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Differential Assembly Properties of Escherichia coli FtsZ and Mycobacterium tuberculosis FtsZ: An Analysis Using Divalent CalciumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The assembly of FtsZ is considered to be a fundamental process during the bacterial cytokinesis. We used several complimentary techniques to probe the assembly of recombinant Escherichia coli FtsZ (EcFtsZ) and Mycobacterium tuberculosis FtsZ (MtbFtsZ) proteins in vitro. As documented earlier, EcFtsZ was found to polymerize at much faster rate than MtbFtsZ. Interestingly, we found that MtbFtsZ produced higher sedimentable polymerized mass than that of the EcFtsZ and that MtbFtsZ formed thicker protofilaments than that of the EcFtsZ. The results indicated that the EcFtsZ polymers are more labile than the MtbFtsZ polymers. Fu...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Jaiswal, R., Panda, D. Tags: Regular Papers Source Type: journals

Association of a Novel Mitochondrial Protein M19 with Mitochondrial NucleoidsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have identified a novel mitochondrial protein, termed M19, by proteomic analysis of mitochondrial membrane proteins from HeLa cells. M19 is highly conserved among vertebrates, and possesses no homologous domains with other known proteins. By northern and western blotting, mouse M19 was shown to be expressed in various tissues, and to be especially abundant in the brain. Human M19 (hM19) is present in mitochondria, and protease-protection experiment showed it to be sublocalized in the matrix space. Carboxy-terminally tagged hM19 appeared as spotted signals within mitochondria and co-localized with signals arising from mi...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Sumitani, M., Kasashima, K., Ohta, E., Kang, D., Endo, H. Tags: Regular Papers Source Type: journals

Expression, Purification and Characterization of Soluble Recombinant Periostin Protein Produced by Escherichia coliEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Periostin is a matricellular protein participating in the tissue remodelling of damaged cardiac tissue after acute myocardial infarction and of the periodontal ligament in mice. However, further studies on the periostin protein have been limited by the intrinsic difficulty of purifying this protein produced in Escherichia coli due to its insolubility. Here, we demonstrate the expression of recombinant periostin protein with high solubility and monodispersity in E. coli. Periostin is composed of an amino-terminal EMI domain, a tandem repeat of 4 fas1 domains (RD1-4), and a carboxyl-terminal region (CTR). We expressed the RD...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Takayama, I., Kii, I., Kudo, A. Tags: Regular Papers Source Type: journals

Importance of Polarisome Proteins in Reorganization of Actin Cytoskeleton at Low pH in Saccharomyces cerevisiaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study further investigated the components involved in this actin reorganization at pH 3.0. Gene deletions on the Sln1p branch of the HOG pathway completely blocked actin depolarization, suggesting that Hog1p activation depends mainly on the osmosensor Sln1p. The protein-synthesis inhibitor cycloheximide did not influence the time course of actin depolarization, suggesting that the depolarization is a direct effect of the HOG pathway. Deletion of the scaffolding protein, Spa2p, or the Spa2p-interacting protein Pea2p, markedly inhibited the depolarization, and further deletion of the formin protein, Bni1p, notably delay...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Motizuki, M., Xu, Z. Tags: Regular Papers Source Type: journals

Differential Usage of the Transport Systems for Folic acid and Methotrexate in Normal Human T-Lymphocytes and Leukemic CellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this study was to investigate different transport systems for FA and MTX, and to delineate their uptake mechanism in MOLT4, K562, Hut78 leukemia cells and normal human T cells. In MOLT4, uptake of MTX was higher than FA, similar to that of K562, Hut78 and normal T cells. In MOLT4 cells, MTX uptake was maximum at pH 7.4 whereas FA uptake was maximum at pH 4.5. Uptake of FA and MTX was significantly inhibited by anions, suggesting anion-dependent transport system. FA uptake was found to be energy dependent whereas MTX uptake was energy independent. RT-PCR and immunofluorescence results demonstrated the prese...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Biswal, B. K., Verma, R. S. Tags: Regular Papers Source Type: journals

Angiotensin II Stimulates KLF5 Phosphorylation and its Interaction with c-Jun Leading to Suppression of p21 Expression in Vascular Smooth Muscle CellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Krüppel-like factor 5 (KLF5) and c-Jun are involved in angiotensin II (Ang II)-induced cell proliferation and play an important role in p21 expression. But the direct and functional implications of KLF5 and c-Jun in regulating p21 expression in vascular smooth muscle cells (VSMCs) are unclear. Here, we show that Ang II upregulated KLF5 and c-Jun expression and inhibited p21 expression in VSMCs, and silencing of KLF5 expression by KLF5-specific small interfering RNA (siRNA) neutralized the inhibitory effects of Ang II on p21 expression. Exposure of VSMCs to Ang II rapidly and strongly stimulated KLF5 phosphorylation, w...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: He, M., Han, M., Zheng, B., Shu, Y.-N., Wen, J.-K. Tags: Regular Papers Source Type: journals

