Multi-layered representation for cell signaling pathways

To understand complex signaling pathways and networks, it is necessary to develop a formal and structured representation of the available information in a format suitable for analysis by software tools. Due to the complexity and incompleteness of the current biological knowledge about cell signaling, such a device must be able to represent cellular pathways at differing levels of details, one level of information abstract enough to convey an essential signaling flow while hiding its details and another level of information detailed enough to explain the underlying mechanisms that account for the signaling flow described at a more abstract level. We have defined a formal ontology for cell-signaling events that allows us to describe these cellular pathways at various levels of abstraction. Using this formal representation, ROSPath (reactive oxygen species-mediated signaling pathway) database system has been implemented and made available on the web (rospath.ewha.ac.kr). ROSPath is a database system for reactive oxygen species (ROS)-mediated cell signaling pathways and signaling processes in molecular detail, which facilitates a comprehensive understanding of the regulatory mechanisms in signaling pathways. ROSPath includes growth factor-, stress-, and cytokine-induced signaling pathways containing about 500 unique proteins (mostly mammalian) and their related protein states, protein complexes, protein complex states, signaling interactions, signaling steps, and pathways. It is a web-based structured repository of information on the signaling pathways of interest and provides a means for managing data produced by large-scale and high-throughput techniques such as proteomics. Also, software tools are provided for querying, displaying, and analyzing pathways, thus furnishing an integrated web environment for visualizing and manipulating ROS-mediated cell-signaling events.     

Database of cell signaling enzymes

This paper describes a database for cell signaling enzymes. Our web database offers methods to study, interpret and compare cell-signaling enzymes. Searching and retrieving data from this database has been made easy and user friendly and it is well integrated with other related databases. We believe the end user will be benefited from this database. AVAILABILITY: http://www.sastra.edu/dcse/index.html.     

Stepping stones in the path of glucocorticoid-driven apoptosis of lymphoid cells

Cumulative work on glucocorticoid (GC) regulation of genes in lymphoid cell cultures has revealed that apoptotic sensitivity to GCs depends on sufficient active GC receptors in the cells. The actions of the ligand-driven GC receptor that lead to apoptosis depend on interactions with other major cell-signaling systems, including the MAPK pathways, the cAMP/PKA pathway, the hedgehog pathway, the mTOR system and the c- myc system. The balance between these systems determines whether a given cell responds to GCs by undergoing apoptosis. A central core of networked genes may be found under GC control in many types of malignant, GC-sensitive cells. The partial core list identified should be tested in clinical cell samples from hematologic malignancies.     

In search of new mutants in cell-signaling systems of the nematodeCaenorhabditis elegans

Development of multicellular organisms is controlled mainly by cell-signaling systems. In this review I first discuss methods of genetic analysis and properties of mutants of cell-signaling systems in general and in the nematodeC. elegans. Then, I describe two of our approaches to isolating new mutants in cell-signaling ofC. elegans. The first approach is to select for mutants that have the same visible phenotype as those in known cell-signaling genes. In a survey of larval lethal mutations we found that there are quite a few mutants in which the inner surface of the body wall is detached from the outer surface of the intestine. Some of them map in genes that are known to act in cell-signaling systems in vulval induction or sex myoblast migration, which are not essential to the growth and survival ofC. elegans. Therefore, we think many of the mutations of the above phenotype disrupt cell-signaling in an unidentified essential function, and also cell-signaling in the non-essential functions. The second approach is to isolate mutants resistant to a drug expected to disturb cell-signaling. As the drug we have chosen sodium fluoride, which depletes calcium ion, activates G-proteins and inactivates some phosphatases. The mutants are grouped into two classes (three and two genes, respectively) according to degree of fluoride-resistance and growth rate of larvae. Although there is so far no direct evidence that these mutants are related to cell-signaling, they show complex epistasis that can be explained by a model consisting of a cell-signaling pathway.     

Making sense of the COP9 signalosome. A regulatory protein complex conserved from Arabidopsis to human

The COP9 signalosome, once defined as a repressor complex of light-activated development in Arabidopsis, has recently been found in humans and is probably present in most multicellular organisms. The COP9 signalosome is closely related to the lid sub-complex of the 26S proteasome in structural composition and probably shares a common evolutionary ancestor. A multifaceted role of the COP9 signalosome in cell-signaling processes is hinted at by its associated novel kinase activity, as well as the involvement of its subunits in regulating multiple cell-signaling pathways and cell-cycle progression. The molecular genetic studies in Arabidopsis suggest that the complex functions as part of a highly conserved regulatory network, whose physiological role in animals remains to be determined.     

