Retroactive signaling in short signaling pathways

In biochemical signaling pathways without explicit feedback connections, the core signal transduction is usually described as a one-way communication, going from upstream to downstream in a feedforward chain or network of covalent modification cycles. In this paper we explore the possibility of a new type of signaling called retroactive signaling, offered by the recently demonstrated property of retroactivity in signaling cascades. The possibility of retroactive signaling is analysed in the simplest case of the stationary states of a bicyclic cascade of signaling cycles. In this case, we work out the conditions for which variables of the upstream cycle are affected by a change of the total amount of protein in the downstream cycle, or by a variation of the phosphatase deactivating the same protein. Particularly, we predict the characteristic ranges of the downstream protein, or of the downstream phosphatase, for which a retroactive effect can be observed on the upstream cycle variables. Next, we extend the possibility of retroactive signaling in short but nonlinear signaling pathways involving a few covalent modification cycles.     

Mapping the human phosphatome on growth pathways

Large‐scale siRNA screenings allow linking the function of poorly characterized genes to phenotypic readouts. According to this strategy, genes are associated with a function of interest if the alteration of their expression perturbs the phenotypic readouts. However, given the intricacy of the cell regulatory network, the mapping procedure is low resolution and the resulting models provide little mechanistic insights. We have developed a new strategy that combines multiparametric analysis of cell perturbation with logic modeling to achieve a more detailed functional mapping of human genes onto complex pathways. A literature‐derived optimized model is used to infer the cell activation state following upregulation or downregulation of the model entities. By matching this signature with the experimental profile obtained in the high‐throughput siRNA screening it is possible to infer the target of each protein, thus defining its ‘entry point’ in the network. By this novel approach, 41 phosphatases that affect key growth pathways were identified and mapped onto a human epithelial cell‐specific growth model, thus providing insights into the mechanisms underlying their function.     

Bmp signaling in molar cusp formation

Tooth cusp is a crucial structure, since the shape of the molar tooth is determined by number, shape, and size of the cusp. Bone morphogenetic protein (Bmp) signaling is known to play a critical role in tooth development, including in initiation. However, it remains unclear whether Bmp signaling is also involved in cusp formation. To address this question, we examined cusp in two different transgenic mouse lines: mice with overexpression of Bmp4 (K14-Bmp4), and those with Bmp inhibitor, Noggin, (K14-Noggin) under keratin14 (K14) promoter. K14-Noggin mice demonstrated extra cusps, whereas reduced number of cusps was observed in K14-Bmp4 mice. To further understand how Bmps are expressed during cusp formation, we performed whole-mount in situ hybridisation analysis of three major Bmps (Bmp2, Bmp4, and Bmp7) in murine maxillary and mandibular molars from E14.5 to P3. The linear expressions of Bmp2 and Bmp4 were observed in both maxillary and mandibular molars at E14.5. The expression patterns of Bmp2 and Bmp4 became significantly different between the maxillary and mandibular molars at E16.5. At P3, all Bmps were expressed in all the cusp regions of the maxillary molar; however, the patterns differed. All Bmps thus exhibited dynamic temporo-spatial expression during the cusp formation. It could therefore be inferred that Bmp signaling is involved in regulating cusp formation.     

Sphingolipid-mediated apoptotic signaling pathways

Various sphingolipids are being viewed as bioactive molecules and/or second messengers. Among them, ceramide (or N-acylsphingosine) and sphingosine generally behave as pro-apoptotic mediators. Indeed, ceramide mediates the death signal initiated by numerous stress agents which either stimulate its de novo synthesis or activate sphingomyelinases that release ceramide from sphingomyelin. For instance, the early generation of ceramide promoted by TNF is mediated by a neutral sphingomyelinase the activity of which is regulated by the FAN adaptor protein, thereby controlling caspase activation and the cell death programme. In addition, the activity of this neutral sphingomyelinase is negatively modulated by caveolin, a major constituent of some membrane microdomains. The enzyme sphingosine kinase also plays a crucial role in apoptosis signalling by regulating the intracellular levels of two sphingolipids having opposite effects, namely the pro-apoptotic sphingosine and the anti-apoptotic sphingosine 1-phosphate molecule. Ceramide and sphingosine metabolism therefore appears as a pivotal regulatory pathway in the determination of cell fate.     

