Biochemical characterization of the novel rice kinesin K23 and its kinetic study using fluorescence resonance energy transfer between an intrinsic tryptophan residue and a fluorescent ATP analogue

We previously demonstrated that the rice kinesin K16, which belongs to the kinesin-7 subfamily, has unique enzymatic properties and atomic structure within key functional regions. In this study, we focused on a novel rice plant kinesin, K23, which also belongs to the kinesin-7 subfamily. The biochemical characterization of the K23 motor domain (K23MD) was studied and compared with the rice kinesin K16 and other related kinesins. K23 exhibits ～45-fold (1.3 Pi mol(-1) site mol(-1) s(-1)) lower microtubule-dependent ATPase activity than conventional kinesins, whereas its affinity for microtubules is comparable with conventional kinesins. MgADP-free K23 is unstable compared with the unusually stable MgADP-free K16MD. The enzymatic properties of K23MD are somewhat different from those of K16. We used a fluorescent ATP analogue 2'(3')-O-(N'-methylanthraniloyl)-ATP (mant-ATP) for the kinetic characterization of K23. The fluorescence of mant-ATP was not significantly altered during its hydrolysis by K23. However, significant fluorescence resonance energy transfer (FRET) between mant-ATP and W21 in the motor domain was observed. The kinetic study using FRET revealed that K23 has unique kinetic characteristics when compared with other kinesins.     

Agronomic use efficiency of N fertilizer in maize-based systems in sub-Saharan Africa within the context of integrated soil fertility management

Traditionally, crop production in sub-Saharan Africa (SSA) depends primarily on mining soil nutrients. Integrated Soil Fertility Management (ISFM) is an approach for intensifying agriculture in SSA that aims at maximizing the agronomic efficiency (AE) of applied nutrient inputs. ISFM contains the following essential components: proper fertilizer management, use of improved varieties, the combined application of organic inputs and fertilizer, and adaptation of input application rates to within-farm soil fertility gradients where these are important. This paper evaluates, through meta-analysis, the impact of these components on the AE of fertilizer N (N-AE), defined as extra grain yield per kg fertilizer N applied, in maize-based systems in SSA. Since N-AE is low for excessive fertilizer N application rates or when fertilizer is applied on fertile, unresponsive soil, as was confirmed by scatter plots against control yields and fertilizer N application rates, such values were removed from the database in order to focus on and elucidate the more variable and complex responses under less than ideal conditions typical for SSA. Compared with local varieties, the use of hybrid maize varieties significantly increased N-AE values (17 and 26 kg (kg N)^?1, respectively) with no differences observed between local and improved, open-pollinated varieties. Mixing fertilizer with manure or compost resulted in the highest N-AE values [36 kg (kg N)^?1] while organic inputs of medium quality also showed significantly higher N-AE values compared with the sole fertilizer treatment but only at low organic input application rates (40 and 23 kg (kg N)^?1, respectively). High quality organic inputs (Class I) and those with a high C-to-N ratio (Class III) or high lignin content (Class IV) did not affect N-AE values in comparison with the sole fertilizer treatment. Application of N fertilizer on infields resulted in significantly higher N-AE values [31 kg (kg N)^?1] compared with the outfields [17 kg (kg N)^?1]. The obtained information indicates that N-AE is amenable to improved management practices and that the various components embedded in the ISFM definition result in improvements in N-AE.     

Dopamine D1 receptor signaling system regulates ryanodine receptor expression after intermittent exposure to methamphetamine in primary cultures of midbrain and cerebral cortical neurons

Regulatory mechanisms of ryanodine receptor (RyR) expression are not well known, although methamphetamine (METH) has been reported to up-regulate RyRs in mouse brain. This study investigate regulatory mechanisms of RyR expression by dopaminergic system using the midbrain and cerebral cortical neurons in primary culture intermittently exposed to METH and dopamine receptor (DR) agonists (1 h/day, for 3 days). Intermittent METH (10 μM) exposure enhanced RyR-1 and -2 proteins and their mRNA, but not RyR-3 expression in the both types of the neurons. These METH-induced increases of RyR proteins and their mRNA were dose-dependently blocked by SCH23390 (a selective D(1) DR antagonist), but not a D(2)DR antagonist sulpiride, suggesting a regulatory role of D(1)DRs in RyR expression by METH in these neurons. In cerebral cortical neurons, intermittent SKF82958 (a selective D(1)DR agonist) exposure increased RyR-1 and -2 proteins and their mRNA, whereas quinpirole (a selective D(2)DR agonist) showed no effects. KT5720, a protein kinase A inhibitor, dose-dependently attenuated the METH-stimulated RyR-1 and -2 expressions in cerebral cortical neurons. METH significantly increased phosphorylation of cAMP-response element-binding protein, which was completely suppressed by SCH23390. These results indicate that RyR-1 and -2 expressions are regulated by D(1)DRs via the signal transduction linked to D(1)DRs.     