Production of n-octanoyl-modified Ghrelin in Cultured Cells Requires Prohormone Processing Protease and Ghrelin O-acyltransferase, as well as n-octanoic AcidEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ghrelin was originally isolated from rat stomach as an endogenous ligand for the GH secretagogue receptor. The major active form of ghrelin is a 28-amino acid peptide modified by an n-octanoic acid on the serine 3 residue, and this lipid modification is essential for the biological activity of ghrelin. However, it is not clear whether prohormone convertase (PC) and ghrelin O-acyltransferase (GOAT) are the minimal requirements for synthesis of acyl-modified ghrelin in cultured cells. By using three cultured cell lines, TT, AtT20 and COS-7, in which the expression levels of processing proteases and GOAT vary, we examined the...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Takahashi, T., Ida, T., Sato, T., Nakashima, Y., Nakamura, Y., Tsuji, A., Kojima, M. Tags: Regular Papers Source Type: journals

NMR Solution Structure of HP0827 (O25501_HELPY) from Helicobacter pylori: Model of the Possible RNA-binding SiteEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The HP0827 protein is an 82-residue protein identified as a putative ss-DNA-binding protein 12RNP2 Precursor from Helicobacter pylori. Here, we have determined 3D structure of HP0827 using Nuclear Magnetic Resonance. It has a ferredoxin-like fold, β1–1–β2–β3–2–β4 (; -helix and β; β-sheet) and ribonucleoprotein (RNP) motifs which are thought to be important in RNA binding. By using structural homologues search and analyzing electrostatic potential of surface, we could compared HP0827 with other RNA-binding proteins (sex-lethal, T-cell restricted intracellular antig...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Jang, S.-B., Ma, C., Lee, J.-Y., Kim, J.-H., Park, S. J., Kwon, A.-R., Lee, B.-J. Tags: Regular Papers Source Type: journals

Mycolyltransferase from Mycobacterium leprae Excludes Mycolate-containing Glycolipid SubstratesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Trehalose dimycolate (TDM) is a major surface-exposed mycolyl glycolipid that contributes to the hydrophobic cell wall architecture of mycobacteria. Nevertheless, because of its potent adjuvant functions, pathogenic mycobacteria appear to have evolved an evasive maneuver to down-regulate TDM expression within the host. We have shown previously that Mycobacterium tuberculosis (M.tb) and Mycobacterium avium (M.av), replace TDM with glucose monomycolate (GMM) by borrowing host-derived glucose as an alternative substrate for the FbpA mycolyltransferase. Mycobacterium leprae (M.le), the causative microorganism of human leprosy,...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Nakao, H., Matsunaga, I., Morita, D., Aboshi, T., Harada, T., Nakagawa, Y., Mori, N., Sugita, M. Tags: Regular Papers Source Type: journals

Importance of the Hydrogen Bonding Network Including Asp52 for Catalysis, as Revealed by Asn59 Mutant Hen Egg-white LysozymesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the catalysis of sugar hydrolysis by hen egg-white lysozyme, Asp52 is thought to stabilize the reaction intermediate. This residue is involved in the well-ordered hydrogen bonding network including Asn46, Asp48, Ser50 and Asn59 on the anti-parallel β-sheet, designated as a ‘platform’, on which the substrate sugar sits. To reveal the role of this hydrogen bonding network in the hydrolysis, we characterized Asn59 mutants by biochemical and crystallographic studies. Surprisingly, the introduction of only a methylene group by the Asn59Gln mutation markedly reduced the bacteriolytic activity and abolished th...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Ose, T., Kuroki, K., Matsushima, M., Maenaka, K., Kumagai, I. Tags: Regular Papers Source Type: journals

Mutational Analysis of the GTP-binding Motif of FlhF which Regulates the Number and Placement of the Polar Flagellum in Vibrio alginolyticusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Precise regulation of the number and placement of flagella is critical for the mono-flagellated bacterium Vibrio alginolyticus to swim efficiently. We previously proposed a model in which the putative GTPase FlhF determines the polar location and generation of the flagellum, the putative ATPase FlhG interacts with FlhF to prevent FlhF from localizing to the pole, and thus FlhG negatively regulates the flagellar number in V. alginolyticus cells. To investigate the role of the GTP-binding motif of FlhF, we generated a series of alanine-replacement mutations at the positions that are highly conserved among homologous proteins...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Kusumoto, A., Nishioka, N., Kojima, S., Homma, M. Tags: Regular Papers Source Type: journals

Characterization and Application of Carbohydrate-binding Modules of {beta}-1,3-xylanase XYL4Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
β-1,3-Xylanase from Vibrio sp. strain AX-4 (XYL4) is a modular enzyme composed of an N-terminal catalytic module belonging to glycoside hydrolase family 26 and two putative carbohydrate-binding modules (CBMs) belonging to family 31 in the C-terminal region. To investigate the functions of these three modules, five deletion mutants lacking individual modules were constructed. The binding assay of these mutants showed that a repeating unit of the CBM was a non-catalytic β-1,3-xylan-binding module, while the catalytic module per se was not likely to contribute to the binding activity when insoluble β-1,3-xylan ...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Kiyohara, M., Sakaguchi, K., Yamaguchi, K., Araki, T., Ito, M. Tags: Regular Papers Source Type: journals

