A role for inositol 1,4,5-trisphosphate in gravitropic signaling and the retention of cold-perceived gravistimulation of oat shoot pulvini

Plants sense positional changes relative to the gravity vector. To date, the signaling processes by which the perception of a gravistimulus is linked to the initiation of differential growth are poorly defined. We have investigated the role of inositol 1,4,5-trisphosphate (InsP(3)) in the gravitropic response of oat (Avena sativa) shoot pulvini. Within 15 s of gravistimulation, InsP(3) levels increased 3-fold over vertical controls in upper and lower pulvinus halves and fluctuated in both pulvinus halves over the first minutes. Between 10 and 30 min of gravistimulation, InsP(3) levels in the lower pulvinus half increased 3-fold over the upper. Changes in InsP(3) were confined to the pulvinus and were not detected in internodal tissue, highlighting the importance of the pulvinus for both graviperception and response. Inhibition of phospholipase C blocked the long-term increase in InsP(3), and reduced gravitropic bending by 65%. Short-term changes in InsP(3) were unimpaired by the inhibitor. Gravitropic bending of oat plants is inhibited at 4 degrees C; however, the plants retain the information of a positional change and respond at room temperature. Both short- and long-term changes in InsP(3) were present at 4 degrees C. We propose a role for InsP(3) in the establishment of tissue polarity during the gravitropic response of oat pulvini. InsP(3) may be involved in the retention of cold-perceived gravistimulation by providing positional information in the pulvini prior to the redistribution of auxin.     

Molecular basis for the ATPase activity of CFTR

CFTR is a member of the ABC (ATP binding cassette) superfamily of transporters. It is a multidomain membrane protein, which utilizes ATP to regulate the flux of its substrate through the membrane. CFTR is distinct in that it functions as a channel and it possesses a unique regulatory R domain. There has been significant progress in understanding the molecular basis for CFTR activity as an ATPase. The dimeric complex of NBD structures seen in prokaryotic ABC transporters, together with the structure of an isolated CF-NBD1, provide a unifying molecular template to model the structural basis for the ATPase activity of CFTR. The dynamic nature of the interaction between the NBDs and the R domain has been revealed in NMR studies. On the other hand, understanding the mechanisms mediating the transmission of information from the cytosolic domains to the membrane and the channel gate of CFTR remains a central challenge.     

Molecular basis underlying the biological effects elicited by extremely low-frequency magnetic field (ELF-MF) on neuroblastoma cells

Extremely low-frequency magnetic fields (ELF-MFs) may affect human health because of the possible associations with leukemia but also with cancer, cardiovascular, and neurological disorders. In the present work, human SH-SY5Y neuroblastoma cells were exposed to a 50 Hz, 1 mT sinusoidal ELF-MF at three different times, that is, 5 days (T5), 10 days (T10), and 15 days (T15) and then the effects of ELF-MF on proteome expression and biological behavior were investigated. Through comparative analysis between treated and control samples, we analyzed the proteome changes induced by ELF-MF exposure. Nine new proteins resolved in sample after a 15-day treatment were involved in a cellular defense mechanism and/or in cellular organization and proliferation such as peroxiredoxin isoenzymes (2, 3, and 6), 3-mercaptopyruvate sulfurtransferase, actin cytoplasmatic 2, t-complex protein subunit beta, ropporin-1A, and profilin-2 and spindlin-1. Our results indicated that ELF-MFs exposure altered the proliferative status and other important cell biology-related parameters, such as cell growth pattern, and cytoskeletal organization. These findings support our hypothesis that ELF radiation could trigger a shift toward a more invasive phenotype.     

Molecular basis of bacteriocins production and activity

Bacteriocins--bacterial proteins or peptides--are envisaged as candidates for the next generation of effective antimicrobials. Analysis of characteristics of natural and genetically engineered bacteriocins with regard to the molecular basis of their production and activity has been performed. Most bacteriocins have narrow spectrum of the inhibitory activity. Some of the broad-spectrum bacteriocins have circular molecular structure (C- and N-terminals of the aminoacid chain are joined by a peptide sequence). Fixed position of molecules' ends possibly accounts for the ability of the proteins to bind with various receptors on the surface of the target cells. Genes encoding bacteriocins and functionally associated proteins can be expressed in heterologous cells including eukaryotic cells. Also there were reports of changing bacteriocin characteristics by the use of site-specific mutagenesis.     

