Self-propagating amyloid as a critical regulator for diverse cellular functions
Amyloids are β-sheet-rich fibrillar protein aggregates characterized by structural properties of self-propagation and strong resistance to detergent and proteinase. Although a number of causative proteins for neurodegenerative disorders are known to undergo amyloid formation, recent studies have revealed that amyloids may also play beneficial roles in cells. Cellular processes that could be regulated by amyloids are diverse and include translational regulation, programmed cell death and protein storage. Yeast prions of Mod5 and Mot3, non-Mendelian extra-chromosomal factors, also show amyloid-like biophysical propertie...
Source: Journal of Biochemistry - May 27, 2014 Category: Biochemistry Authors: Sugiyama, S., Tanaka, M. Tags: JB Reviews Source Type: research
The CD47-SIRP{alpha} signalling system: its physiological roles and therapeutic application
Signal regulatory protein α (SIRPα), also known as SHPS-1/BIT/ CD172a, is an immunoglobulin superfamily protein that binds to the protein tyrosine phosphatases SHP-1 and SHP-2 through its cytoplasmic region. CD47, another immunoglobulin superfamily protein, is a ligand for SIRPα, with the two proteins constituting a cell–cell communication system (the CD47–SIRPα signalling system). SIRPα is particularly abundant in the myeloid-lineage hematopoietic cells such as macrophages or dendritic cells (DCs), whereas CD47 is expressed ubiquitously. Interaction of CD47 (on red blood cells) wi...
Source: Journal of Biochemistry - May 27, 2014 Category: Biochemistry Authors: Murata, Y., Kotani, T., Ohnishi, H., Matozaki, T. Tags: JB Reviews Source Type: research
Biochemical characterization of endonuclease V from the hyperthermophilic archaeon, Pyrococcus furiosus
Endonuclease V (Endo V) is a DNA repair enzyme that recognizes deoxyinosine and cleaves the second phosphodiester bond on the 3' side of the deaminated base lesion. A database search revealed the presence of homologous genes for Endo V in most archaeal species, but the absence in some methanogenic species. We cloned a gene encoding the sequence homologous to Escherichia coli Endo V from the genome of the hyperthermophilic euryarchaeon, Pyrococcus furiosus and purified gene product (PfuEndoV) to homogeneity. In vitro characterization showed that PfuEndoV possesses specific endonuclease activity for the deoxyinosine-containi...
Source: Journal of Biochemistry - April 27, 2014 Category: Biochemistry Authors: Kiyonari, S., Egashira, Y., Ishino, S., Ishino, Y. Tags: Regular Papers Source Type: research
Defining membrane spanning domains and crucial membrane-localized acidic amino acid residues for K+ transport of a Kup/HAK/KT-type Escherichia coli potassium transporter
We examined the topology of Kup from Escherichia coli. Results from the reporter fusion and cysteine labeling assays support a model with 12 membrane-spanning domains. A model for proton-coupled K+ uptake mediated by Kup has been proposed. However, this study did not show any stimulation of Kup activity at low pH and any evidence of involvement of the three His in Kup-mediated K+ uptake. Moreover, replacement of all four cysteines of Kup with serine did not abolish K+ transport activity. To gain insight on crucial residues of Kup-mediated K+ uptake activity, we focused on acidic residues in the predicted external and trans...
Source: Journal of Biochemistry - April 27, 2014 Category: Biochemistry Authors: Sato, Y., Nanatani, K., Hamamoto, S., Shimizu, M., Takahashi, M., Tabuchi-Kobayashi, M., Mizutani, A., Schroeder, J. I., Souma, S., Uozumi, N. Tags: Regular Papers Source Type: research
A novel processing system of sterol regulatory element-binding protein-1c regulated by polyunsaturated fatty acid
In this study, the proteolytic processing of SREBP-1 and -2 was examined by transfection studies of cDNA-encoding mutants in which all the known cleavage sites were disrupted. In cultured cells, sterol-regulated SREBP-2 processing was completely eliminated by mutation of cleavage sites. In contrast, the corresponding SREBP-1c mutants as well as wild type exhibited large amounts of cleaved products in the nuclear extracts from culture cells and murine liver in vivo. The nuclear form of the mutant SREBP-1c was induced by delipidated condition and suppressed by eicosapentaenoic acid, an n-3 PUFA, but not by sterols. This nove...