All hands on deck—the role of chloroplasts, endoplasmic reticulum, and the nucleus in driving plant innate immunity

Plant innate immunity is mediated by cell membrane and intracellular immune receptors that function in distinct and overlapping cell-signaling pathways to activate defense responses. It is becoming increasingly evident that immune receptors rely on components from multiple organelles for the generation of appropriate defense responses. This review analyzes the defense-related functions of the chloroplast, nucleus, and endoplasmic reticulum (ER) during plant innate immunity. It details the role of the chloroplasts in synthesizing defense-specific second messengers and discusses the retrograde signal transduction pathways that exist between the chloroplast and nucleus. Because the activities of immune modulators are regulated, in part, by their subcellular localization, the review places special emphasis on the dynamics and nuclear–cytoplasmic transport of immune receptors and regulators and highlights the importance of this process in generating orderly events during an innate immune response. The review also covers the recently discovered contributions of the ER quality-control pathways in ensuring the signaling competency of cell surface immune receptors or immune regulators.     

A database system for the analysis of biochemical pathways

To provide support for the analysis of biochemical pathways a database system based on a model that represents the characteristics of the domain is needed. This domain has proven to be difficult to model by using conventional data modelling techniques. We are building an ontology for biochemical pathways, which acts as the basis for the generation of a database on the same domain, allowing the definition of complex queries and complex data representation. The ontology is used as a modelling and analysis tool which allows the expression of complex semantics based on a first-order logic representation language. The induction capabilities of the system can help the scientist in formulating and testing research hypotheses that are difficult to express with the standard relational database mechanisms. An ontology representing the shared formalisation of the knowledge in a scientific domain can also be used as data integration tool clarifying the mapping of concepts to the developers of different databases. In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system.     

Pathway recognition and augmentation by computational analysis of microarray expression data

MOTIVATION: We present a system, QPACA (Quantitative Pathway Analysis in Cancer) for analysis of biological data in the context of pathways. QPACA supports data visualization and both fine- and coarse-grained specifications, but, more importantly, addresses the problems of pathway recognition and pathway augmentation. RESULTS: Given a set of genes hypothesized to be part of a pathway or a coordinated process, QPACA is able to reliably distinguish true pathways from non-pathways using microarray expression data. Relying on the observation that only some of the experiments within a dataset are relevant to a specific biochemical pathway, QPACA automates selection of this subset using an optimization procedure. We present data on all human and yeast pathways found in the KEGG pathway database. In 117 out of 191 cases (61%), QPACA was able to correctly identify these positive cases as bona fide pathways with p-values measured using rigorous permutation analysis. Success in recognizing pathways was dependent on pathway size, with the largest quartile of pathways yielding 83% success. In cross-validation tests of pathway membership prediction, QPACA was able to yield enrichments for predicted pathway genes over random genes at rates of 2-fold or better the majority of the time, with rates of 10-fold or better 10-20% of the time. AVAILABILITY: The software is available for academic research use free of charge by email request. SUPPLEMENTARY INFORMATION: Data used in the paper may be downloaded from http://www.jainlab.org/downloads.html     

MNAR plays an important role in ERa activation of Src/MAPK and PI3K/Akt signaling pathways

Estrogens play a critical role in the regulation of cellular proliferation, differentiation, and apoptosis. Evidence indicates that this regulation is mediated by a complex interface of direct control of gene expression (so-called "genomic action") and by regulation of cell-signaling/phosphorylation cascades (referred to as the "non-genomic", or "extranuclear" action). However, the mechanisms of the non-genomic action of estrogens are not well defined. We have recently described the identification of a novel scaffold protein termed MNAR (modulator of non-genomic action of estrogen receptor), that couples conventional steroid receptors with extranuclear signal transduction pathways, thus potentially providing additional and tissue- or cell-specific level of steroid hormone regulation of cell functions. We have demonstrated that the MNAR is required for ER alpha (ERa) interaction with p60(src) (Src), which leads to activation of Src/MAPK pathway. Our new data also suggest that activation of cSrc in response to E2 leads to MNAR phosphorylation, interaction with p85, and activation of the PI3 and Akt kinases. These data therefore suggest that MNAR acts as an important scaffold that integrates ERa action in regulation of important signaling pathways. ERa non-genomic action has been suggested to play a key role in estrogen-induced cardio-, neuro-, and osteo-protection. Therefore, evaluation of the molecular crosstalk between MNAR and ERa may lead to development of functionally selective ER modulators that can separate between beneficial, prodifferentiative effects in bone, the cardiovascular system and the CNS and the "detrimental", proliferative effects in reproductive tissues and organs.     