Ecophysiology of uncultured filamentous anaerobes belonging to the phylum KSB3 that cause bulking in methanogenic granular sludge

A filamentous bulking of a methanogenic granular sludge caused by uncultured filamentous bacteria of the candidate phylum KSB3 in an upflow anaerobic sludge blanket (UASB) system has been reported. To characterize the physiological traits of the filaments, a polyphasic approach consisting of rRNA-based activity monitoring of the KSB3 filaments using the RNase H method and substrate uptake profiling using microautoradiography combined with fluorescence in situ hybridization (MAR-FISH) was conducted. On the basis of rRNA-based activity, the monitoring of a full-scale UASB reactor operated continuously revealed that KSB3 cells became active and predominant (up to 54% of the total 16S rRNA) in the sludge when the carbohydrate loading to the system increased. Batch experiments with a short incubation of the sludge with maltose, glucose, fructose, and maltotriose at relatively low concentrations (approximately 0.1 mM) in the presence of yeast extract also showed an increase in KSB3 rRNA levels under anaerobic conditions. MAR-FISH confirmed that the KSB3 cells took up radioisotopic carbons from [(14)C]maltose and [(14)C]glucose under the same incubation conditions in the batch experiments. These results suggest that one of the important ecophysiological characteristics of KSB3 cells in the sludge is carbohydrate degradation in wastewater and that high carbohydrate loadings may trigger an outbreak of KSB3 bacteria, causing sludge bulking in UASB systems.     

Energetics-based discovery of protein-ligand interactions on a proteomic scale

Biochemical functions of proteins in cells frequently involve interactions with various ligands. Proteomic methods for the identification of proteins that interact with specific ligands such as metabolites, signaling molecules, and drugs are valuable in investigating the regulatory mechanisms of cellular metabolism, annotating proteins with unknown functions, and elucidating pharmacological mechanisms. Here we report an energetics-based target identification method in which target proteins in a cell lysate are identified by exploiting the effect of ligand binding on their stabilities. Urea-induced unfolding of proteins in cell lysates is probed by a short pulse of proteolysis, and the effect of a ligand on the amount of folded protein remaining is monitored on a proteomic scale. As proof of principle, we identified proteins that interact with ATP in the Escherichia coli proteome. Literature and database mining confirmed that a majority of the identified proteins are indeed ATP-binding proteins. Four identified proteins that were previously not known to interact with ATP were cloned and expressed to validate the result. Except for one protein, the effects of ATP on urea-induced unfolding were confirmed. Analyses of the protein sequences and structure models were also employed to predict potential ATP binding sites in the identified proteins. Our results demonstrate that this energetics-based target identification approach is a facile method to identify proteins that interact with specific ligands on a proteomic scale.     

Syntheses of cellotriose and cellotetraose analogues as transition state mimics for mechanistic studies of cellulases

Cellotriose and cellotetraose analogues carrying cyclohexene rings were developed as molecular probes which are expected to mimic the transition state conformation of hydrolysis by cellulases. The cyclohexene ring was placed at the pyranose ring being expected to locate the -1 subsite of the enzyme. In order to evaluate these probes, sulfur derivatives of cellotriose and cellotetraose were also synthesized as the enzyme tolerant analogues which mimic the stable conformations of the natural cellulose. The binding assays using differential scanning calorimetry revealed that introduction of the cyclohexene ring is effective to the complexation with an endoglucanase, NCE5 from Humicola insolens.     

Synthesis and pharmacological evaluation of novel benzoylazole-based PPAR α/γ activators

In our search for new PPARα/γ agonists, we designed and synthesized a series of benzoylazole-based carboxylic acids. Compound 9 showed potent PPARγ partial agonistic activity with modest PPARα agonistic activity. The sodium salt of 9 (9Na) demonstrated potent efficacy in lowering both blood glucose and lipids in an animal model without causing significant body weight gain, a well-known side effect associated with PPARγ full agonists.