5-Aminoimidazole-4-carboxyamide-1-{beta}-D-ribofranoside stimulates the rat enhancer of split- and hairy-related protein-2 gene via atypical protein kinase C lambda
In this study, we examined an issue of whether the SHARP-2 gene expression is regulated by AICAR via the AMPK. AICAR increased the level of SHARP-2 mRNA in H4IIE cells. Whereas an AMPK inhibitor, compound-C, had no effects on the AICAR-induction, inhibitors for both phosphoinositide 3-kinase (PI 3-K) and protein kinase C (PKC) completely diminished the effects of AICAR. Western blot analyses showed that AICAR rapidly activated atypical PKC lambda (aPKC). In addition, when a dominant negative form of aPKC was expressed, the induction of SHARP-2 mRNA level by AICAR was inhibited. Calcium ion is not required for the activatio...
Source: Journal of Biochemistry - March 20, 2016 Category: Biochemistry Authors: Komatsu, Y., Yanagisawa, Y., Moriizumi, M., Tsuchiya, Y., Yokouchi, H., Otsuka, H., Aoyagi, M., Tsukada, A., Kanai, Y., Haneishi, A., Takagi, K., Asano, K., Ono, M., Tanaka, T., Tomita, K., Yamada, K. Tags: Regular Papers Source Type: research
Limitation of tuning the antibody-antigen reaction by changing the value of pH and its consequence for hyperthermia
Distribution of the isoelectric point (pI) was calculated for the hypervariable regions of Fab fragments of the antibody molecules, which structure is annotated in the structural antibody database SabDab. The distribution is consistent with the universal for all organisms dividing the proteome into two sets of acidic and basic proteins. It shows the additional fine structure in a form of the narrow-sized peaks of pI values. This is an explanation why a small change of the environmental pH can have a strong effect on the antibody-antigen affinity. To show this, a typical enzyme-linked immunospecific assay experiment for tes...
Source: Journal of Biochemistry - March 20, 2016 Category: Biochemistry Authors: Mleczko, J., Defort, A., Kozioł, J. J., Nguyen, T. T., Mironczyk, A., Zapotoczny, B., Nowak-Jary, J., Gronczewska, E., Marc, M., Dudek, M. R. Tags: Regular Papers Source Type: research
Exploring the phosphoproteome profiles during Xenopus egg activation by calcium stimulation using a fully automated phosphopeptide purification system
To explore the phosphoproteome profiles during Xenopus egg activation by Ca2+-stimulation, an automated phosphopeptide purification system involving a titania column was improved by introducing 4-step elution with phosphate buffers. The number of detected phosphopeptides in the tryptic digest of a Xenopus egg cytosol fraction on mass spectrometry (MS) was increased 1.5-fold and the percentage of multiply phosphorylated peptides increased from 17 to 24% with introduction of the 4-step elution method. Phosphopeptides were purified by the improved method from tryptic digests of cytosol fractions of Xenopus eggs without and wi...
Source: Journal of Biochemistry - March 20, 2016 Category: Biochemistry Authors: Kanno, T., Furukawa, K., Horigome, T. Tags: Regular Papers Source Type: research
Evolutionary well-conserved region in the signal peptide of parathyroid hormone-related protein is critical for its dual localization through the regulation of ER translocation
Parathyroid hormone-related protein (PTHrP) has two different targeting signals: an N-terminal signal peptide for the endoplasmic reticulum (ER) targeting and an internal nuclear localization signal. The protein not only functions as a secretory protein, but is also found in the nucleus and/or nucleolus under certain conditions. PTHrP signal peptide is less hydrophobic than most signal peptides mainly due to its evolutionarily well-conserved region (QQWS). The substitution of four tandem leucine residues for this conserved region resulted in a significant inhibition of the signal peptide cleavage. At the same time, proport...
Source: Journal of Biochemistry - March 20, 2016 Category: Biochemistry Authors: Amaya, Y., Nakai, T., Miura, S. Tags: Regular Papers Source Type: research
Regulation of bone metabolism by Wnt signals
Wnt ligands play a central role in the development and homeostasis of various organs through β-catenin-dependent and -independent signalling. The crucial roles of Wnt/β-catenin signals in bone mass have been established by a large number of studies since the discovery of a causal link between mutations in the low-density lipoprotein receptor-related protein 5 (Lrp5) gene and alternations in human bone mass. The activation of Wnt/β-catenin signalling induces the expression of osterix, a transcription factor, which promotes osteoblast differentiation. Furthermore, this signalling induces the expression of oste...