Molecular basis of the activity of the phytopathogen pectin methylesterase

We provide a mechanism for the activity of pectin methylesterase (PME), the enzyme that catalyses the essential first step in bacterial invasion of plant tissues. The complexes formed in the crystal using specifically methylated pectins, together with kinetic measurements of directed mutants, provide clear insights at atomic resolution into the specificity and the processive action of the Erwinia chrysanthemi enzyme. Product complexes provide additional snapshots along the reaction coordinate. We previously revealed that PME is a novel aspartic-esterase possessing parallel beta-helix architecture and now show that the two conserved aspartates are the nucleophile and general acid-base in the mechanism, respectively. Other conserved residues at the catalytic centre are shown to be essential for substrate binding or transition state stabilisation. The preferential binding of methylated sugar residues upstream of the catalytic site, and demethylated residues downstream, drives the enzyme along the pectin molecule and accounts for the sequential pattern of demethylation produced by both bacterial and plant PMEs.     

Uptake of glycine by excised pulvini of Mimosa pudica in relation to proton pump activity

Uptake of [³H]-glycine by sections of Mimosa pudica L. pulvini is pH dependent (maximum at pH 5.5) and exhibits biphasic saturation kinetics in the range of concentrations tested (1–75 m M ). Effects of compounds which increase [fusicoccin (FC)] or decrease (uncouplers, ATPase inhibitors) the proton-motive force were tested both on the pH variations induced in the incubation medium and on glycine uptake by the pulvinar tissues: there is a close relationship between the time required for the effect of these compounds on the acidification (for FC) and the pH rise (for the inhibitors) of the medium and that needed respectively for promotion and inhibition of glycine uptake. Experiments with sulfhydryl-reacting compounds show that N-ethylmaleimide induces a large rise in pH in the incubation medium and strongly inhibits glycine uptake, whereas p -chloromercuribenzenesulfonic acid has less effect on these processes. These results argue for a proton-glycine symport mechanism in the pulvinar tissue and thus support the previously postulated involvement of a proton pump in the regulation of pulvinar movement.     

Molecular basis of the selective activity of vitamin D analogues

More than 2,000 synthetic analogues of the biological active form of vitamin D, 1alpha,25-dihydroxyvitamin D(3) (1alpha,25(OH)(2)D(3)), are presently known. Basically, all of them interfere with the molecular switch of nuclear 1alpha,25(OH)(2)D(3) signaling, which is the complex of the vitamin D receptor (VDR), the retinoid X receptor (RXR), and a 1alpha,25(OH)(2)D(3) response element (VDRE). Central element of this molecular switch is the ligand-binding domain (LBD) of the VDR, which can be stabilized by a 1alpha,25(OH)(2)D(3) analogue either in its agonistic, antagonistic, or non-agonistic conformation. The positioning of helix 12 of the LBD is of most critical importance for these conformations. In each of the three conformations, the VDR performs different protein-protein interactions, which then result in a characteristic functional profile. Most 1alpha,25(OH)(2)D(3) analogues have been identified as agonists, a few are antagonists (e.g., ZK159222 and TEI-9647), and only Gemini and some of its derivatives act under restricted conditions as non-agonists. The functional profile of some 1alpha,25(OH)(2)D(3) analogues, such as EB1089 and Gemini, can be modulated by protein and DNA interaction partners of the VDR. This provides them with some selectivity for DNA-dependent and -independent signaling pathways and VDRE structures.     