Vimentin Intermediate Filaments as a Template for Silica Nanotube PreparationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Organic compounds are used as templates to regulate the morphology of inorganic nanostructures. In the present study, we used intermediate filaments (IFs), the major cytoskeleton component of most eukaryotic cells, as a template for hollow silica nanotube preparation. Sol–gel polymerization of tetraethoxysilane proceeded preferentially on the surface of IFs assembled from vimentin protein in vitro, resulting in silica-coated fibres. After removing IFs by calcination, electron microscopy revealed hollow silica nanotubes several micrometers long, with outer diameters of 35–55 nm and an average inner diameter of 1...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Gohara, R., Liu, D., Nakashima, K., Takasaki, Y., Ando, S. Tags: Rapid Communications Source Type: journals

Vascular Endothelium Expresses 3-Mercaptopyruvate Sulfurtransferase and Produces Hydrogen SulfideEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Hydrogen sulfide (H2S) has been recognized as a smooth muscle relaxant. Cystathionine -lyase, which is localized to smooth muscle, is thought to be the major H2S-producing enzyme in the thoracic aorta. Here we show that 3-mercaptopyruvate sulfurtransferase (3MST) and cysteine aminotransferase (CAT) are localized to vascular endothelium in the thoracic aorta and produce H2S. Both 3MST and CAT were localized to endothelium. Lysates of vascular endothelial cells produced H2S from cysteine and -ketoglutarate. The present study provides a new insight into the production and release of H2S as a smooth muscle relaxant from vascul...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Shibuya, N., Mikami, Y., Kimura, Y., Nagahara, N., Kimura, H. Tags: Rapid Communications Source Type: journals

Functional Enhancement by Single-residue Substitution of Streptomyces coelicolor A3(2) H+-translocating PyrophosphataseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
H+-translocating pyrophosphatase converts energy from hydrolysis of pyrophosphate to active H+ transport across biomembranes. Mutational analysis of Streptomyces coelicolor A3(2) enzyme revealed that amino acid substitution of Phe-388 and Ala-514 altered the enzyme activity. Both residues are located at the interface between the transmembrane domains and cytosolic loops, in which the catalytic domain exists. Systematic amino acid substitution was carried out using the Escherichia coli heterologous expression system. Two of the 38 mutant enzymes, F388Y and A514S, showed a high ratio of H+-pump to substrate hydrolysis withou...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Hirono, M., Maeshima, M. Tags: Rapid Communications Source Type: journals

Quality Control Against Misfolded Proteins in the Cytosol: A Network for Cell SurvivalEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Misfolded proteins are toxic to cells and the accumulation of toxic species can lead to protein misfolding diseases, such as neurodegenerative disorders. The toxicity of misfolded proteins is thought to result from the presence of exposed hydrophobic surfaces, which mediate unnecessary binding to normal proteins, interrupting essential interactions between cellular proteins. To prevent toxicity, quality control systems monitor protein folding and remove misfolded species in the cytosol. Molecular chaperones recognize and mask hydrophobic surfaces of misfolded monomers, and transfer them to the ubiquitin–proteasome sy...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Kubota, H. Tags: JB Minireview-Quality Control of the Cellular Protein Systems Source Type: journals

Disulphide Bond Formation in the Intermembrane Space of MitochondriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Proteins of the intermembrane space (IMS) of mitochondria fulfil crucial functions in cellular processes, such as transport of proteins and metal ions, ATP production and apoptotic cell death. All IMS proteins are synthesized in the cytosol and then transported across the mitochondrial outer membrane. A subset of these proteins contains disulphide bonds. For their import into the IMS, they employ a disulphide relay system, made up of two essential proteins, Mia40/Tim40 and the flavin-dependent sulfhydryl-electron transferase Erv1. The disulphide relay system introduces disulphide bonds in substrate proteins triggering thei...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Deponte, M., Hell, K. Tags: JB Minireview-Quality Control of the Cellular Protein Systems Source Type: journals

Disulfide Bond Formation System in Escherichia coliEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The biological kingdoms have evolved elaborate systems that ensure the catalysis of protein disulfide bond (dsb) formation in the cell. Coexisting in the periplasm of Escherichia coli are the DsbA–DsbB disulfide-introducing and DsbC–DsbD disulfide-isomerizing pathways, which promote the oxidative folding of secreted proteins. Recent structural studies of DsbB have illuminated conformational dynamics involved in the effective oxidation of the extremely reduction-prone oxidase, DsbA, as well as the structure of the reaction centre involved in protein Dsb formation de novo in conjunction with ubiquinone. Extensive...
Source: Journal of Biochemistry - November 4, 2009 Category: Biochemistry Authors: Inaba, K. Tags: JB Minireview-Quality Control of the Cellular Protein Systems Source Type: journals

Photocontrol of Calmodulin Interaction with Target Peptides using Azobenzene DerivativeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Calmodulin (CaM), a physiologically important Ca2+-binding protein, participates in numerous cellular regulatory processes. It is dumbbell shaped and contains two globular domains connected by a short -helix. Each of the globular domains has two Ca2+-binding sites, the EF hands. CaM undergoes a conformational change upon binding to Ca2+, which enables it to bind to specific proteins for specific responses. Here, we successfully photocontrolled CaM binding to its target peptide using the photochromic compound N-(4-phenylazophenyl) maleimide (PAM), which reversibly undergoes cis–trans isomerization upon ultraviolet (UV...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Shishido, H., Yamada, M. D., Kondo, K., Maruta, S. Tags: Regular Paper Source Type: journals

