Farnesyl pyrophosphate is a novel transcriptional activator for a subset of nuclear hormone receptors

In silico docking of a chemical library with the ligand-binding domain of thyroid hormone nuclear receptor-beta (TRbeta) suggested that farnesyl pyrophosphate (FPP), a key intermediate in cholesterol synthesis and protein farnesylation, might function as an agonist. Surprisingly, addition of FPP to cells activated TR as well as the classical steroid hormone receptors but not peroxisome proliferative-activating receptors, farnesoid X receptor, liver X receptor, or several orphan nuclear receptors the ligands of which are unknown. FPP enhanced receptor-coactivator binding in vitro and in vivo, and elevation of FPP levels in cells by squalene synthetase or farnesyl transferase inhibitors leads to activation. The FPP effect was blocked by selective receptor antagonists, and in silico docking with 143 nuclear receptor ligand-binding domain structures revealed that FPP only docked with the agonist conformation of those receptors activated by FPP. Our results suggest that certain nuclear receptors maintain a common structural feature that may reflect an action of FPP on an ancient nuclear receptor or that FPP could function as a ligand for one of the many orphan nuclear receptors the ligands of which have not yet been identified. This finding also has potential interesting implications that may, in part, explain the pleotropic effects of statins as well as certain actions of farnesylation inhibitors in cells.     

Yew (Taxus x media Rehd.) cell suspension cultures as a source of taxanes

Natural resources of paclitaxel, an effective anticancer compound, were threatened with extinction soon after the discovery of this valuable substance. Cell suspension cultures derived from different Taxus species have rapidly become an alternative source of paclitaxel and other taxanes. In this paper we provide some insight into cell growth characteristics in cell suspension culture of Taxus x media cv. Hicksii, with emphasis on the effects of jasmonic acid (JA) on taxane production in cell lines with different initial taxane content. Additionally cell growth characteristics of two cell lines was followed during cultivation of cell suspension culture of Taxus x media cv. Hicksii. Packed cell volume (PCV) was shown to be a reliable and efficient alternative for measuring cell growth instead of fresh and dry weight. The initial total taxane content was screened in a number of cell lines, followed by observing the effect of JA on cell mass and total taxane production of selected lines. We showed a great variability in initial taxane content in different cell lines, which decreased during cell suspension maintenance. JA was shown to inhibit cell growth and increase total taxane production (14 to 106 fold).     

Mycorrhizal colonisation in plants from intermittent aquatic habitats

Several plant species with amphibious characteristics from intermittent aquatic habitats were examined for colonisation with arbuscular mycorrhizal fungi (AM), dark septate endophytes (DSE) and the ratio of aerenchyma in root tissue. We studied submerged specimens of Alisma plantago-aquatica, Mentha aquatica, Myosotis scorpioides, Oenanthe fistulosa, Gratiola officinalis, Glyceria fluitans, Sium latifolium and Teucrium scordium. In the first four, we also examined the emerged growth forms, which were grown under experimental conditions. Roots of all species were mycorrhizal and showed AM and DSE colonisation. The results suggest that AM colonisation may also be abundant in plants of aquatic environment. Arbuscules were not found in submerged specimens of M. aquatica, O. fistulosa and S. latifolium. The AM colonisation was generally higher in emerged specimens as compared to submerged ones. The aerenchyma ratio in root cross-sections ranged from 10 to 50% and in most cases did not differ between submerged and emerged specimens. No clear relationship between AM colonisation and aerenchyma ratio was recognized, while a positive correlation between AM and plant available phosphorous was established.     

PredβTM: A Novel β-Transmembrane Region Prediction Algorithm

Predicting the transmembrane regions is an important aspect of understanding the structures and architecture of different β-barrel membrane proteins. Despite significant efforts, currently available β-transmembrane region predictors are still limited in terms of prediction accuracy, especially in precision. Here, we describe PredβTM, a transmembrane region prediction algorithm for β-barrel proteins. Using amino acid pair frequency information in known β-transmembrane protein sequences, we have trained a support vector machine classifier to predict β-transmembrane segments. Position-specific amino acid preference data is incorporated in the final prediction. The predictor does not incorporate evolutionary profile information explicitly, but is based on sequence patterns generated implicitly by encoding the protein segments using amino acid adjacency matrix. With a benchmark set of 35 β-transmembrane proteins, PredβTM shows a sensitivity and precision of 83.71% and 72.98%, respectively. The segment overlap score is 82.19%. In comparison with other state-of-art methods, PredβTM provides a higher precision and segment overlap without compromising with sensitivity. Further, we applied PredβTM to analyze the β-barrel membrane proteins without defined transmembrane regions and the uncharacterized protein sequences in eight bacterial genomes and predict possible β-transmembrane proteins. PredβTM can be freely accessed on the web at http://transpred.ki.si/.     

