Angiopoietins-1 and -2 are both capable of mediating endothelial PAF synthesis: intracellular signalling pathways

Vascular endothelial growth factor (VEGF) is the only angiogenic growth factor capable of inducing an inflammatory response and we have recently demonstrated that its inflammatory effect is mediated by the endothelial synthesis of platelet-activating factor (PAF). Recently discovered, Ang1 and Ang2, upon binding to Tie2 receptor, modulate vascular permeability and integrity, contributing to angiogenesis. Ang1 was initially identified as a Tie2 agonist whereas Ang2 can behave as a context-dependent Tie2 agonist or antagonist. We sought to determine if Ang1 and/or Ang2 could modulate PAF synthesis in bovine aortic endothelial cells (BAEC) and if so, through which intracellular signalling pathways. Herein, we report that Ang1 and Ang2 (1 nM) are both capable of mediating a rapid Tie2 phosphorylation and a rapid, progressive and sustained endothelial PAF synthesis maximal within 4 h (1695% and 851% increase, respectively). Angiopoietin-mediated endothelial PAF synthesis requires the activation of the p38 and p42/44 MAPKs, PI3K intracellular signalling pathways, and a secreted phospholipase A(2) (sPLA(2)-V). Furthermore, angiopoietin-mediated PAF synthesis is partly driven by a relocalization of endogenous VEGF to the cell surface membrane. Our results demonstrate that the angiopoietins constitute another class of angiogenic factors capable of mediating PAF synthesis which may contribute to proinflammatory activities.     

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

Protein complexes represent major functional units for the execution of biological processes. Systematic affinity purification coupled with mass spectrometry (AP‐MS) yielded a wealth of information on the compendium of protein complexes expressed in Saccharomyces cerevisiae. However, global AP‐MS analysis of human protein complexes is hampered by the low throughput, sensitivity and data robustness of existing procedures, which limit its application for systems biology research. Here, we address these limitations by a novel integrated method, which we applied and benchmarked for the human protein phosphatase 2A system. We identified a total of 197 protein interactions with high reproducibility, showing the coexistence of distinct classes of phosphatase complexes that are linked to proteins implicated in mitosis, cell signalling, DNA damage control and more. These results show that the presented analytical process will substantially advance throughput and reproducibility in future systematic AP‐MS studies on human protein complexes.     

Borna disease virus: a unique pathogen and its interaction with intracellular signalling pathways

Borna disease virus (BDV) is a neurotropic RNA virus that establishes non-cytolytic persistent infection in the central nervous system of warm-blooded animals. Depending on the host species and the route of infection, BDV persistence can modulate neuronal plasticity and animal behaviour and/or may provoke a T cell-mediated immunopathological reaction with high mortality. Therefore, BDV functions as a model pathogen to study persistent virus infection in the central nervous system. Here, we review recent evidence showing that BDV interferes with a spectrum of intracellular signalling pathways, which may be involved in viral spread, maintenance of persistence and modulation of neurotransmitter pathways.     

An integrated spectroscopic and wet chemical approach to investigate grass litter decomposition chemistry

The chemical transformations that occur during litter decomposition are key processes for soil organic matter formation and terrestrial biogeochemistry; yet we still lack complete understanding of these chemical processes. Thus, we monitored the chemical composition of Andropogon gerardii (big bluestem grass) litter residue over a 36 month decomposition experiment in a prairie ecosystem using: traditional wet chemical fractionation based upon digestibility, solid state ¹³C nuclear magnetic resonance (NMR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy. The goals of this study were to (1) determine the chemical changes occurring during A. gerardii litter decomposition, and (2) compare the information obtained from each method to assess agreement. Overall, we observed a 97 % mass loss of the original litter, through a two-stage decomposition process. In the first stage, within 12 months, non-structural, cellulose and hemicellulose fractions not encrusted in lignin were preferentially and rapidly lost, while the acid unhydrolyzable residue (AUR) and microbial components increased. During the second stage, 12–36 months, all wet chemical fraction masses decreased equivalently and slowly with time, and the AUR and the lignin-encrusted cellulose fractions decomposition rates were comparable to each other. Method comparisons revealed that wet chemical fractionation did not accurately follow the initial litter structures, particularly lignin, likely because of chemical transformations and accumulation of microbial biomass. FTIR and NMR were able to determine bulk structural characteristics, and aid in elucidating chemical transformations but lacked the ability to measure absolute quantities of structural groups. As a result, we warn from the sole use of wet chemical methods, and strongly encourage coupling them with spectroscopic methods. Our results overall support the traditional chemical model of selective preservation of lignin, but shows that this is limited to the early stages of decomposition, while lignin is not selectively preserved at subsequent stages. Our study also provides important evidence regarding the impact of chemically different litter structures on decomposition rates and pathways.     

