Function of the Yersinia effector YopJ

The Yersinia virulence factor YopJ inhibits the host immune response and induces apoptosis by blocking multiple signaling pathways, including the MAPK and NFkappaB pathways in the infected cell. YopJ is a cysteine protease that cleaves a reversible post-translational modification in the form of ubiquitin or a ubiquitin-like protein. Homologues of YopJ are expressed in animal and plant pathogens, as well as a plant symbiont, suggesting a universal mechanism of regulating or modulating a variety of signaling pathways. The ability of YopJ to block the innate immune response, its activity as a ubiquitin-like protein protease and its activity with respect to mammalian signalling pathways are discussed in this review.     

催化元件和途径的人工设计与组装

催化元件以及由多个催化元件组成的合成途径的设计与组装为人工合成体系的建立奠定了基础,是合成生物学的重要研究内容。除从自然生物中挖掘大量的天然酶和途径可供人工合成体系使用外,将计算生物学、蛋白质工程以及组合生物合成等技术相结合,理性地、有目的地进行催化元件和途径的人工设计与组装,将提供新功能酶以及新物质合成途径。介绍了催化元件和合成途径人工设计与组装的研究策略和最新进展。     

Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems

The structural design of ATP and NADH producing systems, such as glycolysis and the citric acid cycle (TCA), is analysed using optimization principles. It is assumed that these pathways combined with oxidative phosphorylation have reached, during their evolution, a high efficiency with respect to ATP production rates. On the basis of kinetic and thermodynamic principles, conclusions are derived concerning the optimal stoichiometry of such pathways. Extending previous investigations, both the concentrations of adenine nucleotides as well as nicotinamide adenine dinucleotides are considered variable quantities. This implies the consideration of the interaction of an ATP and NADH producing system, an ATP consuming system, a system coupling NADH consumption with ATP production and a system consuming NADH decoupled from ATP production. It is examined in what respect real metabolic pathways can be considered optimal by studying a large number of alternative pathways. The kinetics of the individual reactions are described by linear or bilinear functions of reactant concentrations. In this manner, the steady-state ATP production rate can be calculated for any possible ATP and NADH producing pathway. It is shown that most of the possible pathways result in a very low ATP production rate and that the very efficient pathways share common structural properties. Optimization with respect to the ATP production rate is performed by an evolutionary algorithm. The following results of our analysis are in close correspondence to the real design of glycolysis and the TCA cycle. (1) In all efficient pathways the ATP consuming reactions are located near the beginning. (2) In all efficient pathways NADH producing reactions as well as ATP producing reactions are located near the end. (3) The number of NADH molecules produced by the consumption of one energy-rich molecule (glucose) amounts to four in all efficient pathways. A distance measure and a measure for the internal ordering of reactions are introduced to study differences and similarities in the stoichiometries of metabolic pathways.     

Evidence for the involvement of Plasmodium falciparum proteins in the formation of new permeability pathways in the erythrocyte membrane

The intraerythrocytic developmental stages of the malaria parasite Plasmodium falciparum are responsible for the clinical symptoms associated with malaria tropica. The non-infected human erythrocyte is a terminally differentiated cell that is unable to synthesize proteins and lipids de novo, and it is incapable of importing a number of solutes that are essential for parasite proliferation. Approximately 12-15 h after invasion the parasitized cell undergoes a marked increase in its permeability to a variety of different solutes present in the extracellular milieu. The increase is due to the induction in the erythrocyte membrane of 'new permeability pathways' which have been characterized in some detail in terms of their transport and electrophysiological properties, but which are yet to be defined at a molecular level. Here we show that these pathways are resistant to trypsin but are abolished by treatment of intact infected erythrocytes with chymotrypsin. On resuspension of chymotrypsinized cells in chymotrypsin-free medium the pathways progressively reappear, a process that can be inhibited by cytotoxic agents, and by brefeldin A which inhibits protein secretion. Our results provide evidence for the involvement of parasite encoded proteins in the generation of the pathways, either as components of the pathways themselves or as auxiliary factors.     

Role of amino acids in the translational control of protein synthesis in mammals

Amino acids, long considered simply substrates for protein synthesis, have been recently shown to act as modulators of intracellular signal transduction pathways typically associated with growth-promoting hormones such as insulin and insulin-like growth factor-1. Many of the endpoints of the signaling pathways regulated by amino acids are proteins involved in mRNA translation. Thus, particular amino acids not only serve as substrates for protein synthesis but are also modulators of the process. The focus of this article is to review recent studies that have used intact animals as experimental models to examine the role of amino acids as modulators of signal transduction pathways.     

Hormonal signaling and signal pathway crosstalk in the control of myometrial calcium dynamics

Understanding the basis for the control of myometrial contractant and relaxant signaling pathways is important to understanding how to manage myometrial contractions. Signaling pathways are influenced by the level of expression of the signals and signal pathway components, the location of these components in the appropriate subcellular environment, and covalent modification. Crosstalk between these pathways regulates the effectiveness of signal transduction and represents an important way by which hormones can regulate phenotype. This review deals primarily with signaling pathways that control Ca2+ entry and intracellular release, as well as the interplay between these pathways.     