Source: Journal of Biochemistry - March 20, 2016 Category: Biochemistry Authors: Kobayashi, Y., Uehara, S., Udagawa, N., Takahashi, N. Tags: JB Reviews Source Type: research
Phospho-ubiquitin: upending the PINK-Parkin-ubiquitin cascade
Mitochondria with decreased membrane potential are characterized by defects in protein import into the matrix and impairments in high-efficiency synthesis of ATP. These low-quality mitochondria are marked with ubiquitin for selective degradation. Key factors in this mechanism are PTEN-induced putative kinase 1 (PINK1, a mitochondrial kinase) and Parkin (a ubiquitin ligase), disruption of which has been implicated in predisposition to Parkinson’s disease. Previously, the clearance of damaged mitochondria had been thought to be the end result of a simple cascading reaction of PINK1–Parkin–ubiquitin. However...
Source: Journal of Biochemistry - March 20, 2016 Category: Biochemistry Authors: Matsuda, N. Tags: JB Reviews Source Type: research
Possible role of a histidine residue in the substrate specificity of yeast D-aspartate oxidase
d-Aspartate oxidase (DDO) catalyzes the oxidative deamination of acidic d-amino acids, whereas neutral and basic d-amino acids are substrates of d-amino acid oxidase (DAO). DDO of the yeast Cryptococcus humicola (ChDDO) has much higher substrate specificity to d-aspartate, but the structural features that confer this specificity have not been elucidated. A three-dimensional model of ChDDO suggested that a histidine residue (His56) in the active site might be involved in the unique substrate specificity, possibly through the interaction with the substrate side chain in the active site. His56 mutants with several different a...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Takahashi, S., Shimada, K., Nozawa, S., Goto, M., Abe, K., Kera, Y. Tags: Regular Papers Source Type: research
DNA-binding activity of rat DNA topoisomerase II {alpha} C-terminal domain contributes to efficient DNA catenation in vitro
DNA topoisomerase IIα (topo IIα) is an essential enzyme for resolution of DNA topologies arising in DNA metabolic reactions. In proliferating cells, topo II activities of DNA catenation or decatenation are required for condensation of chromosomes and segregation of chromatids. Recent studies suggest that the C-terminal domain (CTD) of human topo IIα is required for localization to mitotic chromosomes. Here, we show that the CTD of topo IIα is also associated with efficient DNA catenation in vitro, based on comparison of wild-type (WT) rat topo IIα and its deletion mutants. Unlike WT, the CTD t...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Kawano, S., Kato, Y., Okada, N., Sano, K., Tsutsui, K., Tsutsui, K. M., Ikeda, S. Tags: Regular Papers Source Type: research
Induction of intranuclear membranes by overproduction of Opi1p and Scs2p, regulators for yeast phospholipid biosynthesis, suggests a mechanism for Opi1p nuclear translocation
In the yeast Saccharomyces cerevisiae, the expression of phospholipid biosynthetic genes is suppressed by the Opi1p negative regulator. Opi1p enters into the nucleoplasm from the nuclear membrane to suppress the gene expression under repressing conditions. The binding of Opi1p to the nuclear membrane requires an integral membrane protein, Scs2p and phosphatidic acid (PA). Although it is demonstrated that the association of Opi1p with membranes is affected by PA levels, how Opi1p dissociates from Scs2p is unknown. Here, we found that fluorescently labelled Opi1p accumulated on a perinuclear region in an Scs2p-dependent mann...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Masuda, M., Oshima, A., Noguchi, T., Kagiwada, S. Tags: Regular Papers Source Type: research
Sequence and structure analysis of a mirror tRNA located upstream of the cytochrome oxidase I mRNA in mouse mitochondria
RNA fragments corresponding to the mirror tRNA that is located upstream of the cytochrome oxidase I (COXI) gene in the mouse mitochondrial genome were found in the sequences obtained from the mouse brain by the next generation sequencing. RNA fragments corresponding to the 5' terminal of COXI mRNA were also found and it was suggested that the precursor of the COXI mRNA is processed at three residues upstream of the first AUG codon. The mirror tRNA fragment has poly(A) in its 3' terminal and variable 5' terminal, suggesting that this RNA is produced during the 5' processing of COXI mRNA. Secondary structure prediction and N...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Okui, S., Ushida, C., Kiyosawa, H., Kawai, G. Tags: Regular Papers Source Type: research
Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus
The crystal structures of the wild type and catalytic mutant Asp-312->Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (β/α)8-barrel and two β-domains located at both N- and C-terminal ends. The isomaltohexaose–complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (–4 to +2) in the cat...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Suzuki, N., Kishine, N., Fujimoto, Z., Sakurai, M., Momma, M., Ko, J.-A., Nam, S.-H., Kimura, A., Kim, Y.-M. Tags: Regular Papers Source Type: research
Contiguous 2,2,4-triamino-5(2H)-oxazolone obstructs DNA synthesis by DNA polymerases {alpha}, {beta}, {eta}, {iota}, {kappa}, REV1 and Klenow Fragment exo-, but not by DNA polymerase {zeta}
In this study, we analysed translesion synthesis (TLS) across two contiguous Oz molecules (OzOz) using Klenow Fragment exo– (KF exo–) and DNA polymerases (Pols) α, β, , , , and REV1. We found that KF exo– and Pols α, β, and REV1 inserted one nucleotide opposite the 3' Oz of OzOz and stalled at the subsequent extension, and that Pol incorporated no nucleotide. Pol only inefficiently elongated the primer up to full-length across OzOz; the synthesis of most DNA strands stalled at the 3' or 5' Oz of OzOz. Surprisingly, however, Pol efficiently extended the primer up to full-length a...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Suzuki, M., Kino, K., Kawada, T., Oyoshi, T., Morikawa, M., Kobayashi, T., Miyazawa, H. Tags: Regular Papers Source Type: research
Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus
Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus (Tt) and Geobacillus kaustophilus (Gk) were determined. For TtPurM, the maximum resolution was 2.2 Å and the space group was P21212 with four dimers in an asymmetric unit. For GkPurM, the maximum resolution was 2.2 Å and the space group was P21212 with one monomer in asymmetric unit. The biological unit is dimer for both TtPurM and GkPurM and the dimer structures were similar to previously determined structures of PurM in general. For TtPurM, ~50 residues at the amino terminal were disordered in...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Kanagawa, M., Baba, S., Watanabe, Y., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Sampei, G.-i., Kawai, G. Tags: Regular Papers Source Type: research
Determination of cleavage site of Reelin between its sixth and seventh repeat and contribution of meprin metalloproteases to the cleavage
Reelin is a secreted glycoprotein whose function is regulated by proteolysis. One of the specific cleavage sites of Reelin, called C-t, is located approximately between the sixth and seventh Reelin repeat but its exact site was unknown. We here show that a metalloprotease present in the culture supernatant of cerebellar granular neurons (CGN) cleaves Reelin between Ala2688 and Asp2689. A Reelin mutant in which Asp2689 is replaced by Lys (Reelin-DK) is resistant to C-t cleavage by culture supernatant of CGN. From biochemical characteristics and the cleavage site preference, meprin α and meprin β were suggested ca...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Sato, Y., Kobayashi, D., Kohno, T., Kidani, Y., Prox, J., Becker-Pauly, C., Hattori, M. Tags: Regular Papers Source Type: research
GroEL of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31 exhibits GroES and ATP-independent refolding activity
The nitrogen-fixing cyanobacterium, Anabaena L-31 has two Hsp60 proteins, 59 kDa GroEL coded by the second gene of groESL operon and 61 kDa Cpn60 coded by cpn60 gene. Anabaena GroEL formed stable higher oligomer (>12-mer) in the presence of K+ and prevented thermal aggregation of malate dehydrogenase (MDH). Using three protein substrates (MDH, All1541 and green fluorescent protein), it was found that the refolding activity of Anabaena GroEL was lower than that of Escherichia coli GroEL, but independent of both GroES and ATP. This correlated with in vivo data. GroEL exhibited ATPase activity which was enhanced in the pre...
Source: Journal of Biochemistry - February 22, 2016 Category: Biochemistry Authors: Potnis, A. A., Rajaram, H., Apte, S. K. Tags: Regular Papers Source Type: research