Interaction of intracellular signalling and metabolic pathways at inhibition of mitochondrial aconitase by fluoroacetate

Mitochondrial aconitase has been shown to be inactivated under the effects of many compounds and critical states. Fluoroacetate (FA) is the best-known aconitase-inhibiting toxic agent. The biochemistry of the toxic action of FA has been rather well studied; however, no effective therapy has been developed over the past six decades. To search for new approaches to the development of possible antidotes, experiments were carried out in vitro with rat liver mitochondria, Ehrlich ascite tumor (EAT) cells, and cardiomyocytes exposed to FA or fluorocitrate (FC). FA produced its effects at much higher concentrations as compared with FC; in experiments with mitochondria these effects depended on respiratory substrates: with pyruvate, FA induced a slow oxidation and/or a leak of pyridine nucleotides and inhibition of respiration. Oxidation of pyridine nucleotides (PN) was prevented by the incubation of mitochondria with cyclosporin A. Studies of the PN level and dynamics of Ca²⁺ in EAT cells during activation by ATP also revealed the PN leak from mitochondria, which led to a shift in the balance of mitochondrial and cytosolic NAD(P)H under action of FA. Moreover, an increase of cytosolic Ca²⁺ was revealed in the cells exposed to FA, which could be explained by the activation of plasma membrane calcium channels. This mechanism could affect the amplitude and rate of calcium waves in cardiomyocytes under the effects of FA. We emphasize the reciprocal relationship between intracellular PN dynamics and calcium balance and discuss possible pathways of metabolic modulation in the context of development of effective therapy of poisoning with FA and other aconitase inhibitors.     

An integrated agent-mathematical model of the effect of intercellular signalling via the epidermal growth factor receptor on cell proliferation

We have previously developed Epitheliome, a software agent representation of the growth and repair characteristics of epithelial cell populations, where cell behaviour is governed by a number of simple rules. In this paper, we describe how this model has been extended to incorporate an example of a molecular 'mechanism' behind a rule-in this case, how signalling by both endogenous and exogenous ligands of the epidermal growth factor receptor (EGFR) can impact on the proliferation of cell agents. We have developed a mathematical model representing release of endogenous ligand by cells, three-dimensional diffusion of the secreted molecules through a volume of cell culture medium, ligand-receptor binding, and bound receptor internalization and trafficking. Information relating to quantities of molecular species associated with each cell agent is frequently exchanged between the agent and signalling models, and the ratio of bound to free receptors determines cell cycle progression and hence the proliferative behaviour of the cell agents. We have applied this integrated model to examine the effect of plating density on tissue growth via autocrine/paracrine signalling. This predicts that cell growth is dependent on the concentration of exogenous ligand, but where this is limited, then growth becomes dependent on cell density and the availability of endogenous ligand. We have further modified the calcium concentration of the medium to modulate the formation of intercellular bonds between cells and shown that the increased propensity for cells to form colonies in physiological calcium does not result in significantly different patterns of receptor occupancy. In conclusion, our approach demonstrates that by combining agent-based and mathematical modelling paradigms, it is possible to probe the complex feedback relationship between the behaviour of individual cells and their interaction with one another and their environment.     