Factors affecting invertase activity in soils

Summary The rate of reducing sugars released through invertase activity exhibited a buffer pH optimum of 5.0. Generally, the decline in invertase activity in its pH-profile near the optimal pH range was due to a reversible reaction that involved ionization or deionization of the functional groups in the active centre of the protein, but under highly acidic or alkaline conditions (pH<4 to >9) the reduced activity appears to be due to irreversible inactivation of the enzyme. The dependence of the reaction on the amount of enzyme present was linear up to 3 g of soil. By varying the substrate concentration, it was found that the reaction rate of this enzyme approached zero-order kinetics when 145mM of sucrose solution was added to soils. Application of three linear transformations of the Michaelis-Menten equation indicated that the apparent K_m constants varied among the soils studied, but the results obtained by the three plots were similar. By using the Lineweaver-Burk plot, the K_m values in five soils ranged from 16.3 to 42.1 (avg.=24.5) mM and V_max values ranged from 1.98 to 7.37 mg of reducing sugars released/g of soil/24 h. The optimum temperature for invertase activity in soils was observed at 50°C and denaturation of the enzyme began at 55°C. The activation energy (E_a) and enthalpy of activation (H^*) values for invertase activity, expressed in kJ/mole, ranged from 6.1 to 43.1 and 3.5 to 40.5, respectively. The Q₁₀ values for the invertase reaction in soils with a temperature range to 10 to 50°C ranged from 1.08 to 1.96. Under standerd conditions, the accumulation of reducing sugars was linear with time up to 48 h. Among the various pretreatments that affected invertase activity in soils, toluene, TCA, and PMA inhibited the enzyme by an average of 19, 54, and 11%, respectively. Steam-sterilization essentially destroyed soil invertase.     

Method of measuring invertase activity in soils

Summary Invertase (-D-fructofuranoside fructohydrolase, EC [Enzyme Commission] 3.2.1.26) is the enzyme that catalyzes the hydrolysis of sucrose and yields glucose and fructose. The activity of this enzyme was monitored by systematically developing a sensitive and rapid method to detect reducing sugars with the precision of 1.4 to 6.1% C.V. The method involves the colorimetric determination of reducing sugars which react with 3,5-dinitrosalicylic acid when soil is incubated with buffered sucrose solution and toluene at 37°C for 24 h. The detection limit for the method described is 100 g of reducing sugar per ml of soil extract. The color intensity remained constant up to 24 h. Comparative studies showed that the method described was in good agreement to other invertase assay procedures reported in the literature.Studies on the stability and distribution of invertase in soils by using the method described showed that air-drying of field-moist soil samples resulted in decreased activity ranging from 15.3 to 23.7% (avg.=19.8%). Statistical analyses indicated that invertase activity was significantly correlated with total N (r=0.78^***) and organic C (r=0.70^***) in the topsoil of 19 diverse samples. There was no significant correlation between invertase activity and soil pH, cation exchange capacity, percentage of clay and percentage of sand. The activity of this enzyme was concentrated in surface soils and decreased with profile depth. Regression analyses showed that invertase activity was significantly correlated with organic carbon content of three soil profiles examined.     

Increased levels of reactive oxygen species and expression of a cytoplasmic aconitase/iron regulatory protein 1 homolog during the early response of maize pulvini to gravistimulation

The maize (Zea mays L.) stem pulvinus is a disc of tissue located apical to each node that functions to return a tipped stem to a more upright position via increased cell elongation on its lower side. We investigated the possibility that reactive oxygen species (ROS) and hydrogen peroxide (H2O2), in particular, are involved in the gravitropic response of the pulvinus prior to initiation of the growth response by employing the cytochemical stain 3,3'-diaminobenzidine (DAB). DAB polymers were found in the bundle sheath cells of gravistimulated pulvini in association with amyloplasts after 1 min of gravistimulation, and the signal spread throughout the cytosol of these cells by 30 min. Furthermore, treatment of maize stem explants containing pulvini with 1 mm H2O2 on their upper sides caused reversal of bending polarity. Similar, though less dramatic, results were obtained via application of 1 mm ascorbic acid to the lower side of the explants. In addition, we determined that a maize cytoplasmic aconitase/iron regulatory protein 1 (IRP1) homolog is up-regulated in the pulvinus bundle sheath cells after gravistimulation using suppressive subtractive hybridization PCR (SSH PCR), real-time RT-PCR and in situ hybridization. Although we do not yet know the role of the IRP1 homolog in the pulvinus, the protein is known to be a redox sensor in other systems. Collectively, our results point to an increase in ROS quite early in the gravitropic signalling pathway and its possible role in determining the direction of bending of the pulvini. We speculate that an ROS burst may serve to link the physical phenomenon of amyloplast sedimentation to the changes in cellular biochemistry and gene expression that facilitate directional growth.     

