A novel variant of ferredoxin-dependent sulfite reductase having preferred substrate specificity for nitrite in the unicellular red alga Cyanidioschyzon merolae.

Plant NiR (nitrite reductase) and SiR (sulfite reductase) have common structural and functional features. Both enzymes are generally distinguished in terms of substrate specificity for nitrite and sulfite. The genome of Cyanidioschyzon merolae, a unicellular red alga living in acidic hot springs, encodes two SiR homologues, namely CmSiRA and CmSiRB (C. merolae sulfite reductases A and B), but no NiR homologue. The fact that most known SiRs have a low nitrite-reducing activity and that the CmSiRB gene is mapped between the genes for nitrate transporter and nitrate reductase implies that CmSiRB could have a potential to function as a nitrite-reducing enzyme. To verify this hypothesis, we produced a recombinant form of CmSiRB and characterized its enzymatic properties. The enzyme was found to have a significant nitrite-reducing activity, whereas its sulfite-reducing activity was extremely low. As the affinity of CmSiRB for sulfite was higher by 25-fold than that for nitrite, nitrite reduction by CmSiRB was competitively inhibited by sulfite. These results demonstrate that CmSiRB is a unique SiR having a decreased sulfite-reducing activity and an enhanced nitrite-reducing activity. The cellular level of CmSiRB was significantly increased when C. merolae was grown in a nitrate medium. The nitrate-grown C. merolae cells showed a high nitrite uptake from the growth medium, and this consumption was inhibited by sulfite. These combined results indicate that CmSiRB has a significant nitrite-reducing activity and plays a physiological role in nitrate assimilation.

Cell-permeant NAADP: a novel chemical tool enabling the study of Ca2+ signalling in intact cells.

NAADP (nicotinic acid adenine dinucleotide phosphate) is a recently discovered second messenger, and as such, we have much yet to learn about its functions in health and disease. A bottleneck in this basic research is due to NAADP, like all second messengers, being charged to prevent it from leaking out of cells. This makes for effective biology, but imposes difficulties in experiments, as it must be injected, loaded via liposomes, or electroporated, techniques that are highly technically demanding and are possible only in certain single cell preparations. For the better understood second messenger inositol 1,4,5-trisphosphate, great success has been obtained with cell-permeant derivatives where the charged groups are masked through esterification. We now report NAADP-AM as a cell-permeant analogue of NAADP that is taken up into cells and induces NAADP-mediated Ca(2+) signalling. NAADP-AM is a powerful chemical tool that will be of enormous biological utility in a wide range of systems and will greatly facilitate research into the role of NAADP in health and disease.

Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity.

Xylitol dehydrogenase (XDH) is one of several enzymes responsible for assimilating xylose into eukaryotic metabolism and is useful for fermentation of xylose contained in agricultural byproducts to produce ethanol. For efficient xylose utilization at high flux rates, cosubstrates should be recycled between the NAD+-specific XDH and the NADPH-preferring xylose reductase, another enzyme in the pathway. To understand and alter the cosubstrate specificity of XDH, we determined the crystal structure of the Gluconobacter oxydans holoenzyme to 1.9 angstroms resolution. The structure reveals that NAD+ specificity is largely conferred by Asp38, which interacts with the hydroxyls of the adenosine ribose. Met39 stacked under the purine ring and was also located near the 2' hydroxyl. Based on the location of these residues and on sequence alignments with related enzymes of various cosubstrate specificities, we constructed a double mutant (D38S/M39R) that was able to exclusively use NADP+, with no loss of activity.

A streamlined method to predict hepatic clearance using human liver microsomes in the presence of human plasma.

INTRODUCTION: Human liver microsomal incubations are often used to predict the metabolic lability of new chemical entities. The clearance values are scaled-up from in vitro data and mathematically corrected for plasma protein binding, or in some cases the free fraction ratio of plasma to microsomes, using well-established scaling methods such as the well-stirred model. This can be time consuming for multiple compounds since it requires separate experiments to determine in vitro lability, and free fraction. METHODS: We attempted to streamline clearance predictions by combining experiments into one. Firstly, we combined the free fraction experiments into one free fraction ratio by measuring the partitioning of compound between plasma and microsomes, and by applying this experimental ratio to clearance predictions found that it performed at least as well as free fractions determined separately. We also incubated compounds with plasma added to the incubation mixture and compared the predicted clearances to values determined using traditional mathematical protein binding corrections. RESULTS: Consistently, incubations with added plasma resulted in CL predictions closer to literature values than incubations only mathematically corrected for protein binding. For example, incorporating plasma into a ketamine incubation resulted in a CL value of 15.1 mL/min/kg, compared with a value of 10.2 using mathematical binding corrections. The literature value is 16.4 mL/min/kg. DISCUSSION: This work characterizes this new method and compares it to the traditional microsomal incubation method using several literature compounds, and suggests that streamlining the methods may generate quality data faster and with less resource investment.

