Simultaneous detection of DNA-binding proteins using exo-Taq-based reaction

The DNA-binding protein (DBP) has a wide range of roles such as those in DNA repair, recombination, and gene expression. Recently, a microarray-based method has been developed for the high-throughput analysis of DNA-protein interactions. However, to maximize the advantages of this method, the detection process should be improved so that the method can be applied to many proteins without the use of antibody or sample labeling. Previously, we presented a primary report on the detection of DBP, which is applicable to the microarray format. The system consists of three steps: first, the target DBP in the sample solution is incubated with a probe DNA; second, the probe is digested with Exo (Exonuclease) III; finally, the probe is extended withTaq DNA polymerase using fluorescent dye-labeled dUTP as a substrate. The binding DBP protects the probe from digestion by Exo III. Therefore, only the DBP-bound probe allows the following extension. In this study, the simultaneous detection of multiple DBPs was examined, and then the DBPs were analyzed using a crude extract of the cultured cells to demonstrate the general applicability of the method. Our method can be applied to many DBPs using the same procedure and components, whereas in the antibody-based method, the same number of antibodies as DBPs is needed to detect target DBPs in ELISA (enzyme-linked immunosorbent assay). These results suggest that our method is useful for the high-throughput detection of DBPs in the microarray format.     

Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin

The oxygen binding properties of extracellular giant hemoglobins (Hbs) in some annelids exhibit features significantly different from those of vertebrate tetrameric Hbs. Annelid giant Hbs show cooperative oxygen binding properties in the presence of inorganic cations, while the cooperativities of vertebrate Hbs are enhanced by small organic anions or chloride ions. To elucidate the structural basis for the cation-mediated cooperative mechanisms of these giant Hbs, we determined the crystal structures of Ca2+- and Mg2+-bound Hbs from Oligobrachia mashikoi at 1.6 and 1.7 A resolution, respectively. Both of the metal-bound structures were determined in the oxygenated state. Four Ca2+-binding sites and one Mg2+-binding site were identified in each tetramer subassembly. These cations are considered to stabilize the oxygenated form and increase affinity and cooperativity for oxygen binding, as almost all of the Ca2+ and Mg2+ cations were bound at the interface regions, forming either direct or hydrogen bond-mediated interactions with the neighboring subunits. A comparison of the structures of the oxygenated form and the partially unliganded form provides structural insight into proton-coupled cooperativity (Bohr effect) and ligand-induced transitions. Two histidine residues are assumed to be primarily associated with the Bohr effect. With regard to the ligand-induced cooperativity, a novel quaternary rotation mechanism is proposed to exist at the interface region of the dimer subassembly. Interactions among conserved residues Arg E10, His F3, Gln F7, and Val E11, together with the bending motion of the heme molecules, appear to be essential for quaternary rearrangement.     

Regulation of Notch signaling by dynamic changes in the precision of S3 cleavage of Notch-1

Intramembrane proteolysis by presenilin-dependent γ-secretase produces the Notch intracellular cytoplasmic domain (NCID) and Alzheimer disease-associated amyloid-β. Here, we show that upon Notch signaling the intracellular domain of Notch-1 is cleaved into two distinct types of NICD species due to diversity in the site of S3 cleavage. Consistent with the N-end rule, the S3-V cleavage produces stable NICD with Val at the N terminus, whereas the S3-S/S3-L cleavage generates unstable NICD with Ser/Leu at the N terminus. Moreover, intracellular Notch signal transmission with unstable NICDs is much weaker than that with stable NICD. Importantly, the extent of endocytosis in target cells affects the relative production ratio of the two types of NICD, which changes in parallel with Notch signaling. Surprisingly, substantial amounts of unstable NICD species are generated from the Val→Gly and the Lys→Arg mutants, which have been reported to decrease S3 cleavage efficiency in cultured cells. Thus, we suggest that the existence of two distinct types of NICD points to a novel aspect of the intracellular signaling and that changes in the precision of S3 cleavage play an important role in the process of conversion from extracellular to intracellular Notch signaling.     

Preparation of subunits of flavocytochromes c derived from Chlorobium limicola f. thiosulfatophilum and Chromatium vinosum.