Molecular basis for the antagonistic activity of an anti-CXCR4 antibody

Antagonistic antibodies targeting the G-protein C-X-C chemokine receptor 4 (CXCR4) hold promising therapeutic potential in various diseases. We report for the first time the detailed mechanism of action at a molecular level of a potent anti-CXCR4 antagonistic antibody (MEDI3185). We characterized the MEDI3185 paratope using alanine scanning on all 6 complementary-determining regions (CDRs). We also mapped its epitope using CXCR4 mutagenesis to assess the relative importance of the CXCR4 N-terminal peptide, extracellular loops (ECL) and ligand-binding pocket. We show that the interaction between MEDI3185 and CXCR4 is mediated mostly by CDR3H in MEDI3185 and ECL2 in CXCR4. The MEDI3185 epitope comprises the entire ECL2 sequence, lacks any so-called ‘hot-spot’ and is remarkably resistant to mutations. The structure of MEDI3185 variable domains was modeled, and suggested a β-strand/β-strand interaction between MEDI3185 CDR3H and CXCR4 ECL2, resulting in direct steric hindrance with CXCR4 ligand SDF-1. These findings may have important implications for designing antibody therapies against CXCR4.     

Molecular basis of inhibition of the ribonuclease activity in colicin E5 by its cognate immunity protein

Colicin E5 is a tRNA-specific ribonuclease that recognizes and cleaves four tRNAs in Escherichia coli that contain the hypermodified nucleoside queuosine (Q) at the wobble position. Cells that produce colicin E5 also synthesize the cognate immunity protein (Im5) that rapidly and tightly associates with colicin E5 to prevent it from cleaving its own tRNAs to avoid suicide. We report here the crystal structure of Im5 in a complex with the activity domain of colicin E5 (E5-CRD) at 1.15A resolution. The structure reveals an extruded domain from Im5 that docks into the recessed RNA binding cleft in E5-CRD, resulting in extensive interactions between the two proteins. The interactions are primarily hydrophilic, with an interface that contains complementary surface charges between the two proteins. Detailed interactions in three separate regions of the interface account for specific recognition of colicin E5 by Im5. Furthermore, single-site mutational studies of Im5 confirmed the important role of particular residues in recognition and binding of colicin E5. Structural comparison of the complex reported here with E5-CRD alone, as well as with a docking model of RNA-E5-CRD, indicates that Im5 achieves its inhibition by physically blocking the cleft in colicin E5 that engages the RNA substrate.     

Dimethyl sulfoxide elicited increase in cytochrome oxidase activity in rat liver mitochondria in vivo and in vitro

A single intraperitoneal injection of dimethyl sulfoxide (275 mg/100 g body wt.) to rats stimulated cytochrome oxidase activity in liver mitochondria 2-5-fold. The enzyme activity remained at this level for as long as 5 days post-injection. There was however only 10.5% increase in the content of cytochromes a and a3 (as determined spectrophotometrically) in the same period in response to DMSO injection. The addition of either DMSO or dimethyl sulfate (a metabolite of DMSO) to isolated liver mitochondria also caused 2-3-fold increase in cytochrome oxidase activity. The results indicate that enhancement in cytochrome oxidase activity in liver mitochondria after administration of DMSO to rats is on account of activation of cytochrome oxidase caused by structural alterations in mitochondrial membranes rather than de novo synthesis of cytochrome oxidase.