Identification of Radicals Formed in the Reaction Mixture of Bovine Kidney Microsomes with NADPHEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In order to explore the mechanism of myoglobinuric renal toxicity, detection and identification of free radicals was performed for the reaction mixtures of bovine kidney microsomes. EPR measurements showed prominent signals for the control reaction mixture containing 2.0 mg protein/ml bovine kidney microsomes, 5 mM NADPH, 0.1 M 4-POBN and 29 mM phosphate buffer (pH 7.4). Addition of myoglobin (Mb) to the control reaction mixture resulted in increase of EPR peak height. The result indicates that Mb enhances the radical formation. An HPLC–EPR measurement showed three peaks with retention times of 29.4 min (P1), 32.4 mi...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Kumamoto, K., Hirai, T., Kishioka, S., Iwahashi, H. Tags: Regular Paper Source Type: journals

Glutamate64 to Glycine Substitution in G1 {beta}-bulge of Ubiquitin Impairs Function and Stabilizes Structure of the ProteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ubiquitin is a globular protein with a highly conserved sequence. Sequence conservation and compact structure make it an ideal protein for structure–function studies. One of the atypical secondary structural features found in ubiquitin is a parallel G1 β-bulge. Glutamate at 64 is the first residue of this β-bulge and the third residue in a type II turn. However, glycine is seen in these positions in several proteins. To understand the effects of substitution of glutamate64 by glycine on the structure, stability and function of ubiquitin, mutant UbE64G has been constructed and characterized in Saccharomyces ...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Mishra, P., Volety, S., Rao, Ch. M., Prabha, C. R. Tags: Regular Paper Source Type: journals

Structural Insights into the Enzymatic Mechanism of Serine Palmitoyltransferase from Sphingobacterium multivorumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study provides the structural evidence that directly supports our proposed mechanism of the substrate synergism in the SPT reaction. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Ikushiro, H., Islam, M. M., Okamoto, A., Hoseki, J., Murakawa, T., Fujii, S., Miyahara, I., Hayashi, H. Tags: Regular Paper Source Type: journals

Membrane Localization of Protein-Tyrosine Phosphatase 1B is Essential for its Activation of Sterol Regulatory Element-Binding Protein-1 Gene Expression and Consequent HypertriglyceridaemiaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we further investigated the physiological importance of membrane localization of PTP1B in vivo. We found that transient liver-specific overexpression of wild-type PTP1B (PTP1B-WT) using adenovirus-mediated gene transfer was associated with hypertriglyceridaemia and enhanced hepatic SREBP-1 gene expression in mice. However, overexpression of the C-terminal truncated PTP1B (PTP1BCT) failed to increase hepatic SREBP-1 expression or serum triglyceride levels, despite causing insulin resistance. Our results indicate that activation of PTP1B in the liver could induce hypertriglyceridaemia and that anchoring of PTP...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Ugi, S., Shi, K., Nishio, Y., Shimizu, S., Guo, B., Sekine, O., Ikeda, K., Egawa, K., Yoshizaki, T., Nagai, Y., Koya, D., Takada, T., Torii, R., Kimura, H., Kashiwagi, A., Maegawa, H. Tags: Regular Paper Source Type: journals

Crystal Structure of Hypothetical Protein HP0062 (O24902_HELPY) from Helicobacter pylori at 1.65 A ResolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The HP0062 gene encodes a small acidic protein of 86 amino acids with a theoretical pI of 4.6. The crystal structure of hypothetical protein HP0062 from Helicobacter pylori has been determined at 1.65 Å by molecular-replacement method. The crystallographic asymmetric unit contains dimer, in which HP0062 monomer folds into a helix–hairpin–helix structure. The two protomers are primarily held together by extensive hydrophobic interactions in an antiparallel arrangement, forming a four helix bundle. Aromatic residues located at a or g position in the heptad leucine zipper are not major contributor required f...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Jang, S.-B., Kwon, A.-R., Son, W.-S., Park, S. J., Lee, B.-J. Tags: Regular Paper Source Type: journals

Enzymatic Characterization and Comparison of Various Poaceae UDP-GlcA 4-Epimerase IsoformsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study demonstrates that although members of the plant UGlcAE isoforms are highly conserved, the in vitro enzymatic activity of specific Poaceae isoform(s) may be regulated differently by specific nucleotide or nucleotide sugar. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Gu, X., Wages, C. J., Davis, K. E., Guyett, P. J., Bar-Peled, M. Tags: Regular Paper Source Type: journals

Changes in the Conformation of the Vsr Endonuclease Amino-terminal Domain Accompany DNA CleavageEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In Escherichia coli, T/G mismatches arising from deamination of 5-methylcytosine to thymine are converted to CG base pairs by the very short patch (VSP) repair pathway. DNA Polymerase I removes and resynthesizes the mismatched T starting from a 5'-nick created by the Vsr endonuclease. We used limited trypsinolysis to probe conformational changes in the N-terminal domain of Vsr in response to DNA binding, DNA cleavage and interaction with the polymerase. Our data show that the domain becomes trypsin resistant only under conditions that allow DNA cleavage, while interaction with the polymerase restores trypsin sensitivity. W...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Polosina, Y. Y., Cupples, C. G. Tags: Regular Paper Source Type: journals