Synthesis of [³²P]NAADP for the radioreceptor binding assay.

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a major messenger for Ca(2+) mobilization in cells. NAADP-binding proteins are highly selective and have a strong affinity for NAADP. This is the basis of the radioreceptor binding assay, which is used to measure NAADP levels in cells and tissues and to identify cellular stimuli that use NAADP as an intracellular messenger. In the radioreceptor binding assay, radiolabeled NAADP ([(32)P]NAADP) competes with endogenous NAADP present in samples for binding to their receptors. Here, we describe the synthesis of [(32)P]NAADP for use in the radioreceptor binding assay.

Synthesis of NAADP-AM as a membrane-permeant NAADP analog.

Nicotinic acid adenine dinucleotide phosphate (NAADP), like the other major messengers for Ca²âº mobilization, is passively membrane-impermeant. Instead, a cell-permeant acetoxymethyl ester derivative of NAADP (NAADP-AM) can be synthesized as described here and used to study NAADP-mediated Ca²âº release.

Nitric oxide synthase in the pharynx of the planarian Dugesia tigrina.

The distribution of the nicotinamide adenine dinucleotide phosphate-(NADPH) diaphorase reaction, an indicator of nitric oxide synthase activity, was studied in the freshwater planarian Dugesia tigrina (Platyhelminthes). The reaction was restricted to the pharynx, where the inner epithelium was intensely stained and the outer epithelium moderately stained. Neurons that innervated the pharynx were also stained. The enzyme activity was studied by high pressure liquid chromatographic quantitation of the formed citrulline. The presumed nitric oxide synthase was dependent on NADPH, whereas no dependency on Ca2+ and calmodulin could be detected. Tetrahydrobiopterin increased the activity about fivefold to 218.2+/-24.9 fmol/mg protein per min. Nomega-nitro-l-arginine depressed the enzyme activity by about 80%. The results indicate that nitric oxide has a role in the feeding behavior of planarians.

Spatial control of Ca2+ signaling by nicotinic acid adenine dinucleotide phosphate diffusion and gradients.

Intracellular Ca(2+) is able to control numerous cellular responses through complex spatiotemporal organization. Ca(2+) waves mediated by inositol trisphosphate or ryanodine receptors propagate by Ca(2+)-induced Ca(2+) release and therefore do not have an absolute requirement for a gradient in either inositol trisphosphate or cyclic ADP-ribose, respectively. In contrast, we report that although Ca(2+) increases induced by nicotinic acid adenine dinucleotide phosphate (NAADP) are amplified by Ca(2+)-induced Ca(2+) release locally, Ca(2+) waves mediated by NAADP have an absolute requirement for an NAADP gradient. If NAADP is increased such that its concentration is spatially uniform in one region of an egg, the Ca(2+) increase occurs simultaneously throughout this area, and only where there is diffusion out of this area to establish an NAADP gradient is there a Ca(2+) wave. A local increase in NAADP results in a Ca(2+) increase that spreads by NAADP diffusion. NAADP diffusion is restricted at low but not high concentrations of NAADP, indicating that NAADP diffusion is strongly influenced by binding to immobile and saturable sites, probably the NAADP receptor itself. Thus, the range of action of NAADP can be tuned by its concentration from that of a local messenger, like Ca(2+), to that of a global messenger, like IP(3) or cyclic ADP-ribose.

NAD(P)H oxidase inhibiting with apocynin improved vascular reactivity in tail-suspended hindlimb unweighting rat

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Recent studies suggested that reactive oxygen species derived from nicotinamide adenine dinucleotide phosphate (NAD(P)H) oxidase is of functional importance in modulating vascular tone, and we have previously detected excessive superoxide production in tail-suspended hindlimb unweighting (HU) rat cerebral and carotid arteries. HU rat was a widely used model to simulate physiological effects on the vasculature. The present study tended to investigate whether NAD(P)H oxidase inhibition with apocynin influences vasoconstriction, endothelium-dependent relaxation, and nitrite/nitrate (NOx) content in HU rat cerebral and carotid arteries. Vascular contractile and dilate responses were assessed in a myograph organ bath. NOx content in cerebral and carotid arteries was measured. We found enhanced maximal contractile response and impaired endothelium-dependent relaxation in HU rat basilar (P < 0.01) and common carotid artery (P < 0.05); however, chronic treatment of apocynin (50 mg/kg/day) partially reversed abnormal vascular response. Furthermore, 21-day HU increased arterial NOx content (P < 0.01) in cerebral and carotid arteries compared with control rats; however, apocynin treatment restored it toward near-normal values. These data demonstrated that NAD(P)H oxidase-derived oxidative stress mediated abnormal vasoreactivity though nitric oxide mechanism in the settings of simulated microgravity (AU)