Nitric oxide and the enigma of cardiac hypertrophy

In pathological conditions associated with persistent increases in hemodynamic workload (old myocardial infarction, high blood pressure, valvular heart disease), a number of signalling pathways are activated in the heart, all of which promote hypertrophic growth of the heart, characterised at the cellular level by increases in individual cardiac myocyte size. Some of these pathways are required for a successful adaptation to cardiac injury. Other pathways are maladaptive, however, as they lead to progressive contractile dysfunction and heart failure. The free radical gas nitric oxide and natriuretic peptides, both of which are produced in the heart, have emerged as endogenous inhibitors of maladaptive hypertrophy signalling. Overall, it appears that cardiac hypertrophy is controlled by an interplay of pro- and antihypertrophic signalling networks. This delicate balance can tip towards adaptation or heart failure. In the future, patients living with cardiac disease may benefit from therapeutic strategies targeting maladaptive hypertrophy signalling pathways.     

On the Origin of Metabolic Pathways

The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO₂ to monomers used by the first organisms would also be considered an heterotrophic origin. Autotrophy means that the first organisms biosynthesized their cell constituents as well as assembling them. Prebiotic synthetic pathways are all different from the biosynthetic pathways of the last common ancestor (LCA). The steps leading to the origin of the metabolic pathways are closer to prebiotic chemistry than to those in the LCA. There may have been different biosynthetic routes between the prebiotic and the LCAs that played an early role in metabolism but have disappeared from extant organisms. The semienzymatic theory of the origin of metabolism proposed here is similar to the Horowitz hypothesis but includes the use of compounds leaking from preexisting pathways as well as prebiotic compounds from the environment.     

The Regulation of the Autophagic Network and Its Implications for Human Disease

Autophagy has attracted a lot of attention in recent years. More and more proteins and signaling pathways have been discovered that somehow feed into the autophagy regulatory pathways. Regulation of autophagy is complex and condition-specific, and in several diseases, autophagic fluxes are changed. Here, we review the most well-established concepts in this field as well as the reported signaling pathways or components which steer the autophagy machinery. Furthermore, we will highlight how autophagic fluxes are changed in various diseases either as cause for or as response to deal with an altered cellular homeostasis and how modulation of autophagy might be used as potential therapy for such diseases.     

Evidence for the plasticity of arthropod signal transduction pathways

Metazoans are known to contain a limited, yet highly conserved, set of signal transduction pathways that instruct early developmental patterning mechanisms. Genomic surveys that have compared gene conservation in signal transduction pathways between various insects and Drosophila support the conclusion that these pathways are conserved in evolution. However, the degree to which individual components of signal transduction pathways vary among more divergent arthropods is not known. Here, we report our results of a survey of the genome of the two-spotted spider mite Tetranychus urticae, using a set of 294 Drosophila orthologs of genes that function in signal transduction. We find a third of all genes surveyed absent from the spider mite genome. We also identify several novel duplications that have not been previously reported for a chelicerate. In comparison with previous insect surveys, Tetranychus contains a decrease in overall gene conservation, as well as an unusual ratio of ligands to receptors and other modifiers. These findings suggest that gene loss and duplication among components of signal transduction pathways are common among arthropods and suggest that signal transduction pathways in arthropods are more evolutionarily labile than previously hypothesized.     

An overview of data models for the analysis of biochemical pathways

Biochemical pathways such as metabolic, regulatory or signal transduction pathways can be viewed as interconnected processes forming an intricate network of functional and physical interactions between molecular species in the cell. The amount of information available on such pathways for different organisms is increasing very rapidly. This is offering the possibility of performing various analyses on the structure of the full network of pathways for one organism as well as across different organisms, and has therefore generated interest in developing databases for storing and managing this information. Analysing these networks remains far from straightforward owing to the nature of the databases, which are often heterogeneous, incomplete or inconsistent. Pathway analysis is hence a challenging problem in systems biology and in bioinformatics. Various forms of data models have been devised for the analysis of biochemical pathways. This paper presents an overview of the types of models used for this purpose, concentrating on those concerned with the structural aspects of biochemical networks. In particular, the different types of data models found in the literature are classified using a unified framework. In addition, how these models have been used in the analysis of biochemical networks is described. This enables us to underline the strengths and weaknesses of the different approaches, as well as to highlight relevant future research directions.     

PACAP and PDF signaling in the regulation of mammalian and insect circadian rhythms

Endogenous circadian clocks are inherent to all living organisms. They are needed to guarantee successful life since they regulate very important biological processes such as behavior and reproduction. Secretin-like G-protein coupled receptors are very important factors in the signal transduction pathways of circadian clocks. In this review, we will focus on the role of two secretin-like signaling pathways that play an important role in the regulation of the mammalian and the insect clock, respectively: the pituitary adenylate cyclase-activating polypeptide (PACAP) and pigment dispersing factor (PDF) signaling pathways. Both pathways are most likely related although their function in the biological clock differs.     