Insights into the Enzyme-Substrate Interaction in the Norovirus 3C-like ProteaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Glu54 residue of the norovirus 3C-like protease was implicated in proteolysis as a third-member carboxylate of the catalytic triad. The E54L mutant protease cleaved the sequence 133LSFE/AP between the 3B and 3C regions of norovirus polyprotein, but did not cleave the sequence 198ATSE/GK between the 3A and 3B. The 3BC junction mutation (3B-L133A or 3B-F135S) hampered the cleavage by the E54L protease, whereas the 3AB junction mutation (3A-A198L, S200F) allowed the E54L protease to digest. These results indicate that the E54L mutant protease is a substrate-specificity mutant and requires large hydrophobic amino acid resi...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Someya, Y., Takeda, N. Tags: Regular Paper Source Type: journals

Overexpression of Plk3 causes Morphological Change and Cell Growth Suppression in Ras Pathway-activated CellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To unravel the growth inhibition mechanism of Polo-like kinase 3 (Plk3), the effect of overexpression of Plk3 was examined in 293T cells. Cell rounding, changes in actin organization and cellular detachment were induced by Plk3 transfection in a kinase activity-dependent manner. Although apoptosis was not observed, Plk3 overexpression suppressed cellular growth in a long-term colony-forming assay. Because both Plk3 and Ras affect F-actin organization, the effect of co-transfection of Plk3 and Ras was evaluated. Adhesion was synergistically lost by co-transfection of these two genes, compared with transfection of Plk3 alone...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Iida, M., Sasaki, T., Komatani, H. Tags: Regular Paper Source Type: journals

Polymyxin B Identified as an Inhibitor of Alternative NADH Dehydrogenase and Malate: Quinone Oxidoreductase from the Gram-positive Bacterium Mycobacterium smegmatisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Tuberculosis is the leading cause of death due to a single infectious agent in the world and the emergence of multidrug-resistant strains prompted us to develop new drugs with novel targets and mechanism. Here, we screened a natural antibiotics library with Mycobacterium smegmatis membrane-bound dehydrogenases and identified polymyxin B (cationic decapeptide) and nanaomycin A (naphtoquinone derivative) as inhibitors of alternative NADH dehydrogenase [50% inhibitory concentration (IC50) values of 1.6 and 31 µg/ml, respectively] and malate: quinone oxidoreductase (IC50 values of 4.2 and 49 µg/ml, respectively). K...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Mogi, T., Murase, Y., Mori, M., Shiomi, K., Omura, S., Paranagama, M. P., Kita, K. Tags: Regular Paper Source Type: journals

RNA Interference Targeted to the Conserved Dimerization Initiation Site (DIS) of HIV-1 Restricts Virus Escape MutationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Short hairpin RNAs (shRNA) targeting viral or cellular genes can effectively inhibit human immunodeficiency virus type 1 (HIV-1) replication. This inhibition, however, may induce mutations in the targeted gene, leading to rapid escape from the shRNA-induced inhibition. We generated a lymphoid cell line that stably expressed a 19-bp shRNA targeting a well-conserved dimerization initiation site (DIS) of HIV-1, which strongly inhibited viral replication, thereby delaying virus escape. Furthermore, treatment of HIV-1 infection with DIS- and vif-shRNA combination therapy resulted in superior anti-viral responses compared to vif...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Sugiyama, R., Habu, Y., Ohnari, A., Miyano-Kurosaki, N., Takaku, H. Tags: Regular Paper Source Type: journals

Dynamic Expression of Peptidylarginine Deiminase 2 in Human Monocytic Leukaemia THP-1 Cells During Macrophage DifferentiationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Peptidylarginine deiminases (PADs) consist of five enzymes which are widely distributed in human and rodent tissues. The two types of enzymes are found in human peripheral blood cells; PAD4 mainly in granulocytes and monocytes and PAD2 in lymphocytes and macrophages. Little is known about the regulation of PAD expression in macrophages. Here, we report that PAD2 is expressed in human monocytic leukaemia THP-1 cells during differentiation into macrophages by 12-O-tetradecanoylphorbol-13-acetate. During this differentiation, the levels of PAD2 mRNA and protein increased concomitantly, indicating the transcriptional regulatio...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Hojo-Nakashima, I., Sato, R., Nakashima, K., Hagiwara, T., Yamada, M. Tags: Regular Paper Source Type: journals

Protein Quality Control in Chloroplasts: A Current Model of D1 Protein Degradation in the Photosystem II Repair CycleEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The chloroplast originated from endosymbiosis of photosynthetic bacteria. Thus, mechanisms essential for chloroplast biogenesis/homeostasis (protein synthesis, import from cytosol, assembly, and degradation) are predominantly governed by prokaryotic systems. Among these, the quality control system is crucial, because light energy constantly damages photosynthetic proteins and excessive light often limits plant growth by irreversibly inactivating the photosynthetic apparatuses. Here, we overview prokaryotic proteases (FtsH and Deg) which are two enzymes that play critical roles in this system. We particularly focus on Photo...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Kato, Y., Sakamoto, W. Tags: JB Minireviews-Quality Control of the Cellular Protein Systems Source Type: journals