Phosphoproteomics in analyzing signaling pathways

A surprisingly fewer than expected number of genes in the human genome suggests that sophistication of its biologic system is, in part, due to complex regulation of protein activities. The activities of most cellular proteins are regulated by post-translational modifications. One of the most important post-translational modifications is reversible protein phosphorylation, which decorates more than 30% of the proteome and regulates signal transduction pathways under normal conditions as well as in disorders such as diabetes, neurodegenerative diseases, autoimmune diseases and several forms of cancers. This review examines the recent developments in mass spectrometry-based methods for phosphoproteome analysis and its applications for the study of signal transduction pathways. The basic principles of non-mass spectrometry-based methods, such as chemical genetics and flow cytometry-based approaches, are also discussed as well as their specific advantages to signaling studies. Finally, signaling pathways are discussed in the light of large-scale protein interaction studies. The proteomic methods addressed in this review are emerging as some of the essential components in systems biology, which seeks to describe signaling networks through integration of diverse types of data and, in the future, to allow computational simulations of complex biologic pathways in health and disease.     

程序性细胞坏死及其信号通路

细胞凋亡曾被认为是唯一的程序性细胞死亡方式,而坏死是不受信号调控的。但越来越多的证据表明,某些类型的细胞坏死也可受到信号分子的调控,称为程序性细胞坏死,并发现其在免疫功能调控、炎症、感染性疾病中发挥重要作用。本文对程序性细胞坏死的形态特征和信号转导通路及其与免疫系统功能、炎症反应的关系等方面的研究进展作一综述。     

Models of cell signaling pathways

Cellular signaling circuits handle an enormous range of computations. Beyond the housekeeping, replicating and other functions of individual cells, signaling circuits must implement the immensely complex logic of development and function of multicellular organisms. Computer models are useful tools to understand this complexity. Recent studies have extended such models to include electrical, mechanical and spatial details of signaling, and to address the stochastic effects that arise when small numbers of molecules interact. Increasing numbers of models have been developed in close conjunction with experiments, and this interplay gives a deeper and more reliable insight into signaling function.     

Electric field regulated signaling pathways

Physiological electric field (EF) is a potent guidance cue for many physiological development and pathological conditions. The EF induced cellular responses such as migration and proliferation, are considered to be regulated by multiple signaling pathways in a coordinated way. Unlike the signaling transduction regulating the cellular responses toward chemical gradients, the signaling network involved in electric stimulation shows a unique manner, combining the regulation of ion channels, membrane receptors and associated intracellular signaling pathways. This review shall discuss the cellular responses in EF, and summarize the primary signaling network activated during the EF-induced cellular response.     

Phosphoproteomics in analyzing signaling pathways

A surprisingly fewer than expected number of genes in the human genome suggests that sophistication of its biologic system is, in part, due to complex regulation of protein activities. The activities of most cellular proteins are regulated by post-translational modifications. One of the most important post-translational modifications is reversible protein phosphorylation, which decorates more than 30% of the proteome and regulates signal transduction pathways under normal conditions as well as in disorders such as diabetes, neurodegenerative diseases, autoimmune diseases and several forms of cancers. This review examines the recent developments in mass spectrometry-based methods for phosphoproteome analysis and its applications for the study of signal transduction pathways. The basic principles of non-mass spectrometry-based methods, such as chemical genetics and flow cytometry-based approaches, are also discussed as well as their specific advantages to signaling studies. Finally, signaling pathways are discussed in the light of large-scale protein interaction studies. The proteomic methods addressed in this review are emerging as some of the essential components in systems biology, which seeks to describe signaling networks through integration of diverse types of data and, in the future, to allow computational simulations of complex biologic pathways in health and disease.     

Mapping signal transduction pathways by phage display

Rapid identification of proteins that interact with a novel gene product is an important element of functional genomics. Here we describe a phage display-based technique for interaction screening of complex cDNA libraries using proteins or synthetic peptides as baits. Starting with the epidermal growth factor receptor (EGFR) cytoplasmic tail, we identified known protein interactions that link EGFR to the Ras/MAP kinase signal transduction cascade and several novel interactions. This approach can be used as a rapid and efficient tool for elucidating protein networks and mapping intracellular signal transduction pathways.     

Oscillating signaling pathways during embryonic development

Oscillatory signaling pathway activity during embryonic development was first identified in the process of vertebrate somite formation. In mouse, this process is thought to be largely controlled by a cyclic signaling network involving the Notch, FGF, and Wnt pathways. Surprisingly, several recent genetic studies reveal that the core oscillation pacemaker is unlikely to involve periodic activation by these pathways. The mechanism(s) responsible for the production of oscillatory gene activity during somite formation remains, therefore, to be discovered. Oscillatory signaling activity has recently been identified in developmental processes distinct from somite formation. Both the processes of limb development in chick embryos and the maintenance of neural progenitors in mouse embryos involve oscillatory gene activity related to the Notch pathway. These discoveries indicate that oscillatory signaling activities during embryonic development might serve a more general function than previously thought.