An integrated rapid nucleic acid detection assay based on recombinant polymerase amplification for SARS-CoV-2

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel coronavirus that causes the outbreak of coronavirus disease 2019 (COVID-19) (Li et al., 2020a). Viral nucleic acid testing is the standard method for the laboratory diagnosis of COVID-19 (Wu et al., 2020a; Zhu et al., 2020). Currently, a variety of qPCR-based detection kits are used for laboratory-based detection and confirmation of SARS-CoV-2 infection (Corman et al., 2020; Hussein et al., 2020; Ruhan et al., 2020; Veyer et al., 2020). Conventional qPCR involves virus inactivation, nucleic acid extraction, and qPCR amplification procedures. Therefore, the process is complicated, which usually takes longer than 2 h, and requires biosafety laboratories and professional staff. Thus, qPCR is not suitable for use in field or medical units. To reduce the operation steps, automatic integrated qPCR detection systems that combine nucleic acid extraction and qPCR amplification in a sealed cartridge were developed to detect viruses in clinical samples (Li et al., 2020b). However, the detection time is still longer than 1 h. Therefore, rapid nucleic acid detection systems are needed to further improve the detection efficiency.     

Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium

SARS-CoV-2 contains four structural proteins in its genome. These proteins aid in the assembly and budding of new virions at the ER-Golgi intermediate compartment (ERGIC). Current fundamental research efforts largely focus on one of these proteins – the spike (S) protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other structural proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length envelope (E) protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca²⁺, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.     

An integrated computational workflow for efficient and quantitative modeling of renin inhibitors

A new integrated computational workflow that couples the strength of the molecular overlay methods to achieve rapid and automated alignments along with 3D-QSAR techniques like CoMFA and CoMSIA for quantitative binding affinity prediction is presented. The results obtained from such techniques are compared with rule-based Topomer CoMFA method, where possible. The developed 3D-QSAR models were prospectively used to predict the affinities of new compounds designed through R-group deconvolution starting from the core chemical scaffold and subsequent virtual combinatorial library enumeration. The general applicability of the seamless in silico modeling workflow is demonstrated using several datasets reported for small molecule inhibitors of renin.     

Natriuretic peptide signalling: molecular and cellular pathways to growth regulation

The natriuretic peptides (NPs) constitute a family of polypeptide hormones that regulate mammalian blood volume and blood pressure. The ability of the NPs to modulate cardiac hypertrophy and cell proliferation as well is now beginning to be recognized. The NPs interact with three membrane-bound receptors, all of which contain a well-characterized extracellular ligand-binding domain. The R1 subclass of NP receptors (NPR-A and NPR-B) contains a C-terminal guanylyl cyclase domain and is responsible for most of the NPs downstream actions through their ability to generate cGMP. The R2 subclass lacks an obvious catalytic domain and functions primarily as a clearance receptor. This review focuses on the signal transduction pathways initiated by ligand binding and other factors that help to determine signalling specificities, including allosteric factors modulating cGMP generation, receptor desensitization, the activation and function of cGMP-dependent protein kinase (PKG), and identification of potential nuclear or cytoplasmic targets such as the mitogen-activated protein kinase signalling (MAPK) cascade. The inhibition of cardiac growth and hypertrophy may be an important but underappreciated action of the NP signalling system.     

Studies of interaction of intracellular signalling and metabolic pathways under inhibition of mitochondrial aconitase with fluoroacetate

Mitochondrial aconitase has been shown to be inactivated by a spectrum of substances or critical states. Fluoroacetate (FA) is the most known toxic agent inhibiting aconitase. The biochemistry of toxic action of FA is rather well understood, though no effective therapy has been proposed for the past six decades. In order to reveal novel approaches for possible antidotes to be developed, experiments were performed with rat liver mitochondria, Ehrlich ascite tumor cells and cardiomyocytes, exposed to FA or fluorocitrate in vitro. The effect of FA developed at much higher concentrations in comparison with fluorocitrate and was dependent upon respiratory substrates in experiments with mitochondria: with pyruvate, FA induced a slow oxidation and/or leak of pyridine nucleotides and inhibition of respiration. Oxidation of pyridine nucleotides was prevented by incubation of mitochondria with cyclosporin A. Studies of the pyridine nucleotides level and calcium response generated in Ehrlich ascite tumor cells under activation with ATP also revealed a loss of pyridine nucleotides from mitochondria resulting in a shift in the balance of mitochondrial and cytosolic NAD(P)H under exposure to FA. An increase of cytosolic [Ca2+] was observed in the cell lines exposed to FA and is explained by activation of plasma membrane calcium channels; this mechanism, could have an impact on amplitude and rate of Ca2+ waves in cardiomyocytes. Highlighting the reciprocal relationship between intracellular pyridine nucleotides and calcium balance, we discuss metabolic pathway modulation in the context of probable development of an effective therapy for FA poisoning and other inhibitors of aconitase.     