Protein Quality Control in MitochondriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mitochondria are crucial for both life and death of eukaryotic cells. Compromised mitochondrial integrity has severe cellular consequences and is linked to senescence and neurodegenerative disorders in humans. To maintain the functionality of proteins in mitochondria, quality-control mechanisms including signal transduction pathways counteracting mitochondrial stress have evolved. A network of molecular chaperones and proteases monitors protein integrity and prevents accumulation of damaged proteins. In this review, the current knowledge of elaborate defence strategies within mitochondria is summarized. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Tatsuta, T. Tags: JB Minireviews-Quality Control of the Cellular Protein Systems Source Type: journals

Quality Control of Cytoplasmic Membrane Proteins in Escherichia coliEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In Escherichia coli, like in any organism, the cytoplasmic (inner or plasma) membrane proteins play essential roles in transport of small and macro-molecules as well as in transmission of environmental signals across the membrane. Their quality control is critically important for growth and survival of the cell. However, our knowledge about the players and mechanisms of the system is still limited. This review focuses on proteolytic quality control of membrane proteins, in which two membrane-integrated proteases, FtsH and HtpX, with different modes of action, play central roles. The prohibitin family membrane protein compl...
Source: Journal of Biochemistry - October 6, 2009 Category: Biochemistry Authors: Akiyama, Y. Tags: JB Minireviews-Quality Control of the Cellular Protein Systems Source Type: journals

Storage of Gangliosides GM2 and Fucosyl GM1 in the Kidney of MCC Strain of Mastomys (Praomys coucha)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Previously, we histochemically examined the kidney of the MCC strain of mastomys (Praomys coucha) and found the storage of gangliosides. In the present studies, the lipid-bound sialic acid content of gangliosides in the MCC kidney was about 9- to 14-fold higher than that of the control (MWC strain). In the MCC kidney, sialic acids of male gangliosides were composed of N-acetylneuraminic acid at 91.5%; sialic acids of female gangliosides, however, were composed almost entirely of N-glycolylneuraminic acid. TLC of gangliosides showed that the MCC kidney contained four abundant gangliosides (two gangliosides each in males and...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Takimoto, K., Kawamura, N., Kasama, T. Tags: Regular Paper Source Type: journals

Identification and Characterization of a Selective Radioligand for ELOVL6Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ELOVL6, a member of the elongation of very long-chain fatty acids (ELOVL) family, has recently been identified as the rate-limiting enzyme for the elongation of palmitoyl-CoA. ELOVL6 deficient mice are protected from high-fat diet induced insulin resistance, suggesting that ELOVL6 might be a promising target for the treatment of metabolic disorders. Despite the increasing interest in Elovl6 as a therapeutic target, the lack of chemical tools for this enzyme has limited further elucidation of the biochemical and pharmacological properties of ELOVL6. We have identified Compound-A, a potent inhibitor for ELOVL6, by screening ...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Shimamura, K., Takahashi, H., Kitazawa, H., Miyamoto, Y., Nagumo, A., Tang, C., Dean, D., Nagase, T., Sato, N., Tokita, S. Tags: Regular Paper Source Type: journals

CDK11p58 Phosphorylation of PAK1 Ser174 Promotes DLC2 Binding and Roles on Cell Cycle ProgressionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CDK11p58, a CDK11 family Ser/Thr kinase, is a G2/M specific protein and contributed to regulation of cell cycle, transcription and apoptotic signal transduction. Recently, CDK11p58 has been reported to exert important functions in mitotic process, such as the regulation of bipolar spindle formation and sister chromatid cohesion. Here, we identified p21 activated kinase 1 (PAK1) as a new CDK11p58 substrate and we mapped a new phosphorylation site of Ser174 on PAK1. By mutagenesis, we created PAK1174A and PAK1174E, which mimic the dephosphorylated and phosphorylated form of PAK1; further analysis showed PAK1174E could be rec...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Kong, X., Gan, H., Hao, Y., Cheng, C., Jiang, J., Hong, Y., Yang, J., Zhu, H., Chi, Y., Yun, X., Gu, J. Tags: Regular Paper Source Type: journals

Subtilisin-like Proprotein Convertase PACE4 is Required for Skeletal Muscle DifferentiationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Most growth factors stimulate myoblast proliferation and prevent differentiation, whereas insulin-like growth factors (IGFs) promote myoblast differentiation through the phosphatidylinositol 3-kinase (PI3K) pathway. Subtilisin-like proprotein convertases (SPCs) are involved in cell growth and differentiation via activation of pro-growth factors. However, the role of SPCs in myogenesis remains poorly understood. Here we show that PACE4, a member of the SPC family, plays a critical role in myogenic differentiation of C2C12 cells. PACE4 mRNA levels increased markedly during myogenesis, whereas the expression of other member o...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Yuasa, K., Masuda, T., Yoshikawa, C., Nagahama, M., Matsuda, Y., Tsuji, A. Tags: Regular Paper Source Type: journals