Source: Journal of Biochemistry - April 27, 2014 Category: Biochemistry Authors: Nakakuki, M., Kawano, H., Notsu, T., Imada, K., Mizuguchi, K., Shimano, H. Tags: Regular Papers Source Type: research
Evaluation of the stability of an SR398/GroES chaperonin complex
The stability of an SR398/GroES chaperonin complex was examined. As was expected, based on the finding of previous studies, the SR398/GroES complex was extremely stable in the presence of an excess amount of free adenosine 5'-[-thio]triphosphate (ATPS) or adenosine 5'-(β,-imido)triphosphate (AMPPNP). However, the complex was not stable in the absence of nucleotides. These results indicate that ATPS and AMPPNP repeatedly associated to and dissociated from the complex in a non-cooperative manner. This nucleotide exchange did not induce the dissociation of GroES and substrate from SR398, suggesting the importance of the ...
Source: Journal of Biochemistry - April 27, 2014 Category: Biochemistry Authors: Ishino, S., Kawata, Y., Ikegami, T., Matsuzaki, K., Hoshino, M. Tags: Regular Papers Source Type: research
Calcium-dependent structural changes in human reticulocalbin-1
In this study, we established a new bacterial expression and purification procedure for hRCN1. We observed that hRCN1 binds Ca2+ in a cooperative manner and the Ca2+ binding caused an increase in the α-helix content of hRCN1. On the other hand, hRCN1 did not change the structure with Mg2+ loading. hRCN1 is a monomeric protein, and its overall structure became more compact upon Ca2+ binding, as revealed by gel-filtration column chromatography and small-angle X-ray scattering. This is the first report of conformational changes in the CREC family upon Ca2+ binding. Our data suggest that CREC family member interactions w...
Source: Journal of Biochemistry - April 27, 2014 Category: Biochemistry Authors: Suzuki, N., Ban, S., Itoh, E., Chen, S., Imai, F. L., Sawano, Y., Miyakawa, T., Tanokura, M., Yonezawa, N. Tags: Regular Papers Source Type: research
Roles of mitochondrial ubiquitin ligase MITOL/MARCH5 in mitochondrial dynamics and diseases
Accumulating evidence indicate physiological significance of mitochondrial dynamics such as mitochondrial fusion and division, the dynamic movement of mitochondria along microtubules and interaction of mitochondria with the endoplasmic reticulum. A disruption in mitochondrial dynamics leads to a functional deterioration of mitochondria, resulting in a variety of diseases including neurodegenerative disorders. We previously identified a mitochondrial ubiquitin ligase MITOL/MARCH5, which belongs to the membrane-associated RING-CH E3 ubiquitin ligase (MARCH) family (also called MARCH5). MITOL plays an important role in the re...
Source: Journal of Biochemistry - April 27, 2014 Category: Biochemistry Authors: Nagashima, S., Tokuyama, T., Yonashiro, R., Inatome, R., Yanagi, S. Tags: JB Review Source Type: research
Phase separation of myelin sheath in Triton X-114 solution: predominant localization of the 21.5-kDa isoform of myelin basic protein in the lipid raft-associated domain
In this study, we have developed a new method for phase separation of myelin. The non-ionic detergent Triton X-114 is used to solubilize myelin sheath which then undergoes phase separation to yield four fractions. The lipid raft-associated proteins and lipids in each fraction were analysed by immunoblotting and lipid analysis, respectively. The present method gives two lipid raft-enriched fractions, one of them was found to contain only lipid raft-associated galactocerebroside and cholesterol as the major lipids. The 21.5-kDa MBP isoforms (21.5 MBP), both unphosphorylated and phosphorylated, were exclusively contained in t...
Source: Journal of Biochemistry - March 26, 2014 Category: Biochemistry Authors: Uruse, M., Yamamoto, M., Sugawa, M., Matsuura, K., Sato, Y., Seiwa, C., Watanabe, K., Aiso, S., Asou, H. Tags: Regular Papers Source Type: research
Photocontrol of the mitotic kinesin Eg5 using a novel S-trityl-L-cysteine analogue as a photochromic inhibitor
In this study, we synthesized a novel photochromic S-trityl-l-cysteine analogue, 4-(N-(2-(N-acetylcysteine-S-yl) acetyl) amino)-4'- (N-(2-(N-(triphenylmethyl)amino)acetyl)amino)azobenzene (ACTAB), composed of a trityl group, azobenzene and N-acetyl-l-cysteine, which exhibits cis–trans photoisomerization in order to photocontrol the function of Eg5. ACTAB exhibited cis–trans photoisomerization upon alternating irradiation at two different wavelengths in the visible range, 400 and 480 nm. ACTAB induced reversible changes in the inhibitory activity of ATPase and motor activities correlating with the cis–tran...
