Interstrand crosslink-induced homologous recombination carries an increased risk of deletions and insertions

Homology directed repair (HDR) defends cells against the toxic effects of two-ended double strand breaks (DSBs) and one-ended DSBs that arise when replication progression is inhibited, for example by encounter with DNA lesions such as interstrand crosslinks (ICLs). HDR can occur via various mechanisms, some of which are associated with an increased risk of concurrent sequence rearrangements that can lead to deletions, insertions, translocations and loss of heterozygosity. Here, we compared the risk of HDR-associated sequence rearrangements that occur spontaneously versus in response to exposure to an agent that induces ICLs. We describe the creation of two fluorescence-based direct repeat recombination substrates that have been targeted to the ROSA26 locus of embryonic stem cells, and that detect the major pathways of homologous recombination events, e.g., gene conversions with or without crossing over, repair of broken replication forks, and single strand annealing (SSA). SSA can be distinguished from other pathways by application of a matched pair of site-specifically integrated substrates, one of which allows detection of SSA, and one that does not. We show that SSA is responsible for a significant proportion of spontaneous homologous recombination events at these substrates, suggesting that two-ended DSBs are a common spontaneous recombinogenic lesion. Interestingly, exposure to mitomycin C (an agent that induces ICLs) increases the proportion of HDR events associated with deletions and insertions. Given that many chemotherapeutics induce ICLs, these results have important implications in terms of the risk of chemotherapy-induced deleterious sequence rearrangements that could potentially contribute to secondary tumors.     

The presence of Drosophila melanogaster sex peptide-like immunoreactivity in the accessory glands of male Helicoverpa armigera

In this study a highly specific polyclonal antibody to DrmSP was produced and used to develop and standardize a sensitive direct ELISA. Structure-activity studies revealed that the antiserum is specific to the N-terminal of DrmSP. This ELISA was used for the detection of DrmSP-like immunoreactivity in the reproductive tissues of male Helicoverpa armigera moths at femtomole levels. Two positive immunoreactive peaks were found in HPLC purified extracts of male accessory glands. The immunoreactive peak, which contained a higher amount of immunoreactivity, was also found to be pheromonostatic in PBAN-injected decapitated females as well as in intact female moths during their peak pheromone production. Lower levels of DrmSP-like immunoreactivity were found in younger males (1-2 day-old) when compared to older males (3-7 day-old).     

Quantification of compartmented metabolic fluxes in developing soybean embryos by employing biosynthetically directed fractional (13)C labeling, two-dimensional [(13)C, (1)H] nuclear magnetic resonance, and comprehensive isotopomer balancing

Metabolic flux quantification in plants is instrumental in the detailed understanding of metabolism but is difficult to perform on a systemic level. Toward this aim, we report the development and application of a computer-aided metabolic flux analysis tool that enables the concurrent evaluation of fluxes in several primary metabolic pathways. Labeling experiments were performed by feeding a mixture of U-(13)C Suc, naturally abundant Suc, and Gln to developing soybean (Glycine max) embryos. Two-dimensional [(13)C, (1)H] NMR spectra of seed storage protein and starch hydrolysates were acquired and yielded a labeling data set consisting of 155 (13)C isotopomer abundances. We developed a computer program to automatically calculate fluxes from this data. This program accepts a user-defined metabolic network model and incorporates recent mathematical advances toward accurate and efficient flux evaluation. Fluxes were calculated and statistical analysis was performed to obtain sds. A high flux was found through the oxidative pentose phosphate pathway (19.99 +/- 4.39 micromol d(-1) cotyledon(-1), or 104.2 carbon mol +/- 23.0 carbon mol per 100 carbon mol of Suc uptake). Separate transketolase and transaldolase fluxes could be distinguished in the plastid and the cytosol, and those in the plastid were found to be at least 6-fold higher. The backflux from triose to hexose phosphate was also found to be substantial in the plastid (21.72 +/- 5.00 micromol d(-1) cotyledon(-1), or 113.2 carbon mol +/-26.0 carbon mol per 100 carbon mol of Suc uptake). Forward and backward directions of anaplerotic fluxes could be distinguished. The glyoxylate shunt flux was found to be negligible. Such a generic flux analysis tool can serve as a quantitative tool for metabolic studies and phenotype comparisons and can be extended to other plant systems.     

