that initial binding and uptake of Hh is independent of and segregated from the processes of signal transduction and activation.     

Crosstalk between jasmonic acid, ethylene and Nod factor signaling allows integration of diverse inputs for regulation of nodulation

Plant hormones interact at many different levels to form a network of signaling pathways connected by antagonistic and synergistic interactions. Ethylene and jasmonic acid both act to regulate the plant's responsiveness to a common set of biotic stimuli. In addition ethylene has been shown to negatively regulate the plant's response to the rhizobial bacterial signal, Nod factor. This regulation occurs at an early step in the Nod factor signal transduction pathway, at or above Nod factor-induced calcium spiking. Here we show that jasmonic acid also inhibits the plant's responses to rhizobial bacteria, with direct effects on Nod factor-induced calcium spiking. However, unlike ethylene, jasmonic acid not only inhibits spiking but also suppresses the frequency of calcium oscillations when applied at lower concentrations. This effect of jasmonic acid is amplified in the ethylene-insensitive mutant skl, indicating an antagonistic interaction between these two hormones for regulation of Nod factor signaling. The rapidity of the effects of ethylene and jasmonic acid on Nod factor signaling suggests direct crosstalk between these three signal transduction pathways. This work provides a model by which crosstalk between signaling pathways can rapidly integrate environmental, developmental and biotic stimuli to coordinate diverse plant responses.     

Additive Effects of PDGF Receptor β Signaling Pathways in Vascular Smooth Muscle Cell Development

The platelet-derived growth factor β receptor (PDGFRβ) is known to activate many molecules involved in signal transduction and has been a paradigm for receptor tyrosine kinase signaling for many years. We have sought to determine the role of individual signaling components downstream of this receptor in vivo by analyzing an allelic series of tyrosine–phenylalanine mutations that prevent binding of specific signal transduction components. Here we show that the incidence of vascular smooth muscle cells/pericytes (v/p), a PDGFRβ-dependent cell type, can be correlated to the amount of receptor expressed and the number of activated signal transduction pathways. A decrease in either receptor expression levels or disruption of multiple downstream signaling pathways lead to a significant reduction in v/p. Conversely, loss of RasGAP binding leads to an increase in this same cell population, implicating a potential role for this effector in attenuating the PDGFRβ signal. The combined in vivo and biochemical data suggest that the summation of pathways associated with the PDGFRβ signal transduction determines the expansion of developing v/p cells.     

Notch signal transduction: a real rip and more

The Notch signaling pathway functions in a wide variety of processes that regulate tissue patterning and morphogenesis in developing vertebrates and invertebrates. Research on the mechanism of ligand-induced Notch signal transduction has revealed a novel and essential element in the signal cascade. Some recent findings support a model in which sequential proteolytic cleavage serves to regulate Notch signal transduction.