The subunits of Chlorobium limicala f. thiosulfatophilum cytochrome c-553 and of Chromatium vinosum cytochrome c-552 have been obtained. Chlorobium cytochrome c-553 is split into the cytochrome and flavoprotein subunits by treatment with trichloroacetic acid; after the cytochrome is precipitated by 1–2% trichloroacetic acid, the cytochrome subunit is extractable with buffer, while the flavoprotein subunit is not dissolved. The subunits of Chromatium cytochrome c-552 can not be obtained by the trichloroacetic acid-treatment. The flavoprotein subunit of the Chromatium cytochrome is obtained by isoelectric focusing in the presence of 6 M urea and 1% mercaptoethanol, while the cytochrome subunit is prepared by gel filtration in the presence of 6 M urea with Sephacryl S-200. Molecular weights of the cytochrome and flavoprotein subunits from the Chlorobium cytochrome are 11,000 and 47,000, respectively, while those of the two subunits from the Chromatium cytochrome are 21,000 and 46,000, respectively. The molecule of each flavocytochrome c is composed of one molecule of each of the cytochrome and flavoprotein subunits.     

Selective Inhibition by Ethanol of Mitochondrial Calcium Influx Mediated by Uncoupling Protein-2 in Relation to N-Methyl-D-Aspartate Cytotoxicity in Cultured Neurons

Background

We have shown the involvement of mitochondrial uncoupling protein-2 (UCP2) in the cytotoxicity by N-methyl-D-aspartate receptor (NMDAR) through a mechanism relevant to the increased mitochondrial Ca²⁺ levels in HEK293 cells with acquired NMDAR channels. Here, we evaluated pharmacological profiles of ethanol on the NMDA-induced increase in mitochondrial Ca²⁺ levels in cultured murine neocortical neurons.

Methodology/Principal Findings

In neurons exposed to glutamate or NMDA, a significant increase was seen in mitochondrial Ca²⁺ levels determined by Rhod-2 at concentrations of 0.1 to 100 µM. Further addition of 250 mM ethanol significantly inhibited the increase by glutamate and NMDA in Rhod-2 fluorescence, while similarly potent inhibition of the NMDA-induced increase was seen after exposure to ethanol at 50 to 250 mM in cultured neurons. Lentiviral overexpression of UCP2 significantly accelerated the increase by NMDA in Rhod-2 fluorescence in neurons, without affecting Fluo-3 fluorescence for intracellular Ca²⁺ levels. In neurons overexpressing UCP2, exposure to ethanol resulted in significantly more effective inhibition of the NMDA-induced increase in mitochondrial free Ca²⁺ levels than in those without UCP2 overexpression, despite a similarly efficient increase in intracellular Ca²⁺ levels irrespective of UCP2 overexpression. Overexpression of UCP2 significantly increased the number of dead cells in a manner prevented by ethanol in neurons exposed to glutamate. In HEK293 cells with NMDAR containing GluN2B subunit, more efficient inhibition was similarly induced by ethanol at 50 and 250 mM on the NMDA-induced increase in mitochondrial Ca²⁺ levels than in those with GluN2A subunit. Decreased protein levels of GluN2B, but not GluN2A, subunit were seen in immunoprecipitates with UCP2 from neurons with brief exposure to ethanol at concentrations over 50 mM.

Conclusions/Significance

Ethanol could inhibit the interaction between UCP2 and NMDAR channels to prevent the mitochondrial Ca²⁺ incorporation and cell death after NMDAR activation in neurons.     

Identification of OS-2 MAP kinase-dependent genes induced in response to osmotic stress, antifungal agent fludioxonil, and heat shock in Neurospora crassa

Two-component signal transduction comprising of OS-1 (histidine kinase), OS-4 (MAPKK kinase), OS-5 (MAPK kinase), and OS-2 (MAP kinase) plays an important role in osmotic regulation in Neurospora crassa. To identify the genes regulated downstream of OS-2 MAP kinase, quantitative real-time RT-PCR analysis was conducted in selected genes based on Hog1 MAP kinase regulated genes in yeast. In response to osmotic stress and fludioxonil, expression of six genes that for glycerol synthesis (gcy-1, gcy-3, and dak-1), gluconeogenesis (fbp-1 and pck-1), and catalase (ctt-1) was activated in the wild-type strain, but not in the os-2 mutant. A heat shock treatment also induced their expression in the same way. Consisting with the gene expression, the enzyme activity of glycerol dehydrogenase, but not glycerol-3-phosphate dehydrogenase, was increased in response to osmotic stress and fludioxonil in the wild-type strain. OS-2 was phosphorylated by the OS-1 cascade in response to relatively low osmotic stress and fludioxonil. However, OS-2 phosphorylation by heat shock and a higher osmotic stress was found in the os-1 mutant normally but not in the os-4 and os-5 mutants. These results suggested that non-OS-1 signaling activates OS-2 in an OS-4-dependent manner in such conditions.     

