Wnt signal transduction pathways

The Wnt signaling pathway is an ancient and evolutionarily conserved pathway that regulates crucial aspects of cell fate determination, cell migration, cell polarity, neural patterning and organogenesis during embryonic development. The Wnts are secreted glycoproteins and comprise a large family of nineteen proteins in humans hinting to a daunting complexity of signaling regulation, function and biological output. To date major signaling branches downstream of the Fz receptor have been identified including a canonical or Wnt/β-catenin dependent pathway and the non-canonical or β-catenin-independent pathway which can be further divided into the Planar Cell Polarity and the Wnt/Ca²⁺ pathways, and these branches are being actively dissected at the molecular and biochemical levels. In this review, we will summarize the most recent advances in our understanding of these Wnt signaling pathways and the role of these pathways in regulating key events during embryonic patterning and morphogenesis.     

Wnt signal transduction pathways

The Wnt signaling pathway is an ancient and evolutionarily conserved pathway that regulates crucial aspects of cell fate determination, cell migration, cell polarity, neural patterning and organogenesis during embryonic development. The Wnts are secreted glycoproteins and comprise a large family of nineteen proteins in humans hinting to a daunting complexity of signaling regulation, function and biological output. To date major signaling branches downstream of the Fz receptor have been identified including a canonical or Wnt/β-catenin dependent pathway and the non-canonical or β-catenin-independent pathway which can be further divided into the Planar Cell Polarity and the Wnt/Ca²⁺ pathways, and these branches are being actively dissected at the molecular and biochemical levels. In this review, we will summarize the most recent advances in our understanding of these Wnt signaling pathways and the role of these pathways in regulating key events during embryonic patterning and morphogenesis.Key words: Wnt, frizzled, dishevelled, canonical, non-canonical, β-catenin, Planar Cell Polarity     

Leptin-induced signal transduction pathways

Leptin is a multifunctional cytokine and hormone that primarily acts in the hypothalamus and plays a key role in the regulation of food intake and energy expenditure. In addition, it has direct effects on many cell types on the periphery. Leptin acts through its receptor, the product of the db gene, which has six isoforms. Only one of them (OB-Rb) has full signalling capabilities and is able to activate the Jak/STAT pathway, the major pathway used by leptin to exert its effects. However, some signalling events can be initiated by the short isoforms. Besides Jak/STAT, other pathways, such as MAPK and the 5'-AMP-activated protein kinase (AMPK) pathway, are also involved in leptin signalling. Leptin also interacts with insulin signalling. In this paper, we give an overview of the signal transduction mechanisms that are related to the actions of leptin.     

Apoptotic signal transduction: emerging pathways.

Apoptosis is a counterbalance to mechanisms of cell proliferation and is critically important in regulation of the immune system, development, and normal tissue homeostasis. Mammalian signal transduction pathways affecting apoptosis are more complex than their counterparts in the nematode Caenorhabditis elegans, a valuable model system that has provided powerful initial insights into key molecules regulating apoptosis. Despite this complexity, substantial progress has been made in recent years towards defining the nature and detail of signalling pathways bringing about apoptosis in mammalian cells. In particular, the identity and precise substrate specificities of a large family of caspase enzymes, implicated as critical components of the apoptotic machinery, have been defined. In addition, the mechanism by which the cell surface Fas receptor mediates induction of apoptosis, via activation of caspases, has recently been elucidated. A prominent role for mitochondria in cell death pathways has also recently emerged, a clear theme being that mitochondria can trigger degradative events by the release of apoptogenic proteins (e.g., cytochrome c) from the intermembrane space to the cytosol. This review focuses on recent progress in these areas and discusses integration of this knowledge in our overall understanding of the processes that control apoptosis.     

Integrin-mediated signal transduction pathways.

Integrins serve as adhesion receptors for extracellular matrix proteins and also transduce biochemical signals into the cell. They regulate a variety of cellular functions, including spreading, migration, proliferation and apoptosis. Many signaling pathways downstream of integrins have been identified and characterized and are discussed here. In particular, integrins regulate many protein tyrosine kinases and phosphatases, such as FAK and Src, to coordinate many of the cell processes mentioned above. The regulation of MAP kinases by integrins is important for cell growth or other functions, and the putative roles of Ras and FAK in these pathways are discussed. Phosphatidylinositol lipids and their modifying enzymes, particularly PI 3-kinase, are strongly implicated as mediators of integrin-regulated cytoskeletal changes and cell migration. Similarly, actin cytoskeleton regulation by the Rho family of GTPases is coordinated with integrin signaling to regulate cell spreading and migration, although the exact relationship between these pathways is not clear. Finally, intracellular pH and calcium fluxes by integrins are suggested to affect a variety of cellular proteins and functions.     