Cortisol synthesis in epidermis is induced by IL-1 and tissue injury

Glucocorticoids (GCs) are known inhibitors of wound healing. In this study we report the novel finding that both keratinocytes in vitro and epidermis in vivo synthesize cortisol and how this synthesis regulates wound healing. We show that epidermis expresses enzymes essential for cortisol synthesis, including steroid 11 β-hydroxylase (CYP11B1), and an enzyme that controls negative feedback mechanism, 11β-hydroxysteroid dehydrogenase 2 (11βHSD2). We also found that cortisol synthesis in keratinocytes and skin can be stimulated by ACTH and inhibited by metyrapone (CYP11B1 enzyme inhibitor). Interestingly, IL-1β, the first epidermal signal of tissue injury, induces the expression of CYP11B1 and increases cortisol production by keratinocytes. Additionally, we found induction of CYP11B1 increased production of cortisol and activation of GR pathway during wound healing ex vivo and in vivo using human and porcine wound models, respectively. Conversely, inhibition of cortisol synthesis during wound healing increases IL-1β production, suggesting that cortisol synthesis in epidermis may serve as a local negative feedback to proinflammatory cytokines. Local GCs synthesis, therefore, may provide control of the initial proinflammatory response, preventing excessive inflammation upon tissue injury. Inhibition of GC synthesis accelerated wound closure in vivo, providing the evidence that modulation of cortisol synthesis in epidermis may be an important regulatory mechanism during wound healing.     

New insights into globoids of protein storage vacuoles in wheat aleurone using synchrotron soft X-ray microscopy

Mature developed seeds are physiologically and biochemically committed to store nutrients, principally as starch, protein, oils, and minerals. The composition and distribution of elements inside the aleurone cell layer reflect their biogenesis, structural characteristics, and physiological functions. It is therefore of primary importance to understand the mechanisms underlying metal ion accumulation, distribution, storage, and bioavailability in aleurone subcellular organelles for seed fortification purposes. Synchrotron radiation soft X-ray full-field imaging mode (FFIM) and low-energy X-ray fluorescence (LEXRF) spectromicroscopy were applied to characterize major structural features and the subcellular distribution of physiologically important elements (Zn, Fe, Na, Mg, Al, Si, and P). These direct imaging methods reveal the accumulation patterns between the apoplast and symplast, and highlight the importance of globoids with phytic acid mineral salts and walls as preferential storage structures. C, N, and O chemical topographies are directly linked to the structural backbone of plant substructures. Zn, Fe, Na, Mg, Al, and P were linked to globoid structures within protein storage vacuoles with variable levels of co-localization. Si distribution was atypical, being contained in the aleurone apoplast and symplast, supporting a physiological role for Si in addition to its structural function. These results reveal that the immobilization of metals within the observed endomembrane structures presents a structural and functional barrier and affects bioavailability. The combination of high spatial and chemical X-ray microscopy techniques highlights how in situ analysis can yield new insights into the complexity of the wheat aleurone layer, whose precise biochemical composition, morphology, and structural characteristics are still not unequivocally resolved.     

Structural analysis of a peptide fragment of transmembrane transporter protein bilitranslocase

Using a combination of genomic and post-genomic approaches is rapidly altering the number of identified human influx carriers. A transmembrane protein bilitranslocase (TCDB 2.A.65) has long attracted attention because of its function as an organic anion carrier. It has also been identified as a potential membrane transporter for cellular uptake of several drugs and due to its implication in drug uptake, it is extremely important to advance the knowledge about its structure. However, at present, only the primary structure of bilitranslocase is known. In our work, transmembrane subunits of bilitranslocase were predicted by a previously developed chemometrics model and the stability of these polypeptide chains were studied by molecular dynamics (MD) simulation. Furthermore, sodium dodecyl sulfate (SDS) micelles were used as a model of cell membrane and herein we present a high-resolution 3D structure of an 18 amino acid residues long peptide corresponding to the third transmembrane part of bilitranslocase obtained by use of multidimensional NMR spectroscopy. It has been experimentally confirmed that one of the transmembrane segments of bilitranslocase has alpha helical structure with hydrophilic amino acid residues oriented towards one side, thus capable of forming a channel in the membrane.     