群感效应与链霉菌次生代谢调控

群感效应是细菌协调群体行为的一种外界信号传递机制,在细菌中普遍存在,参与细胞的多种生理过程。链霉菌中也存在群感效应,在抗生素等次生代谢产物的生物合成中起重要的调控作用;从自诱导信号分子的结构到信号传递机制都存在一定多样性,其中以A-因子为代表的γ-丁酸内酯类信号分子的作用机制研究最为深入。近几年在链霉菌中发现的PI-因子、M-因子以及一些特定的代谢产物则代表几类结构较新颖的信号分子,通过群感效应机制调控次生代谢过程;链霉菌中还发现胆固醇氧化酶、甘油等分子具有信号分子特征,不排除是通过群感效应来参与抗生素生物合成调控。本文主要就参与链霉菌次生代谢调控的几类群感效应系统的研究状况进行综述,重点阐述各类群感信号分子的结构和信号传递机制的不同,并对链霉菌群感效应的研究趋势以及在抗生素高产菌遗传育种中的应用前景进行了展望。     

PaVESy: Pathway Visualization and Editing System

A data managing system for editing and visualization of biological pathways is presented. The main component of PaVESy (Pathway Visualization and Editing System) is a relational SQL database system. The database design allows storage of biological objects, such as metabolites, proteins, genes and respective relations, which are required to assemble metabolic and regulatory biological interactions. The database model accommodates highly flexible annotation of biological objects by user-defined attributes. In addition, specific roles of objects are derived from these attributes in the context of user-defined interactions, e.g. in the course of pathway generation or during editing of the database content. Furthermore, the user may organize and arrange the database content within a folder structure and is free to group and annotate database objects of interest within customizable subsets. Thus, we allow an individualized view on the database content and facilitate user customization. A JAVA-based class library was developed, which serves as the database programming interface to PaVESy. This API provides classes, which implement the concepts of object persistence in SQL databases, such as entries, interactions, annotations, folders and subsets. We created editing and visualization tools for navigation in and visualization of the database content. User approved pathway assemblies are stored and may be retrieved for continued modification, annotation and export. Data export is interfaced with a range of network visualization programs, such as Pajek or other software allowing import of SBML or GML data format. AVAILABILITY: http://pavsey.mpimp-golm.mpg.de     

AraCyc: a biochemical pathway database for Arabidopsis

AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).     

Peptide-based fluorescent sensors of protein kinase activity: design and applications

Protein kinases control the flow of information through cell-signaling pathways. A detailed analysis of their behavior enhances our ability to understand normal cellular states and to devise therapeutic interventions for diseases. The design and application of "Environmentally-Sensitive", "Deep-Quench" and "Self-Reporting" sensor systems for studying protein kinase activity are described. These sensors allow real-time activity measurements in a continuous manner for a wide variety of kinases. As these sensors can be adapted from an in vitro screen to imaging kinase activity in living cells, they support both preliminary and later stages of drug discovery.     

Granulosa cell apoptosis: conservation of cell signaling in an avian ovarian model system

Ovarian follicle atresia in all vertebrates studied to date is mediated via apoptosis, a process that is often initiated within the granulosa cell layer. While follicle atresia is considered a normal physiological process to insure the greatest chance for ovulation of fertilizable oocytes, abnormally high rates of atresia result in chronic infertility and/or premature termination of fertility (e.g., menopause). Although the vast majority of research to elucidate the molecular ordering of cell signaling during the process of granulosa cell apoptosis has been conducted in mammalian model systems, there is ample evidence to demonstrate that many of the proteins, enzymes and cell-signaling pathways are common to ovarian follicles from avian species. The following review will discuss evidence for the conservation of cellular processes that regulate the fate of granulosa cells from the avian, versus mammalian, ovary during follicle development.     

Novel molecular targets for prevention of obesity and osteoporosis

Evidence from both epidemiological studies and basic research suggests that obesity and osteoporosis are interrelated. Though there is an increase in the prevalence of these disorders, a limited number of treatments are available, one of the reasons being the complexity of the pathways involved and difficulty in identifying a single molecular target. Due to adverse effects of pharmaceuticals, intake of herbal drugs by patients without a physician's recommendation is increasing globally. Lack of success with targeted monotherapy has encouraged scientists to determine whether combinations of phytochemicals that interfere with numerous cell-signaling pathways can be a more effective approach to treat complex diseases. For example, evidence is emerging that specific combinations of phytochemicals are far more effective than single compounds in decreasing adipogenesis and promoting bone formation. Since multiple pathways are dysfunctional in obesity and osteoporosis, an ideal approach for preventing and treating these diseases may be to use a combination of phytochemicals to address several targets simultaneously.     

Automated metabolic reconstruction for Methanococcus jannaschii

We present the computational prediction and synthesis of the metabolic pathways in Methanococcus jannaschii from its genomic sequence using the PathoLogic software. Metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. We predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. These assignments represent significantly improved enzyme and pathway predictions compared with previous metabolic reconstructions, and some key metabolic reactions, previously missing, have been identified. Our results, in the form of enzymatic assignments and metabolic pathway predictions, form a database (MJCyc) that is accessible over the World Wide Web for further dissemination among members of the scientific community.