Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase.

The structure of the RNA-dependent RNA polymerase (RdRP) from the rabbit hemorrhagic disease virus has been determined by x-ray crystallography to a 2.5-A resolution. The overall structure resembles a "right hand," as seen before in other polymerases, including the RdRPs of polio virus and hepatitis C virus. Two copies of the polymerase are present in the asymmetric unit of the crystal, revealing active and inactive conformations within the same crystal form. The fingers and palm domains form a relatively rigid unit, but the thumb domain can adopt either "closed" or "open" conformations differing by a rigid body rotation of approximately 8 degrees. Metal ions bind at different positions in the two conformations and suggest how structural changes may be important to enzymatic function in RdRPs. Comparisons between the structures of the alternate conformational states of rabbit hemorrhagic disease virus RdRP and the structures of RdRPs from hepatitis C virus and polio virus suggest novel structure-function relationships in this medically important class of enzymes.     

Pescador: the PEptides in Solution ConformAtion Database: Online Resource

In recent years a large body of data has been obtained from Nuclear Magnetic Resonance and Circular Dichroism experiments on the influence of the amino acid sequence and various other parameters on the conformational state of peptides in solution. Interpreting the experimental data in terms of the conformational populations of the peptides remains a key problem, for which current solutions leave appreciable room for improvement. Considering that making this body of data available for surveys and analysis should be instrumental in tackling the problem, we undertook the development of Pescador: The `PEptides in Solution ConformAtion Database: Online Resource'. Pescador contains data from NMR and CD spectroscopy on peptides in solution as well as information on the structural parameters derived from these data. It also features specialized Web-based tools for data deposition, and means for readily accessing the stored information for analysis purposes. To illustrate the use of the database in deriving information for the conformational analysis of peptides, we show how the alpha proton -values stored in Pescador and measured by NMR for different peptides in different laboratories can be used to derive a new set of `random coil' chemical shift values. Firstly, we show these values to be very similar to those obtained experimentally for model peptides in water, and their variation with increasing Tri-Fluoro-Ethanol (TFE) concentration is similar to that reported for model peptides. We show, furthermore, that the chemical shift data in Pescador can be used to derive correction factors that take into account effects of neighboring residues. These correction factors compare favorably with those recently derived from a series of model GGXGG peptides Schwarzinger_e-valuesstoredinPescadorandmeasuredbyNMRfordifferentpeptidesindifferentlaboratoriescanbeusedtoderiveanewsetof`randomcoil'chemicalshiftvalues.Firstly,weshowthesevaluestobeverysimilartothoseobtainedexperimentallyformodelpeptidesinwater,andtheirvariationwithincreasingTri-Fluoro-Ethanol(TFE)concentrationissimilartothatreportedformodelpeptides.Weshow,furthermore,thatthechemicalshiftdatainPescadorcanbeusedtoderivecorrectionfactorsthattakeintoaccounteffectsofneighboringresidues.ThesecorrectionfactorscomparefavorablywiththoserecentlyderivedfromaseriesofmodelGGXGGpeptides Schwarzinger _etal. These encouraging results suggest that, as the quantity of NMR data on peptide deposited in Pescador increases, surveys of these data should be a valuable means of deriving key parameters for the analysis of peptide conformation.     

NMR experiments for the measurement of proton-proton and carbon-carbon residual dipolar couplings in uniformly labelled oligosaccharides

A 2D-HSQC-carbon selective/proton selective-constant time COSY, 2D-HSQC-(sel C, sel H)-CT COSY experiment, which is applicable to uniformly ¹³C isotopically enriched samples (U-¹³C) of oligosaccharides or oligonucleotides is proposed for the measurement of proton–proton RDC in crowded regions of 2D-spectra. In addition, a heteronuclear constant time-COSY experiment, ¹³C-¹³C CT-COSY, is proposed for the measurement of one bond carbon–carbon RDC in these molecules. These two methods provide an extension, to U-¹³C molecules, of the original homonuclear constant time-COSY experiment proposed by Tian et al. (1999) for saccharides. The combination of a number of these RDC with NOE data may provide the method of choice to study oligosaccharide conformation in the free and receptor-bound state.     