Molecular Cloning, Expression and Characterization of A Novel Mouse SULT6 Cytosolic SulfotransferaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
By searching the mouse EST database, we identified a novel mouse cytosolic sulfotransferase (SULT) cDNA (RIKEN cDNA 2410078J06). Sequence analysis revealed that this new SULT belongs to the cytosolic SULT6 gene family. The recombinant form of this newly identified SULT, designated SULT6B1, was expressed using the pGEX-4T-1 glutathione S-transferase fusion system and purified from transformed BL21 Escherichia coli cells. Purified mouse SULT6B1 exhibited sulfonating activity toward thyroxine and bithionol among a variety of endogenous and xenobiotic compounds tested as substrates. pH optimum of purified mouse SULT6B1 was det...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Takahashi, S., Sakakibara, Y., Mishiro, E., Kouriki, H., Nobe, R., Kurogi, K., Yasuda, S., Liu, M.-C., Suiko, M. Tags: Regular Paper Source Type: journals

Crystallographic and Mutational Analyses of Substrate Recognition of Endo-{alpha}-N-acetylgalactosaminidase from Bifidobacterium longumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Endo--N-acetylgalactosaminidase (endo--GalNAc-ase), a member of the glycoside hydrolase (GH) family 101, hydrolyses the O-glycosidic bonds in mucin-type O-glycan between -GalNAc and Ser/Thr. Endo--GalNAc-ase from Bifidobacterium longum JCM1217 (EngBF) is highly specific for the core 1-type O-glycan to release the disaccharide Galβ1-3GalNAc (GNB), whereas endo--GalNAc-ase from Clostridium perfringens (EngCP) exhibits broader substrate specificity. We determined the crystal structure of EngBF at 2.0 Å resolution and performed automated docking analysis to investigate possible binding modes of GNB. Mutational analy...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Suzuki, R., Katayama, T., Kitaoka, M., Kumagai, H., Wakagi, T., Shoun, H., Ashida, H., Yamamoto, K., Fushinobu, S. Tags: Regular Paper Source Type: journals

Siccanin Rediscovered as a Species-Selective Succinate Dehydrogenase InhibitorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To identify antibiotics targeting to respiratory enzymes, we carried out matrix screening of a structurally varied natural compound library with Pseudomonas aeruginosa membrane-bound respiratory enzymes. We identified a succinate dehydrogenase inhibitor, siccanin (IC50, 0.9 µM), which is a potent antibiotic against some pathogenic fungi like Trichophyton mentagrophytes and inhibits their mitochondrial succinate dehydrogenase. We found that siccanin was effective against enzymes from P. aeruginosa, P. putida, rat and mouse mitochondria but ineffective or less effective against Escherichia coli, Corynebacterium glutami...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Mogi, T., Kawakami, T., Arai, H., Igarashi, Y., Matsushita, K., Mori, M., Shiomi, K., Omura, S., Harada, S., Kita, K. Tags: Regular Paper Source Type: journals

TRAF-Interacting Protein with a Forkhead-Associated Domain B (TIFAB) Is a Negative Regulator of the TRAF6-Induced Cellular FunctionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Tumour necrosis factor receptor-associated factor (TRAF)-interacting protein with a forkhead-associated domain (TIFA) activates TRAF6 to induce NF-B activation. TIFA-related protein, TIFAB, is highly expressed in the spleen and inhibits TIFA-mediated TRAF6 activation. However, little is known about cell types that express TIFAB and its function in those cells. Here, we show that TIFAB is mainly expressed in B cells rather than T cells in the spleen and that the expression level was much higher in dendritic cells (DCs) and macrophages than that in splenic lymphocytes. TIFAB expression was downregulated when B cells, DCs or ...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Matsumura, T., Kawamura-Tsuzuku, J., Yamamoto, T., Semba, K., Inoue, J.-i. Tags: Regular Paper Source Type: journals

Human C21orf63 is a Heparin-binding ProteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Human C21orf63 is a type-1 transmembrane protein of hitherto unknown function, with two repeats of putative ‘galactose-binding lectin domains'. By using glycan microarray analysis and other assays, we found that human C21orf63 interacts with heparin and to a lesser extent with heparan sulphate. The C-terminal galactose-binding lectin domain of C21orf63 is necessary for heparin binding. The inability of other human proteins with galactose-binding lectin domains to interact with heparin suggests that heparin binding is a unique property of C21orf63. Results of real-time polymerase chain reaction and tissue immunostaini...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Mitsunaga, K., Harada-Itadani, J., Shikanai, T., Tateno, H., Ikehara, Y., Hirabayashi, J., Narimatsu, H., Angata, T. Tags: Regular Paper Source Type: journals

Domain-dependent Interaction of Eukaryotic Initiation Factor eIF4A for Binding to Middle and C-terminal Domains of eIF4GEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The interactions of recombinant human eIF4A (4A) and its N- and C-terminal side domains (AN and AC, respectively) with the middle- and C-terminal-domain-linked fragment (GMC) of eIF4G and its middle and C-terminal domains (GM and GC, respectively) were investigated by surface plasmon resonance (SPR) analysis and isothermal titration calorimetry (ITC). It is remarkable that the kinetic parameter-dependent SPR profile observed for the 4A–GMC pair was quite different from the steady affinity profiles of the 4A–GM/GC pairs, suggesting the simultaneous contribution of the middle and C-terminal domains of eIF4G for t...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Fujita, Y., Oe, M., Tutsumino, T., Morino, S., Imataka, H., Tomoo, K., Ishida, T. Tags: Regular Paper Source Type: journals