An integrated modeling-experimental strategy for the analysis of metabolic pathways

An inherent problem in studying the behavior of a metabolic pathway is the impossibility of developing a complete, detailed model that includes all the cellular processes that have an impact on the set of fluxes in such a pathway. Lacking this, one requires some means of modeling the interactions between a metabolic pathway and other cellular processes for the purpose of analyzing pathway characteristics within the cell (e.g., determining sensitivity coefficients for various steps in the pathway) with a minimal amount of time and effort. A general framework is developed for studying these issues in a rigorous manner. Using this framework, detailed knowledge about a metabolic pathway (i.e., a set of rate expressions for steps in the pathway) can be combined with the results from a relatively simple set of experiments in order to obtain estimates for the sensitivity of the pathway to enzyme activities, inhibition constants, and other parameters that determine the pathway's behavior, while accounting for the pathway's interaction with the rest of the cellular metabolism. A model system representing amino acid production is used to illustrate the problem and to provide results based on computational experiments. The modeling strategy described here should be useful in genetic design to improve pathway fluxes and metabolic network selectivity.     

Auxin cross-talk: integration of signalling pathways to control plant development

Plants sense and respond to endogenous signals and environmental cues to ensure optimal growth and development. Plant cells must integrate the myriad transduction events into a comprehensive network of signalling pathways and responses. The phytohormone auxin occupies a central place within this transduction network, frequently acting in conjunction with other signals, to co-ordinately regulate cellular processes such as division, elongation and differentiation. As a non-cell autonomous signal, auxin also interacts with other signalling pathways to regulate inter-cellular developmental processes. As part of this especially themed edition of Plant Molecular Biology, we will review examples of `cross-talk' between auxin and other signalling pathways. Given the current state of knowledge, we have deliberately focused our efforts reviewing auxin interactions with other phytohormone and light signalling pathways. We conclude by discussing how new genomic approaches and the Arabidopsis genome sequence are likely to impact this area of research in the future.     

Roles of Rac and cytosolic phospholipase A2 in the intracellular signalling in response to titanium particles

Titanium (Ti) particle is one of the prosthetic materials commonly used in implantation and has frequently been implicated in pathogenesis such as periprosthetic osteolysis. In the present study, we undertook to understand the intracellular signalling pathway stimulated by exogenous Ti at Rat-2 fibroblasts. By reporter gene analysis following transient transfections, exogenous Ti was shown to stimulate c-fos serum response element (SRE)-dependent luciferase activities in a dose-dependent manner. In addition, Ti-induced SRE activation was shown to be dramatically repressed by RacN17, a dominant negative mutant of Rac1, suggesting that Rac GTPase is essential for the signalling of Ti to c-fos SRE. Furthermore, pretreatment with MAFP, an inhibitor of cytosolic phospholipase A(2) (cPLA(2)), MK886, an inhibitor of 5-lipoxygenase (5-LO), or indomethacin, a general inhibitor of cyclooxygenase (COX), also significantly repressed Ti-induced SRE activation, suggesting mediatory roles of cPLA(2) and subsequent arachidonic acid (AA) metabolisms to leukotrienes (LTs) and prostaglandins (PGs) in the Ti signalling to c-fos SRE. Consistent with these results, intracellular levels of leukotriene B(4) (LTB(4)) and prostaglandin E(2) (PGE(2)) were Rac-dependently elevated in cells exposed to Ti particles.