Novel tetrahydro-thieno pyridyl oxazolidinone: an antibacterial agent

Synthesis of a number of 4,5,6,7-tetrahydro-thieno[3,2-c]pyridine substituted oxazolidinones have been reported. They have been screened against a panel of Gram-positive pathogens including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. A SAR has been developed. Compound 15 showed comparable activity (MIC) to linezolid and superior to eperezolid.     

An examination of the moisture sorption characteristics of commercial magnesium stearate

The objective of this study was to characterize the moisture sorption of magnesium stearate and the morphological changes, if any, resulting from moisture sorption. Six samples of commercial magnesium stearate USP were examined. Moisture sorption isotherms were obtained at 25°C and 5% to 98% relative humidity (RH) using a moisture balance. Changes in crystal form resulting from moisture sorption were determined by x-ray diffraction. There were differences in the shape of the isotherm, reversibility of moisture uptake, and shape of the hysteresis loop in the isotherms of crystalline and amorphous magnesium stearates. The isotherm of crystalline magnesium stearate was almost parallel to the pressure axis until and RH of ∼80%. The isotherm of the amorphous sample was characterized by continuous uptake of water over the entire range of RH. Exposure of amorphous magnesium stearate to RH greater than 70% resulted in the formation of the trihydrate. The trihydrate was converted into the anhydrous form when heated to a temperature of 100°C to 105°C. The trihydrate could be generated by exposing the anhydrate to RH higher than 70%.     

Evidence in support of lysine 77 and histidine 96 as acid-base catalytic residues in saccharopine dehydrogenase from Saccharomyces cerevisiae

Saccharopine dehydrogenase (SDH) catalyzes the final reaction in the α-aminoadipate pathway, the conversion of l-saccharopine to l-lysine (Lys) and α-ketoglutarate (α-kg) using NAD? as an oxidant. The enzyme utilizes a general acid-base mechanism to conduct its reaction with a base proposed to accept a proton from the secondary amine of saccharopine in the oxidation step and a group proposed to activate water to hydrolyze the resulting imine. Crystal structures of an open apo form and a closed form of the enzyme with saccharopine and NADH bound have been determined at 2.0 and 2.2 ? resolution, respectively. In the ternary complex, a significant movement of domain I relative to domain II that closes the active site cleft between the two domains and brings H96 and K77 into the proximity of the substrate binding site is observed. The hydride transfer distance is 3.6 ?, and the side chains of H96 and K77 are properly positioned to act as acid-base catalysts. Preparation of the K77M and H96Q single-mutant and K77M/H96Q double-mutant enzymes provides data consistent with their role as the general acid-base catalysts in the SDH reaction. The side chain of K77 initially accepts a proton from the ε-amine of the substrate Lys and eventually donates it to the imino nitrogen as it is reduced to a secondary amine in the hydride transfer step, and H96 protonates the carbonyl oxygen as the carbinolamine is formed. The K77M, H976Q, and K77M/H96Q mutant enzymes give 145-, 28-, and 700-fold decreases in V/E(t) and >103-fold increases in V?/K(Lys)E(t) and V?/K(α-kg)E(t) (the double mutation gives >10?-fold decreases in the second-order rate constants). In addition, the K77M mutant enzyme exhibits a primary deuterium kinetic isotope effect of 2.0 and an inverse solvent deuterium isotope effect of 0.77 on V?/K(Lys). A value of 2.0 was also observed for (D)(V?/K(Lys))(D?O) when the primary deuterium kinetic isotope effect was repeated in D?O, consistent with a rate-limiting hydride transfer step. A viscosity effect of 0.8 was observed on V?/K(Lys), indicating the solvent deuterium isotope effect resulted from stabilization of an enzyme form prior to hydride transfer. A small normal solvent isotope effect is observed on V, which decreases slightly when repeated with NADD, consistent with a contribution from product release to rate limitation. In addition, V?/K(Lys)E(t) is pH-independent, which is consistent with the loss of an acid-base catalyst and perturbation of the pK(a) of the second catalytic group to a higher pH, likely a result of a change in the overall charge of the active site. The primary deuterium kinetic isotope effect for H96Q, measured in H?O or D?O, is within error equal to 1. A solvent deuterium isotope effect of 2.4 is observed with NADH or NADD as the dinucleotide substrate. Data suggest rate-limiting imine formation, consistent with the proposed role of H96 in protonating the leaving hydroxyl as the imine is formed. The pH-rate profile for V?/K(Lys)E(t) exhibits the pK(a) for K77, perturbed to a value of ～9, which must be unprotonated to accept a proton from the ε-amine of the substrate Lys so that it can act as a nucleophile. Overall, data are consistent with a role for K77 acting as the base that accepts a proton from the ε-amine of the substrate lysine prior to nucleophilic attack on the α-oxo group of α-ketoglutarate, and finally donating a proton to the imine nitrogen as it is reduced to give saccharopine. In addition, data indicate a role for H96 acting as a general acid-base catalyst in the formation of the imine between the ε-amine of lysine and the α-oxo group of α-ketoglutarate.     