Alpha4beta1 integrin/ligand interaction inhibits alpha5beta1-induced stress fibers and focal adhesions via down-regulation of RhoA and induces melanoma cell migration

We have studied the function of the Hep III fibronectin domain in the cytoskeletal response initiated by alpha5beta1 integrin-mediated adhesion. Melanoma cells formed stress fibers and focal adhesions on the RGD-containing FNIII7-10 fragment. Coimmobilization of FNIII4-5, a fragment spanning Hep III and containing the alpha4beta1 ligand H2 with FNIII7-10, or addition of soluble FNIII4-5 to cells preattached to FNIII7-10, inhibited stress fibers and induced cytoplasmic protrusions. This effect involved alpha4beta1 since: 1) mutations in H2 reverted the inhibition; 2) other alpha4beta1 ligands (CS-1, VCAM-1), an anti-alpha4 mAb, or alpha4 expression in HeLa cells inhibited stress fibers. This activity was apparently cryptic in fibronectin or large fibronectin fragments, but exposed upon proteolytic degradation. Indeed purified peptic fragments containing H2, inhibited stress fibers when mixed with FNIII7-10 or fibronectin. RhoA activation with LPA or transfection with V14RhoA reverted the inhibitory effect and induced stress fibers on FNIII7-10+FNIII4-5. Furthermore, addition of alpha4beta1 ligands to FNIII7-10, down-regulated RhoA and activated p190RhoGAP, which localized to cytoplasmic protrusions. alpha4beta1/ligand interaction induced cell migration, monitored by video microscopy and wound healing assays. These data indicate that alpha4beta1 provides an antagonistic signal to alpha5beta1 by interfering with the RhoA activation pathway and this leads to melanoma cell migration.     

Cloning and expression of a lipoxygenase from <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> 42A2

In order to produce (S) 10-monohydroxy-8E-octadecenoic acid (MHOD) from oleic acid, a full-length probable lipoxygenase cDNA from Pseudomonas aeruginosa 42A2 was cloned and expressed in Escherichia coli BL21(DE3). The recombinant protein was purified by affinity chromatography to electrophoretic homogeneity and specifically stained. Its molecular mass was 70 kDa. The activity of the rec-LOX with oleic acid was about 30% of that of the prefered substrate, linoleic acid (100%). Bacterial LOX forms a new subfamily in the lipoxygenase phylogenetic tree.     

Characterization and cDNA cloning of monomeric lectins that correspond to the B-Chain of a type 2 ribosome-inactivating protein from the bark of Japanese elderberry (Sambucus sieboldiana)

Two monomeric lectins, SSA-b-3 and SSA-b-4, were purified from the bark tissue of Japanese elderberry, Sambucus sieboldiana. SDS-PAGE of the purified lectins showed the presence of single bands of 35 and 33 kDa for SSA-b-3 and SSA-b-4, respectively, irrespective of the presence of reducing agent. MS analysis as well as gel filtration of these lectins indicated that they exist mostly as monomeric lectins. Analysis of the N-terminal amino acid sequences of SSA-b-3 and SSA-b-4 yielded an identical sequence, indicating their close structural relationship. Four cDNA clones with extensive homology were obtained from the bark cDNA library and indicated to encode SSA-b-3 or SSA-b-4 from the comparison with the N-terminal sequences of these lectins. These clones were classified into two groups, three for SSA-b-3 and one for SSA-b-4, based on the predicted isoelectric points. The amino acid sequences of the encoded polypeptides were almost identical with the B-chain of a type 2 ribosome-inactivating protein from the same bark tissue, sieboldin-b, except for the absence of a small peptide containing a cystein residue, which is critical for the heteromeric dimerization with an A-subunit. Carbohydrate binding specificity and biological activity of these lectins are also reported.     

