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.     

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.     

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.     

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     

Roles of the His-Asp phosphorelay signal transduction system in controlling cell growth and development in Aspergillus nidulans

The His-Asp phosphorelay signal transduction system has been identified in most organisms, including bacteria, yeasts, fungi, and plants, except for animals. This system is important in adaptation to stress, control of cell growth, and induction of development in response to environmental changes. On the basis of genomic information, it has been found that Aspergillus nidulans, a model species of fungi, includes 15 histidine kinases (HKs), one histidine-containing phosphotransmitter protein (HPt), and four response regulators (RRs) as factors related to the signal transduction system. In this review, it is explain that the His-Asp phosphorelay system is important in controlling cell growth (responses to fungicides, the induction of asexual and sexual development, and so on) under different growth conditions with reference to A. nidulans.     

In silico reconstruction of the amino acid metabolic pathways of Trypanosoma cruzi

Trypanosoma cruzi is the epidemiological agent of Chagas' disease, affecting most of Central and South America, constituting a significant health and socio-economic problem. The parasite has a metabolism largely based on the consumption of amino acids, which participate in a diversity of metabolic pathways, leading to many crucial compounds for the survival of this parasite. Study of its enzymes has the potential to disclose new therapeutic targets and foster the development of new drugs. In this study, we employed computational approaches to reconstruct in silico the amino acid metabolic pathways of T. cruzi, aiming to link genomic information with functional information. For that, protein sequences from 570 EC classes belonging to 25 different pathways in general amino acid metabolism were downloaded from KEGG. A subset of 471 EC classes had at least one sequence deposited. Clustering of the proteins belonging to each EC class was performed using a similarity-based approach implemented in the tool AnEnPi. Reconstruction of the metabolic pathways comprising the amino acid metabolism of T. cruzi was performed by analyzing the output of BLASTP, using as query the dataset of predicted proteins of T. cruzi against all sequences of each individual cluster. This approach allowed us to identify 764 T. cruzi proteins probably involved in the metabolism of amino acids as well as the identification of several putative cases of analogy. Furthermore, we were able to identify several enzymatic activities of T. cruzi that were not previously included in KEGG.     

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.     

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.     

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.     

SakA MAP kinase is involved in stress signal transduction,sexual development and spore viability in Aspergillus nidulans

In eukaryotic cells, environmental stress signals are transmitted by evolutionarily conserved MAPKs, such as Hog1 in the budding yeast Saccharomyces cerevisiae, Spc1 in the fission yeast Schizosaccharomyces pombe and p38/JNK in mammalian cells. Here, we report the identification of the Aspergillus nidulans sakA gene, which encodes a member of the stress MAPK family. The sakA gene is able to complement the S. pombe spc1- defects in both osmo-regulation and cell cycle progression. Moreover, SakA MAPK is activated in response to osmotic and oxidative stress in both S. pombe and A. nidulans. However, in contrast to hog1 and spc1 mutants, the sakA null mutant is not sensitive to high osmolarity stress, indicating a different regulation of the osmostress response in this fungus. On the other hand, the DeltasakA mutant shows development and cell-specific phenotypes. First, it displays premature steA-dependent sexual development. Second, DeltasakA mutant produces asexual spores that are highly sensitive to oxidative and heat shock stress and lose viability upon storage. Indeed, SakA is transiently activated early after induction of conidiation. Our results indicate that SakA MAPK is involved in stress signal transduction and repression of sexual development, and is required for spore stress resistance and survival.     

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.     

Characterization of the pH signal transduction pathway gene palA of Aspergillus nidulans and identification of possible homologs.

We have cloned the palA gene of Aspergillus nidulans, one of six genes participating in ambient pH signal transduction in a regulatory circuit mediating pH regulation of gene expression. The derived 798-residue PalA protein is 29.4% identical over its entire length to a hypothetical protein from the nematode Caenorhabditis elegans and also has possible yeast homologs.     

Jasmonic acid in wound signal transduction pathways

Wounding induces expression of genes encoding defense-related proteins involved in wound healing. An intensive survey has been carried out to clarify the initial signal transduction pathways that mediate this stress to expression of genes. In this context, signal molecules that intermediate in the wound signal to cellular response have been actively searched for. Jasmonic acid (JA) has been considered to be a key signal molecule in this pathway. Systemin, ABA, ethylene, and electrical current have been suggested to function by transmitting the wound signal to JA. A mitogen-activated protein kinase has been shown to respond rapidly to wounding, and proposed to function as one of the key enzymes involved in JA biosynthesis. Transgenic plants overexpressing a gene encoding a Rab-type, small GTP-binding protein contained 6-fold higher levels of cytokinins than wild-type plants, and responded to wounding by rapidly producing JA and, uncommonly, accumulating salicylic acid (SA), a pathogenic signal. These phenomena observed in the transgenic plants were reproduced when wild-type plants were wounded in the presence of the synthetic cytokinin, benzylaminopurine, suggesting that cytokinins are indispensable in the control of endogenous levels of JA and SA.