Distinctive effects of cadmium on glucosinolate profiles in Cd hyperaccumulator Thlaspi praecox and non-hyperaccumulator Thlaspi arvense

We investigated the hypothesis that continuous water application allows favorable and steady water content and hydraulic conductivity in the root zone, thus enabling higher water potential in the soil–root interface (ψ_root). Elevated ψ_root increases transpiration (T) and prevents yield loss due to stomatal closure or to low root osmotic potential that develops in response to low ψ_root. We assume further, that the advantage of continuous water application is more pronounced for young plants, where water uptake per root length and competition on resources in the root system is higher. We investigated this hypothesis by examining the average water content of the root zone and T as a function of time for sunflowers grown under varied irrigation frequencies experimentally and in a modeled simulations, and by solving for the necessary effective root length and ψ_root for each case. High frequency water application was shown to positively affect root water uptake efficiency and yield, especially when plants were young. Irrigation frequency affected growth through the water content in the bulk soil (θ_soil) which in turn affects ψ_root. A low θ_soil and coupled low hydraulic conductivity decreased T and yield. Moreover, a decreased θ_soil caused low ψ_root, inefficient allocation of energy and carbohydrates and eventual yield loss. It was likely that these phenomena were more pronounced with young plants due to higher water uptake per root length.     

The influence of jasmonic acid on biophysical properties of potato leaf protoplasts and roots

Summary Jasmonic acid (JA) and its derivatives are a novel group of plant endogenous growth regulators. In our experiments some new data about the physiological effects of JA were obtained using electron paramagnetic resonance spectroscopy. Experiments were performed on potato plants (Solanum tuberosum L. cv. Vesna) grown in vitro. Different quantities of JA (0.1–10 M) were added to the growth medium. Root samples of plants grown on media supplemented with JA showed a more rapid spin probe N-oxyl-2,2,6,6-tetramethyl piperidine reduction than the control plants, which is a possible indicator of altered root permeability. Samples of leaf protoplasts were probed with methyl ester of 5-doxyl-haxadecanoic acid. We observed a membrane fluidity decrease in protoplasts isolated from plants grown on higher concentrations of JA (1 and 10 M).Abbreviations JA jasmonic acid - Me-JA methyl jasmonate - EPR electron paramagnetic resonance - RubisCO ribulose-1,5-biphosphate carboxylase/oxigenase - MeFASL(10,3) methyl ester of 5-doxyl-hexadecanoic acid - MES (2(N-morpholino)ethanesulfonic acid) - TEMPO N-oxyl-2,2,6,6-tetramethyl piperidine     

Dual-specificity phosphatases in the hypo-osmotic stress response of keratin-defective epithelial cell lines

Although mutations in intermediate filament proteins cause many human disorders, the detailed pathogenic mechanisms and the way these mutations affect cell metabolism are unclear. In this study, selected keratin mutations were analysed for their effect on the epidermal stress response. Expression profiles of two keratin-mutant cell lines from epidermolysis bullosa simplex patients (one severe and one mild) were compared to a control keratinocyte line before and after challenge with hypo-osmotic shock, a common physiological stress that transiently distorts cell shape. Fewer changes in gene expression were found in cells with the severely disruptive mutation (55 genes altered) than with the mild mutation (174 genes) or the wild type cells (261 genes) possibly due to stress response pre-activation in these cells. We identified 16 immediate-early genes contributing to a general cell response to hypo-osmotic shock, and 20 genes with an altered expression pattern in the mutant keratin lines only. A number of dual-specificity phosphatases (MKP-1, MKP-2, MKP-3, MKP-5 and hVH3) are differentially regulated in these cells, and their downstream targets p-ERK and p-p38 are significantly up-regulated in the mutant keratin lines. Our findings strengthen the case for the expression of mutant keratin proteins inducing physiological stress, and this intrinsic stress may affect the cell responses to secondary stresses in patients' skin.