Possible involvement of mitochondrial uncoupling protein-2 in cytotoxicity mediated by acquired N-methyl-d-aspartate receptor channels

We have previously shown the possible involvement of mitochondrial membrane potential disruption in the mechanisms underlying the neurotoxicity seen after activation of N-methyl-d-aspartate (NMDA) receptors (NMDAR) in primary cultured rat hippocampal neurons. In this study, we attempted to demonstrate a pivotal role of mitochondrial uncoupling protein-2 (UCP2) as a determinant of the NMDA neurotoxicity by using acquired NMDAR channels artificially orchestrated in HEK293 cells. In cells with overexpression of UCP2, immunoreactive UCP2 was exclusively detected at intracellular locations stained with the mitochondrial marker MitoTracker. In cells with acquired NMDAR channels, exposure to either NMDA or the calcium ionophore A23187 similarly led to a significant increase in cytosolic Ca(2+) levels determined by Fluo-3 imaging irrespective of the overexpression of UCP2. By contrast, NMDA, but not A23187, was significantly more effective in increasing mitochondrial Ca(2+) levels determined by Rhod-2 fluorescence imaging in cells transfected with NMDAR subunit and UCP2 expression vectors than in those without UCP2 overexpression. Overexpression of UCP2 significantly increased the number of cells stained with propidium iodide in cultures with acquired NMDAR channels, but failed to significantly affect that in cells exposed to A23187. Immunocytochemical and immunoprecipitation analyses similarly revealed the possible interaction between GluN1 subunit and UCP2 in HEK293 cells with acquired NMDAR channels and UCP2 overexpression. These results suggest that UCP2 could play a role as a determinant of the neurotoxicity mediated by NMDAR through a mechanism related to the unidentified interaction with the essential GluN1 subunit toward modulation of mitochondrial Ca(2+) levels in neurons.     

Foamy Virus Envelope Protein Is a Substrate for Signal Peptide Peptidase-like 3 (SPPL3)

Signal peptide peptidase (SPP), its homologs, the SPP-like proteases SPPL2a/b/c and SPPL3, as well as presenilin, the catalytic subunit of the γ-secretase complex, are intramembrane-cleaving aspartyl proteases of the GxGD type. In this study, we identified the 18-kDa leader peptide (LP18) of the foamy virus envelope protein (FVenv) as a new substrate for intramembrane proteolysis by human SPPL3 and SPPL2a/b. In contrast to SPPL2a/b and γ-secretase, which require substrates with an ectodomain shorter than 60 amino acids for efficient intramembrane proteolysis, SPPL3 cleaves mutant FVenv lacking the proprotein convertase cleavage site necessary for the prior shedding. Moreover, the cleavage product of FVenv generated by SPPL3 serves as a new substrate for consecutive intramembrane cleavage by SPPL2a/b. Thus, human SPPL3 is the first GxGD-type aspartyl protease shown to be capable of acting like a sheddase, similar to members of the rhomboid family, which belong to the class of intramembrane-cleaving serine proteases.     

External morphology of the posterior end, the "opisthosoma", of the beard worm Oligobrachia mashikoi (Pogonophora)

The entire length of the beard worm, Oligobrachia mashikoi (Pogonophora), including the posterior end, the "opisthosoma" was collected successfully. This species is exclusive to Tsukumo Bay in Ishikawa Prefecture, Japan. Although the portion preceding the opisthosoma was similar to a fine filament, it abruptly assumed a shape similar to a shovel and appeared to be composed of many segmental structures. The number of segments exceeded 50. The dorsal side of the opisthosoma differed from that of the ventral side in morphology. The opisthosoma was equipped with 4 lines of setae arranged longitudinally and a sucker on the tip. When considering the fact that the Family Oligobrachiidae is the most primitive group of pogonophores, the external morphology of the opisthosoma is interesting as it may be reminiscent of the ancestral condition. This is the first report of the opisthosoma in Oligobrachiidae.