Investigation of the Role of a Conserved Glycine Motif in the Saccharomyces cerevisiae Xylose Reductase

All yeast xylose reductases, with the exception of that from Schizosaccharomyces pombe, possess the catalytic and coenzyme-binding elements from both the aldo–keto reductase and short-chain dehydrogenase–reductase (SDR) enzyme families in their primary sequences. In the Saccharomyces cerevisiae xylose reductase (XR), the SDR-like coenzyme-binding GXXXGXG motif (Gly motif) is located between residues 128 and 134, with the third Gly residue being replaced by an Asp. We used site-directed mutagenesis to study the role of this SDR-like Gly motif in the S. cerevisiae xylose reductase. Site-directed mutagenesis of the individual conserved Gly residue positions (G128A, G132A, D134G, and D134A) did not significantly affect the specific activity, kinetic constants (K_m, K_cat, and K_cat/K_m), or dissociation constants (K_d) in any of the variants compared with the wild type. Deletion of the entire Gly motif produced an unstable protein that could not be purified. These results indicate that the SDR-like Gly motif likely provides support to the overall structure of the enzyme, but it does not contribute directly to coenzyme binding in this XR.     

Polymorphic microsatellite DNA markers for Banksia hookeriana (Proteaceae)

We developed 11 polymorphic microsatellite DNA markers for an Australian native shrub Banksia hookeriana (Proteaceae). The number of alleles per locus in 37 individuals varied from three to 17, observed and expected heterozygosities ranged from 0.297 to 0.838 and from 0.279 to 0.900, respectively. Two loci (BH‐B5 and BH‐B107) showed significant deviation from Hardy–Weinberg equilibrium (P < 0.05), and null alleles may be present at these two loci. All loci showed independent inheritance.     

Characterization of biocontrol traits in the entomopathogenic nematode Heterorhabditis georgiana (Kesha strain), and phylogenetic analysis of the nematode’s symbiotic bacteria

Our objective was to estimate the biocontrol potential of the recently discovered entomopathogenic nematode species Heterorhabditis georgiana (Kesha strain). Additionally, we conducted a phylogenetic characterization of the nematode’s symbiotic bacterium. In laboratory experiments, we compared H. georgiana to other entomopathogenic nematodes for virulence, environmental tolerance (to heat, desiccation, and cold), and host seeking ability. Virulence assays targeted Acheta domesticus, Agrotis ipsilon, Diaprepes abbreviatus, Musca domestica, Plodia interpunctella, Solenopsis invicta, and Tenebrio molitor. Each assay included H. georgiana and five or six of the following species: Heterorhabditis floridensis, Heterorhabditis indica, Heterorhabditis mexicana, Steinernema carpocapsae, Steinernema feltiae, Steinernema rarum, and Steinernema riobrave. Environmental tolerance assays included Heterorhabditis bacteriophora, H. georgiana, H. indica, S. carpocapsae, S. feltiae, and S. riobrave (except cold tolerance did not include S. carpocapsae or S. riobrave). Host seeking ability was assessed in H. bacteriophora, H. georgiana, S. carpocapsae, and Steinernema glaseri, all of which showed positive orientation to the host with S. glaseri having greater movement toward the host than S. carpocapsae (and the heterorhabditids being intermediate). Temperature range data (tested at 10, 13, 17, 25, 30 and 35 °C) indicated that H. georgiana can infect Galleria mellonella between 13 and 35 °C (with higher infection at 17–30 °C), and could reproduce between 17 and 30 °C (with higher nematode yields at 25 °C). Compared with other nematode species, H. georgiana expressed low or intermediate capabilities in all virulence and environmental tolerance assays indicating a relatively low biocontrol potential. Some novel observations resulted from comparisons among other species tested. In virulence assays, H. indica caused the highest mortality in P. interpunctella followed by S. riobrave; S. carpocapsae caused the highest mortality in A. domesticus followed by H. indica; and S. riobrave was the most virulent nematode to S. invicta. In cold tolerance, S. feltiae exhibited superior ability to cause mortality in G. mellonella (100%) at 10 °C, yet H. bacteriophora and H. georgiana exhibited the ability to produce attenuated infections at 10 °C, i.e., the infections resumed and produced mortality at 25 °C. In contrast, H. indica did not show an ability to cause attenuated infections. Based on the phylogenetic analysis, the bacterium associated with H. georgiana was identified as Photorhabdus luminescens akhurstii.     