Supporting role of lysine 13 and glutamate 16 in the acid-base mechanism of saccharopine dehydrogenase from Saccharomyces cerevisiae

Saccharopine dehydrogenase (SDH) catalyzes the NAD+ dependent oxidative deamination of saccharopine to form lysine (Lys) and α-ketoglutarate (α-kg). The active site of SDH has a number of conserved residues that are believed important to the overall reaction. Lysine 13, positioned near the active site base (K77), forms a hydrogen bond to E78 neutralizing it, and contributing to setting the pKa of the catalytic residues to near neutral pH. Glutamate 16 is within hydrogen bond distance to the Nε atom of R18, which has strong H-bonding interactions with the α-carboxylate and α-oxo groups of α-kg. Mutation of K13 to M and E16 to Q decreased kcat by about 15-fold, and primary and solvent deuterium kinetic isotope effects measured with the mutant enzymes indicate hydride transfer is rate limiting for the overall reaction. The pH-rate profiles for K13M exhibited no pH dependence, consistent with an increase in negative charge in the active site resulting in the perturbation in the pKas of catalytic groups. Elimination of E16 affects optimal positioning of R18, which is involved in binding and holding α-kg in the correct conformation for optimum catalysis. In agreement, a ΔΔG°' of 2.60 kcal/mol is estimated from the change in Kα-kg for replacing E16 with Q.     

Divergent effects of compounds on the hydrolysis and transpeptidation reactions of γ-glutamyl transpeptidase

A novel class of inhibitors of the enzyme γ-glutamyl transpeptidase (GGT) were evaluated. The analog OU749 was shown previously to be an uncompetitive inhibitor of the GGT transpeptidation reaction. The data in this study show that it is an equally potent uncompetitive inhibitor of the hydrolysis reaction, the primary reaction catalyzed by GGT in vivo. A series of structural analogs of OU749 were evaluated. For many of the analogs, the potency of the inhibition differed between the hydrolysis and transpeptidation reactions, providing insight into the malleability of the active site of the enzyme. Analogs with electron withdrawing groups on the benzosulfonamide ring, accelerated the hydrolysis reaction, but inhibited the transpeptidation reaction by competing with a dipeptide acceptor. Several of the OU749 analogs inhibited the transpeptidation reaction by slow onset kinetics, similar to acivicin. Further development of inhibitors of the GGT hydrolysis reaction is necessary to provide new therapeutic compounds.     

Biodegradation of 2-Chlorophenol by Rhodopseudomonas palustris

A phototrophic bacterial culture that assimilates 2-chlorophenol (2-CP) was enriched from effluents of paper and wood industry. The isolated bacterium was identified as Rhodopseudomonas palustris based on its morphological characteristics, biochemical reactions, and fatty acid methyl ester gas chromatography (FAME-GC) analysis. The bacterium R. palustris being photoheterotrophic in nutrition was also able to switch between phototropic, aerobic, and anaerobic modes of metabolism, as evidenced by modulation of the bacterial photopigments. The switching of anaerobic to aerobic metabolism was evidenced by the presence of catechol, a product of aerobic oxidation of 2-CP in the spent medium and the disappearance of photopigment-specific absorbance in the organism. R. palustris degraded about 97% of the supplemented 2-CP from the culture medium in 40 days along with production of an exo-polysaccharide, which probably provides protection from substrate toxicity and enhances its bioavailability. Thin-layer chromatography (TLC) and gas chromoatography–mass spectrometry (GC-MS) analysis of the R. palustris spent medium extracts indicated the presence of phenol. The GC-MS data also indicated that phenol is metabolized through an ortho-cleavage pathway. Further analysis of the R. palustris cell-free extracts for enzymes showed the presence of a chlorophenol dehalogenase (CD) and a chlorophenol nicotinamide adenine dinucleotide phosphate (NADPH)-oxidoreductase (CNOR) with respective specific activities of 0.114 and 0.26 μmol/min/mg, suggesting an initial reductive dechlorination step during 2-CP catabolism. The study thus highlights the important roles of phototrophic bacteria in the decontamination of environmental pollutants from the polluted sites.