Source: Journal of Biochemistry - March 26, 2014 Category: Biochemistry Authors: Ishikawa, K., Tohyama, K., Mitsuhashi, S., Maruta, S. Tags: Regular Papers Source Type: research
A long non-coding RNA transcribed from conserved non-coding sequences contributes to the mouse prolyl oligopeptidase gene activation
Prolyl oligopeptidase (POP) is a multifunctional protease which is involved in many physiological events, but its gene regulatory mechanism is poorly understood. To identify novel regulatory elements of the POP gene, we compared the genomic sequences at the mouse and human POP loci and found six conserved non-coding sequences (CNSs) at adjacent intergenic regions. From these CNSs, four long non-coding RNAs (lncRNAs) were transcribed and the expression pattern of one (lncPrep+96kb) was correlated with that of POP. lncPrep+96kb was transcribed as two forms due to the different transcriptional start sites and was localized at...
Source: Journal of Biochemistry - March 26, 2014 Category: Biochemistry Authors: Matsubara, S., Kurihara, M., Kimura, A. P. Tags: Regular Papers Source Type: research
Overexpression of autotaxin, a lysophosphatidic acid-producing enzyme, enhances cardia bifida induced by hypo-sphingosine-1-phosphate signaling in zebrafish embryo
Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are second-generation lysophospholipid mediators that exert multiple biological functions through their own cognate receptors. They are both present in the blood stream, activate receptors with similar structures (endothelial differentiation gene receptors), have similar roles in the vasculature and are vasoactive. However, it is unclear whether these lysophospholipid mediators cross-talk downstream of each receptor. Here, we provide in vivo evidence that LPA signaling counteracted S1P signaling. When autotaxin (Atx), an LPA-producing enzyme, was overexpressed i...
Source: Journal of Biochemistry - March 26, 2014 Category: Biochemistry Authors: Nakanaga, K., Hama, K., Kano, K., Sato, T., Yukiura, H., Inoue, A., Saigusa, D., Tokuyama, H., Tomioka, Y., Nishina, H., Kawahara, A., Aoki, J. Tags: Regular Papers Source Type: research
Loss of Tsc1 accelerates malignant gliomagenesis when combined with oncogenic signals
Glioblastomas frequently harbour genetic lesions that stimulate the activity of mammalian target of rapamycin complex 1 (mTORC1). Loss of heterozygosity of tuberous sclerosis complex 1 (TSC1) or TSC2, which together form a critical negative regulator of mTORC1, is also seen in glioblastoma; however, it is not known how loss of the TSC complex affects the development of malignant gliomas. Here we investigated the role of Tsc1 in gliomagenesis in mice. Tsc1 deficiency up-regulated mTORC1 activity and suppressed the proliferation of neural stem/progenitor cells (NSPCs) in a serial neurosphere-forming assay, suggesting that Ts...
Source: Journal of Biochemistry - March 26, 2014 Category: Biochemistry Authors: Yamada, D., Hoshii, T., Tanaka, S., Hegazy, A. M., Kobayashi, M., Tadokoro, Y., Ohta, K., Ueno, M., Ali, M. A. E., Hirao, A. Tags: Regular Papers Source Type: research
Calcineurin-NFAT activation and DSCR-1 auto-inhibitory loop: how is homoeostasis regulated?
Calcineurin-nuclear factor of activated T cells (NFAT) signalling plays a critical role not only in the immune and nervous systems, but also in cardiovascular development and pathological endothelial cell activation during angiogenesis or inflammation. Studies in NFAT-null mice demonstrated that there is high redundancy between functions of the different NFAT family members. Deletion of only one NFAT causes mild phenotypes, but compound deletions of multiple NFAT family members leads to severe abnormalities in multiple organ systems. Genome-wide transcription analysis revealed that many NFAT target genes are related to cel...
Source: Journal of Biochemistry - March 26, 2014 Category: Biochemistry Authors: Minami, T. Tags: JB Review Source Type: research
Construction of functional fragments of the cytoplasmic loop with the C-terminal region of PomA, a stator component of the Vibrio Na+ driven flagellar motor
In this study, to investigate the function of the cytoplasmic domain of PomA, we constructed a series of fragments that flank the cytoplasmic loop of PomA between the second and third transmembrane (TM) domains (A-loop) and the C-terminal region, and expressed them in Escherichia coli together with PomA and PotB (a chimeric protein of PomB and MotB). We observed a dominant-negative effect of one PomA fragment on motility. We confirmed that these PomA fragments localized both in the membrane fraction and in the cytoplasmic fraction, and induced bacterial growth delay. Effect of additional point and deletion mutations into t...
Source: Journal of Biochemistry - March 2, 2014 Category: Biochemistry Authors: Onoue, Y., Abe-Yoshizumi, R., Gohara, M., Kobayashi, S., Nishioka, N., Kojima, S., Homma, M. Tags: Regular Papers Source Type: research