Down-regulation of rat brain adenosine A1 receptors at the end of pregnancy

The status of the adenosine A1 receptor/adenylyl cyclase (A1R/AC) transduction pathway in rat brain was analysed at the end of pregnancy using different approaches. Pregnancy at term caused a significant decrease in the Bmax value obtained by saturation binding assays using [3H]DPCPX as radioligand, suggesting a down-regulation of adenosine A1 receptor. Moreover, A1 receptor immunodetection in pregnant rat membranes and the level of mRNA coding A1 receptor were significantly decreased. This loss of A1 receptor was associated with a significant increase in receptor affinity, since the KD value from the [3H]DPCPX saturation curve and Ki for N6-cyclohexyladenosine (CHA) were decreased in pregnant rats. Surprisingly, CHA-mediated inhibition of adenylyl cyclase was increased, reflecting enhanced receptor responsiveness. On the other hand, immunoblotting of different alphaGi-protein isoforms revealed a significant increase in alphaGi3 level in membranes from pregnant rats. Pre-incubation of membranes with anti-alphaGi3 antibody blocked the guanosine triphosphate (GTP) or CHA inhibitory effect on adenylyl cyclase in both pregnant and non-pregnant rats, pointing to alphaGi3 as the main isoform involved in the A1 receptor response. These results suggest that, at the end of pregnancy, there is a down-regulation of adenosine A1 receptors counterbalanced with a strengthened functionality, probably due to an increase in both alphaGi3 protein and receptor affinity.     

Variations in water status, gas exchange, and growth in Rosmarinus officinalis plants infected with Glomus deserticola under drought conditions

The influence of the arbuscular mycorrhizal fungus Glomus deserticola on the water relations, gas exchange parameters, and vegetative growth of Rosmarinus officinalis plants under water stress was studied. Plants were grown with and without the mycorrhizal fungus under glasshouse conditions and subjected to water stress by withholding irrigation water for 14 days. Along the experimental period, a significant effect of the fungus on the plant growth was observed, and under water stress, mycorrhizal plants showed an increase in aerial and root biomass compared to non-mycorrhizal plants. The decrease in the soil water potential generated a decrease in leaf water potential (psi(l)) and stem water potential (psi(x)) of mycorrhizal and non-mycorrhizal plants, with this decrease being lower in mycorrhizal water-stressed plants. Mycorrhization also had positive effects on the root hydraulic conductivity (Lp) of water stressed plants. Furthermore, mycorrhizal-stressed plants showed a more important decrease in osmotic potential at full turgor (psi(os)) than did non-mycorrhizal-stressed plants, indicating the capacity of osmotic adjustment. Mycorrhizal infection also improved photosynthetic activity (Pn) and stomatal conductance (g(s)) in plants under water stress compared to the non-mycorrhizal-stressed plants. A similar behaviour was observed in the photochemical efficiency of PSII (Fv/Fm) with this parameter being lower in non-mycorrhizal plants than in mycorrhizal plants under water stress conditions. In the same way, under water restriction, mycorrhizal plants showed higher values of chlorophyll content than did non-mycorrhizal plants. Thus, the results obtained indicated that the mycorrhizal symbiosis had a beneficial effect on the water status and growth of Rosmarinus officinalis plants under water-stress conditions.     

In vitro deregulation of markers characteristic of human prostate epithelial cells

We have screened primary cultures of human prostate for the expression of markers reported to be characteristic of specific cell lineages in vivo, in order to ascertain whether human prostate cells in vitro maintain and reflect their in vivo differentiated phenotypes and to evaluate the homogeneity of the populations of cells that can be derived from this tissue. Using single and dual stain immunofluorescent microscopy to analyse very early organoid and subsequently derived monolayer stage cultures, we have observed that expression of markers characteristic of human prostate epithelial cells in vivo is deregulated within 48h, indicating that dissociation of human prostate tissue and cultivation of prostate epithelial cells in culture can result in promiscuous expression of cell type specific markers of prostate epithelial cells. These observations have important implications for studies of cell lineage and differentiation of prostate cells in vitro.     

The atypical PKC-interacting protein p62 is an important mediator of RANK-activated osteoclastogenesis

The atypical PKCs (aPKCs) have been implicated genetically in at least two independent signaling cascades that control NF-kappa B and cell polarity, through the interaction with the adapters p62 and Par-6, respectively. P62 binds TRAF6, which plays an essential role in osteoclastogenesis and bone remodeling. Recently, p62 mutations have been shown to be the cause of the 5q35-linked Paget's disease of bone, a genetic disorder characterized by aberrant osteoclastic activity. Here we show that p62, like TRAF6, is upregulated during RANK-L-induced osteoclastogenesis and that the genetic inactivation of p62 in mice leads to impaired osteoclastogenesis in vitro and in vivo, as well as inhibition of IKK activation and NF-kappa B nuclear translocation. In addition, RANK-L stimulation leads to the inducible formation of a ternary complex involving TRAF6, p62, and the aPKCs. These observations demonstrate that p62 is an important mediator during osteoclastogenesis and induced bone remodeling.