FT-IR Spectroscopic Studies on the Molecular Mechanism for Substrate Specificity/Activation of Medium-Chain Acyl-CoA DehydrogenaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The interactions of acyl-CoA with medium-chain acyl-CoA dehydrogenases (MCADs) reconstituted with artificial FADs—i.e. 8-CN-, 7,8-Cl2-, 8-Cl-, 8-OCH3- and 8-NH2-FAD—were investigated by UV-visible absorption and FT-IR measurements. Although 8-NH2-FAD-MCAD did not oxidize acyl-CoA the wavelength of the absorption maximum of the flavin was altered by acyl-CoAs binding. Thus, 8-NH2-FAD-MCAD is one of the attractive materials for investigation of enzyme–substrate (ES) interaction in ES complex (the complex of oxidized MCAD with acyl-CoA). FT-IR difference spectra between non-labelled and [1-13C]-labelled acyl...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Nishina, Y., Sato, K., Tamaoki, H., Setoyama, C., Miura, R., Shiga, K. Tags: Regular Paper Source Type: journals

Fatty Acids Bound to Recombinant Tear Lipocalin and Their Role in Structural StabilizationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A variant of human tear lipocalin was expressed in Escherichia coli, and the bound fatty acids were analysed by gas chromatography, mass spectroscopy and nuclear magnetic resonance spectroscopy. Five major fatty acids were identified as hexadecanoic acid (palmitic acid, PA), cis-9-hexadecenoic acid (palmitoleic acid), 9,10-methylenehexadecanoic acid, cis-11-octadecenoic acid (vaccenic acid) and 11,12-methyleneoctadecanoic acid (lactobacillic acid). The composition of the bound fatty acids was similar to the fatty acid composition of E. coli extract, suggesting that the binding affinities are similar for these fatty acids. ...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Tsukamoto, S., Fujiwara, K., Ikeguchi, M. Tags: Regular Paper Source Type: journals

RecX is Involved In the Switch between DNA Damage Response and Normal Metabolism in D. radioduransEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Apart from inhibiting RecA activity through protein–protein interactions, Deinococcus radiodurans RecX inhibits the expression of RecA and two other anti-oxidant proteins. To identify the repertoire of proteins regulated by RecX, comparative proteomic studies were undertaken on a wild-type strain (R1) and recX null mutant (RecX–). Two-dimensional electrophoresis followed by MALDI-TOF identification revealed 35 differentially expressed proteins, including 12 up-regulated and 23 down-regulated proteins in the mutant. The 12 up-regulated proteins are DNA repair proteins, stress response proteins, and metabolism-re...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Sheng, D., Jao, J., Li, M., Xu, P., Zhang, J. Tags: Regular Paper Source Type: journals

DNA Helicase Activity in Purified Human RECQL4 ProteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Human RECQL4 protein was expressed in insect cells using a baculovirus protein expression system and it was purified to near homogeneity. The protein sedimented at a position between catalase (230 kDa) and ferritin (440 kDa) in glycerol gradient centrifugation, suggesting that it forms homo-multimers. Activity to displace annealed 17-mer oligonucleotide in the presence of ATP was co-sedimented with hRECQL4 protein. In ion-exchange chromatography, both DNA helicase activity and single-stranded DNA-dependent ATPase activity were co-eluted with hRECQL4 protein. The requirements of ATP and Mg for the helicase activity were dif...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Suzuki, T., Kohno, T., Ishimi, Y. Tags: Regular Paper Source Type: journals

NMR Structure of the Heterodimer of Bem1 and Cdc24 PB1 Domains from Saccharomyces CerevisiaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bem1 and Cdc24 of the budding yeast Saccharomyces cerevisiae interact with each other through PB1–PB1 heterodimer formation to regulate the establishment of cell polarity. Here we present the tertiary structure of the heterodimer of Bem1 and Cdc24 PB1 domains determined by NMR spectroscopy. To avoid ambiguity in the NMR spectral analysis, we first prepared a mutant of the Cdc24 PB1 domain that had truncated loops. The mutant provided well dispersed spectra without spectral overlapping, thus allowing unambiguous spectral assignments for structure determination. We confirmed that the loop deletion-mutant was quite simi...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Ogura, K., Tandai, T., Yoshinaga, S., Kobashigawa, Y., Kumeta, H., Ito, T., Sumimoto, H., Inagaki, F. Tags: Regular Paper Source Type: journals

Nestin Serves as a Prosurvival Determinant that is Linked to the Cytoprotective Effect of Epidermal Growth Factor in Rat Vascular Smooth Muscle CellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nestin is an intermediate filament protein mainly expressed in muscle and neural progenitors. Recently, we reported that nestin is expressed in rat vascular smooth muscle cells (VSMCs), disappears after serum-deprivation and then is re-expressed again following EGF stimulation. As the function of nestin in VSMCs remains unknown, its anti-apoptotic function was investigated in this study. We first showed that cell viability of nestin-depleted cells following H2O2 treatments decreased by nestin RNAi. Further DNA laddering analysis and flow cytometry results demonstrated that this loss of cell viability was mediated through a...
Source: Journal of Biochemistry - August 25, 2009 Category: Biochemistry Authors: Huang, Y.-L., Wu, C.-M., Shi, G.-Y., Wu, G. C.-C., Lee, H., Jiang, M.-J., Wu, H.-L., Yang, H.-Y. Tags: Regular Paper Source Type: journals