Knowledge representation of signal transduction pathways

MOTIVATIONS: Signal transduction is the common term used to define a diverse topic that encompasses a large body of knowledge about the biochemical mechanisms. Since most of the knowledge of signal transduction resides in scientific articles and is represented by texts in natural language or by diagrams, there is the need of a knowledge representation model for signal transduction pathways that can be as readily processed by a computer as it is easily understood by humans. RESULTS: A signal transduction pathway representation model is presented. It is based on a compound graph structure and is designed to handle the diversity and hierarchical structure of pathways. A prototype knowledge base was implemented on a deductive database and a number of biological queries are demonstrated on it.     

Power-law models of signal transduction pathways

The mathematical modelling of signal transduction pathways has become a valuable aid to understanding the complex interactions involved in intracellular signalling mechanisms. An important aspect of the mathematical modelling process is the selection of the model type and structure. Until recently, the convention has been to use a standard kinetic model, often with the Michaelis-Menten steady state assumption. However this model form, although valuable, is only one of a number of choices, and the aim of this article is to consider the mathematical structure and essential features of an alternative model form--the power-law model. Specifically, we analyse how power-law models can be applied to increase our understanding of signal transduction pathways when there may be limited prior information. We distinguish between two kinds of power law models: a) Detailed power-law models, as a tool for investigating pathways when the structure of protein-protein interactions is completely known, and; b) Simplified power-law models, for the analysis of systems with incomplete structural information or insufficient quantitative data for generating detailed models. If sufficient data of high quality are available, the advantage of detailed power-law models is that they are more realistic representations of non-homogenous or crowded cellular environments. The advantages of the simplified power-law model formulation are illustrated using some case studies in cell signalling. In particular, the investigation on the effects of signal inhibition and feedback loops and the validation of structural hypotheses are discussed.     

Two-component signal transduction pathways in Arabidopsis

The two-component system, consisting of a histidine (His) protein kinase that senses a signal input and a response regulator that mediates the output, is an ancient and evolutionarily conserved signaling mechanism in prokaryotes and eukaryotes. The identification of 54 His protein kinases, His-containing phosphotransfer proteins, response regulators, and related proteins in Arabidopsis suggests an important role of two-component phosphorelay in plant signal transduction. Recent studies indicate that two-component elements are involved in plant hormone, stress, and light signaling. In this review, we present a genome analysis of the Arabidopsis two-component elements and summarize the major advances in our understanding of Arabidopsis two-component signaling.     

Phytochrome and UV signal transduction pathways

The phytochromes are the best studied plant photoreceptors, controlling a wide variety of responses at both whole plant and single cell levels. Three signal transduction pathways, dependent on cGMP and/or calcium, have been found to be utilized by phytochrome to control the expression of genes required for chloroplast development (e.g., CAB and FNR) and anthocyanin biosynthesis (e.g., CHS). In particular, cGMP is a second messenger positively regulating CHS gene expression whilst calcium and calmodulin act as negative regulators. In addition to phytochrome regulation of CHS we have begun to examine the signal transduction pathways utilized by UV photoreceptors. In contrast to phytochrome-mediated responses, results indicate a role for calcium and calmodulin as positive regulators of CHS gene expression in UV light.     

Wound signal transduction pathways in plants

A significant advancement in our knowledge and understanding of wound-signaling pathways in plants has been made recently. Essential role in the explanation of these processes came from the genetic screens and analysis of mutants which are defective in either jasmonic acid (JA) biosynthesis, JA perception or systemin function. Plants equally react to wound in the tissues directly damaged (local response) as well as in the non-wounded areas (systemic response). Jasmonides and in particular the most studied JA, produced by the octadecanoid pathway, are responsible for the systemic response. Jasmonides functioning as long-distance signal particles transmit the information about wound to distant, non-wounded tissues where defense response is invoked. Peptyd - systemin, identified in some Solanaceous species, acts locally to the wounded area to elicit the production of JA. Jasmonic acid-dependent and -independent wound signal transduction pathways have been identified and partially characterized. JA-dependent wound signaling pathways are responsible for the activation of systemic responses, whereas JA-independent wound signaling pathways, activated close to wound side, have a role in reparation of damaged tissue and in defense against pathogens.     