Evaluation of synthetic female attractants against Ceratitis capitata (Diptera: Tephritidae) in sticky coated spheres and McPhail type traps

In field experiments conducted in a citrus orchard in Chios, Greece, we tested the efficacy of yellow, sticky, plastic, hollow spheres baited with long-lasting dispensers of the food attractants ammonium acetate, 1,4-diaminobutane (putrescine), and trimethylamine (FA-3) to capture adults of the Mediterranean fruit fly, Ceratitis capitato (Wiedemann) (Diptera: Tephritidae). Yellow spheres (7.5 cm in diameter) baited internally or externally with FA-3 were approximately 30 and approximately 12 times more attractive for females and males respectively than unbaited spheres. However, they were approximately 3 times less attractive for both sexes than plastic McPhail type traps baited with the same attractants and provided with water and a drop of a surfactant in their bases (wet traps), and only 1.5 and 2.8 times less attractive for females and males, respectively, than likewise-baited McPhail type traps provided with a killing agent (dimethyl dichlorovinyl phosphate) but not water in their bases (dry trap). Baited spheres were more C. capitata female selective than either wet or dry McPhail traps. The importance of these findings in developing lure and kill devices for the Mediterranean fruit fly is discussed.     

Active-site characteristics of CYP2C19 and CYP2C9 probed with hydantoin and barbiturate inhibitors

Three series of N-3 alkyl substituted phenytoin, nirvanol, and barbiturate derivatives were synthesized and their inhibitor potencies were tested against recombinant CYP2C19 and CYP2C9 to probe the interaction of these ligands with the active sites of these enzymes. All compounds were found to be competitive inhibitors of both enzymes, although the degree of inhibitory potency was generally much greater towards CYP2C19. Inhibitor stereochemistry did not markedly influence K(i) towards CYP2C9, and log P adequately predicted inhibitor potency for this enzyme. In contrast, stereochemistry was an important factor in determining inhibitor potency towards CYP2C19. (S)-(+)-N-3-Benzylnirvanol and (R)-(-)-N-3-benzylphenobarbital emerged as the most potent and selective CYP2C19 inhibitors, with K(i) values of < 250nM--at least two orders of magnitude greater inhibitor potency than towards CYP2C9. Both inhibitors were metabolized preferentially at their C-5 phenyl substituents, indicating that CYP2C19 prefers to orient the N-3 substituents away from the active oxygen species. These features were incorporated into expanded CoMFA models for CYP2C9, and a new, validated CoMFA model for CYP2C19.     

Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex

Cytochrome bc(1) is an integral membrane protein complex essential for cellular respiration and photosynthesis; it couples electron transfer from quinol to cytochrome c to proton translocation across the membrane. Specific bc(1) inhibitors have not only played crucial roles in elucidating the mechanism of bc(1) function but have also provided leads for the development of novel antibiotics. Crystal structures of bovine bc(1) in complex with the specific Q(o) site inhibitors azoxystrobin, MOAS, myxothiazol, stigmatellin and 5-undecyl-6-hydroxy-4,7-dioxobenzothiazole were determined. Interactions, conformational changes and possible mechanisms of resistance, specific to each inhibitor, were defined. Residues and secondary structure elements that are capable of discriminating different classes of Q(o) site inhibitors were identified for the cytochrome b subunit. Directions in the displacement of the cd1 helix of cytochrome b subunit in response to various Q(o) site inhibitors were correlated to the binary conformational switch of the extrinsic domain of the iron-sulfur protein subunit. The new structural information, together with structures previously determined, provide a basis that, combined with biophysical and mutational data, suggest a modification to the existing classification of bc(1) inhibitors. bc(1) inhibitors are grouped into three classes: class P inhibitors bind to the Q(o) site, class N inhibitors bind to the Q(i) site and the class PN inhibitors target both sites. Class P contains two subgroups, Pm and Pf, that are distinct by their ability to induce mobile or fixed conformation of iron-sulfur protein.     

Structural insights into the interaction between prion protein and nucleic acid

The infectious agent of transmissible spongiform encephalopathies (TSE) is believed to comprise, at least in part, the prion protein (PrP). Other molecules can modulate the conversion of the normal PrP(C) into the pathological conformer (PrP(Sc)), but the identity and mechanisms of action of the key physiological factors remain unclear. PrP can bind to nucleic acids with relatively high affinity. Here, we report small-angle X-ray scattering (SAXS) and nuclear magnetic resonance spectroscopy measurements of the tight complex of PrP with an 18 bp DNA sequence. This double-stranded DNA sequence (E2DBS) binds with nanomolar affinity to the full-length recombinant mouse PrP. The SAXS data show that formation of the rPrP-DNA complex leads to larger values of the maximum dimension and radius of gyration. In addition, the SAXS studies reveal that the globular domain of PrP participates importantly in the formation of the complex. The changes in NMR HSQC spectra were clustered in two major regions: one in the disordered portion of the PrP and the other in the globular domain. Although interaction is mediated mainly through the PrP globular domain, the unstructured region is also recruited to the complex. This visualization of the complex provides insight into how oligonucleotides bind to PrP and opens new avenues to the design of compounds against prion diseases.     