Retrograde trafficking and plasma membrane recycling pathways of the budding yeast Saccharomyces cerevisiae

The endosomal system functions as a network of protein and lipid sorting stations that receives molecules from endocytic and secretory pathways and directs them to the lysosome for degradation, or exports them from the endosome via retrograde trafficking or plasma membrane recycling pathways. Retrograde trafficking pathways describe endosome‐to‐Golgi transport while plasma membrane recycling pathways describe trafficking routes that return endocytosed molecules to the plasma membrane. These pathways are crucial for lysosome biogenesis, nutrient acquisition and homeostasis and for the physiological functions of many types of specialized cells. Retrograde and recycling sorting machineries of eukaryotic cells were identified chiefly through genetic screens using the budding yeast Saccharomyces cerevisiae system and discovered to be highly conserved in structures and functions. In this review, we discuss advances regarding retrograde trafficking and recycling pathways, including new discoveries that challenge existing ideas about the organization of the endosomal system, as well as how these pathways intersect with cellular homeostasis pathways.     

Origins and Evolution of Pathways of Anaerobic Metabolism in the Animal Kingdom

Energetic characteristics and functional roles define two maintypes of anaerobicpathways in the animal kingdom: high efficiency/lowrates of energy production pathways geared to anoxia survival(aspartate-succinate and glucose-succinate pathways), and lowefficiency?/high rates of energy production pathways gearedto maintaining or increasing metabolic activity (multiple opinepathways and lactate pathway). The aspartate-succinate and opinepathways require both amino acids and carbohydrate as substrates,whereas the glucose-succinate and lactate pathways are dependenton carbohydrate only. Phylogenetic, functional and chemicalconsiderations indicate an evolutionary progression from aminoacid-linked to carbohydrate-based anaerobic pathways. The tauropineand strombine pathwaysare possibly the most ancient opine pathwaysso far discovered, and the octopine pathway the most advanced.The roles of the aspartate-succinate and opine pathways mayoriginally have been not too dissimilar. A hierarchy of "ratesof energy production pathways" of phosphagen > lactate >octopine > other opine pathways is proposed, which definesmuch of their phylogenetic selection and how they are used.The different properties of phosphocreatine compared to otherphosphagens is indicated to have been a key factor in the emergenceof vertebrates     

Targeting stem cell signaling pathways for drug discovery: advances in the Notch and Wnt pathways

Signaling pathways transduce extracellular stimuli into cells through molecular cascades to regulate cellular functions.In stem cells,a small number of pathways,notably those of TGF-?/BMP,Hedgehog,Notch,and Wnt,are responsible for the regulation of pluripotency and differentiation.During embryonic development,these pathways govern cell fate specifications as well as the formation of tissues and organs.In adulthood,their normal functions are important for tissue homeostasis and regeneration,whereas aberrations result in diseases,such as cancer and degenerative disorders.In complex biological systems,stem cell signaling pathways work in concert as a network and exhibit crosstalk,such as the negative crosstalk between Wnt and Notch.Over the past decade,genetic and genomic studies have identified a number of potential drug targets that are involved in stem cell signaling pathways.Indeed,discovery of new targets and drugs for these pathways has become one of the most active areas in both the research community and pharmaceutical industry.Remarkable progress has been made and several promising drug candidates have entered into clinical trials.This review focuses on recent advances in the discovery of novel drugs which target the Notch and Wnt pathways.     

Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock

In this study, we modify and extend the bilevel optimization framework OptKnock for identifying gene knockout strategies in the Escherichia coli metabolic network, leading to the overproduction of representative amino acids and key precursors for all five families. These strategies span not only the central metabolic network genes but also the amino acid biosynthetic and degradation pathways. In addition to gene deletions, the transport rates of carbon dioxide, ammonia, and oxygen, as well as the secretion pathways for key metabolites, are introduced as optimization variables in the framework. Computational results demonstrate the importance of manipulating energy-producing/consuming pathways, controlling the uptake of nitrogen and oxygen, and blocking the secretion pathways of key competing metabolites. The identified pathway modifications include not only straightforward elimination of competing reactions but also a number of nonintuitive knockouts quite distant from the amino acid-producing pathways. Specifically, OptKnock suggests three reactions (i.e., pyruvate kinase, phosphotransacetylase, and ATPase) for deletion, in addition to the straightforward elimination of 2-ketoglutarate dehydrogenase, to generate a glutamate-overproducing mutant. Similarly, phosphofructokinase and ATPase are identified as promising knockout targets to complement the removal of pyruvate formate lyase and pyruvate dehydrogenase for enhancing the yield of alanine. Although OptKnock in its present form does not consider regulatory constraints, it does provide useful suggestions largely in agreement with existing practices and, more importantly, introduces a framework for incorporating additional modeling refinements as they become available.