MicroRNA与肿瘤相关的信号转导通路

信号转导通路在细胞代谢、生长、增殖、应激、发育和凋亡等生命活动中具有极为重要的作用。干扰这些通路将可能影响细胞的正常发育, 甚至导致肿瘤。MicroRNA(miRNA)是近年来在真核生物中发现的、在转录后水平负调节基因表达的一类长度约22个核苷酸的非编码小RNA, 其靶基因数目众多, 生物学功能广泛。在多种肿瘤中发现了miRNA的异常表达, 提示后者与肿瘤发生有关, 可能机制为调控癌基因或肿瘤抑制基因的表达。此外亦发现miRNA的靶基因有许多作用于肿瘤相关的信号转导通路。miRNA在肿瘤发生过程中的重要调控功能预示其将成为人类癌症诊断和治疗方面的新星。     

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

We report the development of a publicly accessible, curated nucleotide sequence database of hypocrealean entomopathogenic fungi. The goal is to provide a platform for users to easily access sequence data from taxonomic reference strains. The database can be used to accurately identify unknown entomopathogenic fungi based on sequence data for a variety of phylogenetically informative loci. The database provides full multi-locus sequence alignment capabilities. The initial release contains data compiled for 525 strains covering the phylogenetic diversity of three important entomopathogenic families: Clavicipitaceae, Cordycipitaceae, and Ophiocordycipitaceae. Furthermore, Entomopathogen ID can be expanded to other fungal clades of insect pathogens, as sequence data becomes available. The database will allow isolate characterisation and evolutionary analyses. We contend that this freely available, web-accessible database will facilitate the broader community to accurately identify fungal entomopathogens, which will allow users to communicate research results more effectively.     

Simulating the evolution of signal transduction pathways

We use a generic model of a network of proteins that can activate or deactivate each other to explore the emergence and evolution of signal transduction networks and to gain a basic understanding of their general properties. Starting with a set of non-interacting proteins, we evolve a signal transduction network by random mutation and selection to fulfill a complex biological task. In order to validate this approach we base selection on a fitness function that captures the essential features of chemotactic behavior as seen in bacteria. We find that a system of as few as three proteins can evolve into a network mediating chemotaxis-like behavior by acting as a "derivative sensor". Furthermore, we find that the dynamics and topology of such networks show many similarities to the natural chemotaxis pathway, that the response magnitude can increase with increasing network size and that network behavior shows robustness towards variations in some of the internal parameters. We conclude that simulating the evolution of signal transduction networks to mediate a certain behavior may be a promising approach for understanding the general properties of the natural pathway for that behavior.     

GPCR和CaCC信号传导中的钙信号网络

G蛋白偶联受体(G protein-coupled receptor,GPCR)作为最大的一类人膜蛋白受体家族和最重要的药物靶标而倍受关注,其中钙离子在细胞内信号传导级联放大中起了关键的作用。阐述了GPCR和钙激活的氯离子通道蛋白(calcium-activated chloride channel,CaCC)中的钙信号网络与生理功能以及如何干扰阻断该网络,为药物设计和很多疾病的治疗提供了依据。     

Modeling and simulation in signal transduction pathways: a systems biology approach

Modeling, the heart of systems biology, of complex processes (example: signal transduction) is a wide scientific discipline where many approaches from different areas are confronted with the aim of better understanding, identifying and modeling of complex data coming from various sources. The purpose of this paper is to introduce the basic steps of systems biology view towards signaling pathways, which mainly deals with the computational tools. The paper emphasizes the modeling and simulation approach in the signal transduction pathways using the topologies of the biochemical reactions with an overview of the different types of software platforms. Finally, we demonstrated the epidermal growth factor receptor signaling pathway model as an example to study the growth factor mediated signaling system with biological experiments. This paper will enables new comers to underline the strengths of the computational approaches towards signal transduction, as well as to highlight the systems biology research directions.     

Targeting signal transduction pathways by chemopreventive agents

Cancer is a dynamic process that involves many complex factors, which may explain why a "magic bullet" cure for cancer has not been found. Death rates are still rising for many types of cancers, which possibly contributes to the increased interest in chemoprevention as an alternative approach to the control of cancer. This strategy for cancer control is based on the presumption that because cancer develops through a multi-step process, each step may be a prospective target for reversing or suppressing the process. Thus, the design and development of chemopreventive agents that act on specific and/or multiple molecular and cellular targets is gaining support as a rational approach to control cancer. Nutritional or dietary factors have attracted a great deal of interest because of their perceived ability to act as highly effective chemopreventive agents. They are professed as being generally safe and may have efficacy as chemopreventive agents by preventing or reversing premalignant lesions and/or reducing second primary tumor incidence. Many of these dietary compounds appear to act on multiple target signaling pathways. Some of the most interesting and well documented are resveratrol and components of tea, including EGCG, theaflavins and caffeine. This review will focus on recent work regarding three well-accepted cellular/molecular mechanisms that may at least partially explain the effectiveness of selected food factors, including those indicated above, as chemopreventive anti-promotion agents. These food compounds may act by: (1) inducing apoptosis in cancer cells; (2) inhibiting neoplastic transformation through the inhibition of AP-1 and/or NF-kappaB activation; and/or (3) suppressing COX-2 overexpression in cancer cells.