Activation of MAP kinases by calcium-dependent and calcium-independent pathways. Stimulation by thapsigargin and epidermal growth factor.

In order to determine the effect of calcium mobilization on mitogen-activated protein (MAP) kinase activation, we have treated human foreskin fibroblasts (HSWP cells) and human epidermal carcinoma (A431) cells with thapsigargin. Intracellular free calcium was monitored by single cell image analysis using fura-2 and correlated with MAP kinase stimulation as assessed by immunoprecipitation, kinase renaturation assays and immunoblotting. Thapsigargin stimulated the 44- and 42-kDa MAP kinase isozymes in both cell types with kinetics that were slightly delayed relative to enzyme stimulated by epidermal growth factor. Removal of external calcium did not significantly affect the activation of the MAP kinases by thapsigargin, indicating that intracellular calcium mobilization is sufficient to stimulate the enzymes. However, treatment of cells with EGTA under conditions which deplete both intra- and extracellular calcium inhibited stimulation by thapsigargin but not epidermal growth factor. Stimulation of the MAP kinases by the calcium ionophore ionomycin paralleled the activation observed with thapsigargin in both calcium-containing and calcium-free conditions. These results indicate that there are at least two independent pathways for stimulation of MAP kinase: one that is dependent on intracellular calcium mobilization, and one that is mediated by the tyrosine kinase epidermal growth factor receptor and is calcium-independent.     

Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO.

Shotgun proteomics is rapidly becoming one of the most efficient and popular tools to examine protein expression in cells. Numerous laboratories now have a wide array of low- and high-performance mass spectrometry instrumentation necessary to complete proteome-wide projects. Often these laboratories have time and financial constraints that prohibit all projects from being conducted on high-performance state-of-the-art mass spectrometers. Here, we compare shotgun proteomic results using a direct 'lyse, digest and analyse' approach on a high-performance mass spectrometer (i.e. the LTQ-FT) with the results from a much lower-performance instrument (i.e. the LCQ-DUO) where, for the latter, various traditional protein pre-fractionation steps and gas-phase fractionation were used to increase the proteome coverage. Our results demonstrate that shotgun proteomic analyses conducted on the lower-performance LCQ-DUO mass spectrometer could adequately characterize a PhoP constitutive strain of Salmonella typhimurium if proteome pre-fractionation steps and gas-phase fractionation were included.     

Effects of zomepirac and indomethacin on renal blood flow and electrolyte excretion in anesthetized monkeys

Zomepirac sodium is a new inhibitor of prostaglandin cyclooxygenase with an $\text{in vitro}$ potency equivalent to indomethacin. Since inhibitors of prostaglandin synthesis have marked effects on renal hemodynamics, zomepirac may be expected to reduce renal blood flow (RBF) in a manner similar to indomethacin. This study compares the effects of zomepirac and indomethacin on RBF and electrolyte excretion in anesthetized Rhesus monkeys. Each experiment consisted of a control period followed by 3 or 4 drug treatment periods in which increasing doses of zomepirac (0.5 to 20 mg/kg) or indomethacin (0.5 to 10 mg/kg were given. Indomethacin (5 mg/kg) reduced RBF by 22% and the higher dose (10 mg/kg) reduced RBF by an additional 13%. Zomepirac had little effect on RBF in doses as high as 20 mg/kg. At any given dose the mean plasma concentration of zomepirac was equal to or greater than indomethacin. Peak indomethacin concentration was 48 μg/ml after the 10 mg/kg dose while the peak zomepirac, after 20 mg/kg, was 158 μg/ml. Neither drug had a significant effect on either glomerular filtration rate or excretion rate of sodium or potassium. Thus, zomepirac had only minimal effects on RBF while indomethacin decreased RBF of anesthetized monkeys in a manner qualitatively similar to its effect in other species. The minimal renal effects caused by zomepirac relative to indomethacin in this primate may indicate a therapeutic advantage for zomepirac in man.