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Journal of Biochemistry

Tokuhiro Chano, Sofia Avnet
RAB39A is a Rab small GTPase that localizes at distinct subcellular compartments and regulates intracellular membrane trafficking pathways in vertebrate cells. RAB39A interacts with various molecules and modulates vesicular trafficking that regulates multiple biological pathways such as neuronal differentiation and/or autophagy. Among these pathways are Hippo and Notch signalings, microtubular organization, and mitophagy/autophagy. Although RAB39A has never been studied in cancer biology, it has been recently shown to promote cancer stemness and tumorigenesis...
April 10, 2018: Journal of Biochemistry
Takamichi Sato, Ryo Takano, Kazuhiro Tokunaka, Kan Saiga, Arihiro Tomura, Hidemitsu Sugihara, Toshihiko Hayashi, Yasutada Imamura, Makoto Morita
Expression of type IV collagen α1 chain in non-triple helical form, NTH α1(IV), is observed in cultured human cells, human placenta, and rabbit tissues. Biological functions of NTH α1(IV) are most likely to be distinct from type IV collagen, since their biochemical characteristics are quite different. To explore the biological functions of NTH α1(IV), we prepared some anti-NTH α1(IV) antibodies. In the course of characterization of these antibodies, one antibody, #141, bound to a polypeptide of 140 kDa in size in addition to NTH α1(IV)...
April 5, 2018: Journal of Biochemistry
Kar Yan Soh, Jacelyn Mei San Loh, Thomas Proft
Streptococcus pyogenes nuclease A (SpnA) and streptococcal 5' nucleosidase A (S5nA) are two recently described virulence factors from the human pathogen S. pyogenes. In-vitro studies have shown that SpnA is a nuclease that cleaves ssDNA and dsDNA, including the DNA backbone of neutrophil extracellular traps. S5nA was shown to hydrolyse AMP and ADP, but not ATP, to generate the immunomodulatory molecule adenosine. S5nA also generates the macrophage-toxic deoxyadenosine from dAMP. However, detailed in vivo studies of the two enzymes have been hampered by difficulties with using current animal models for this exclusive human pathogen...
April 5, 2018: Journal of Biochemistry
Tomoya Uchida, Masaaki Kanemori
Heat shock protein 70 (Hsp70) chaperone systems consist of Hsp70, Hsp40, and a nucleotide-exchange factor and function to help unfolded proteins achieve their native conformations. Typical Hsp40s assume a homodimeric structure and have both chaperone and cochaperone activity. The dimeric structure is critical for chaperone function, whereas the relationship between the dimeric structure and cochaperone function is hardly known. Here, we examined whether two intact protomers are required for cochaperone activity of Hsp40 using an Escherichia coli Hsp70 chaperone system consisting of DnaK, DnaJ, and GrpE...
April 4, 2018: Journal of Biochemistry
Takuto Suito, Kohjiro Nagao, Masataka Hatano, Kenichi Kohashi, Aiko Tanabe, Hiromichi Ozaki, Jun Kawamoto, Tatsuo Kurihara, Tetsuo Mioka, Kazuma Tanaka, Yuji Hara, Masato Umeda
It is commonly observed that freshwater fish contain lower amounts of omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs), such as eicosapentaenoic acid (EPA, C20:5n-3) and docosahexaenoic acid (DHA, C22:6n-3), than marine fish species. In this study, we performed a detailed comparative analysis of phospholipids (PLs) and triacylglycerols (TAGs) from Gymnogobius isaza, a freshwater goby endemic to Lake Biwa inhabiting the lake bottom, and Gymnogobius urotaenia, a related goby that inhabits the shore of Lake Biwa...
March 15, 2018: Journal of Biochemistry
Ryota Yamagami, Ryota Miyake, Ayaka Fukumoto, Misa Nakashima, Hiroyuki Hori
TrmFO catalyzes the formation of 5-methyluridine at position 54 in tRNA and uses N5, N10-methylenetetrahydrofolate (CH2THF) as the methyl group donor. We found that the trmFO gene disruptant strain of Thermus thermophilus, an extremely-thermophilic eubacterium, can grow faster than the wild-type strain in the synthetic medium at 70 °C (optimal growth temperature). Nucleoside analysis revealed that the majority of modifications were appropriately introduced into tRNA, showing that the limited nutrients are preferentially consumed in the tRNA modification systems...
March 10, 2018: Journal of Biochemistry
Nao Sakurai, Shunsuke Nishio, Yuka Akiyama, Shinji Miyata, Kenzi Oshima, Daita Nadano, Tsukasa Matsuda
Casein is the major milk protein to nourish infants but, in certain population, it causes cow's milk allergy, indicating the uptake of antigenic casein and their peptides through the intestinal epithelium. Using human intestinal Caco-2 cell monolayers, the apical-to-basal transepithelial transport of casein was investigated. Confocal microscopy using component-specific antibodies showed that αs1-casein antigens became detectable as punctate signals at the apical-side cytoplasm and reached to the cytoplasm at a tight-junction level within a few hours...
February 27, 2018: Journal of Biochemistry
Satoru Nirasawa, Kazuhiko Nakahara, Saori Takahashi
Paenidase is the first microorganism-derived D-aspartyl endopeptidase that specifically recognizes an internal D-Asp residue to cleave [D-Asp]-X peptide bonds. Using peptide sequences obtained from the protein, we performed PCR with degenerate primers to amplify the paenidase I-encoding gene. Nucleotide sequencing revealed that mature paenidase I consists of 322 amino acid residues and that the protein is encoded as a pro-protein with a 197-amino-acid N-terminal extension compared to the mature protein. Paenidase I exhibits amino acid sequence similarity to several penicillin-binding proteins...
February 27, 2018: Journal of Biochemistry
Akihiko Kanou, Koichiro Kako, Keiko Hirota, Akiyoshi Fukamizu
No abstract text is available yet for this article.
February 19, 2018: Journal of Biochemistry
Zhao Peng, Miyu Takeshita, Nao Shibata, Hideaki Tada, Yoshikazu Tanaka, Jun Kaneko
Staphylococcus aureus bi-component pore-forming toxins consist of S- and F-components, and form hetero-octameric beta-barrel pores on target blood cell membranes. Among them, γ-hemolysin (Hlg2 and LukF) and LukED (LukE and LukD) possess hemolytic activity, whereas the Panton -Valentine leukocidin (LukS-PV and LukF-PV) does not lyse human erythrocytes.Here, we focused on four loop structures in the rim domain of S-component, namely loops -1, -2, -3, and -4, and found that replacement of loop-4 in both Hlg2 and LukE with that of LukS-PV abolished their hemolytic activity...
February 17, 2018: Journal of Biochemistry
Akshari Gupta, Daiju Kitagawa
Several decades of centriole research have revealed the beautiful symmetry present in these microtubule-based organelles, which are required to form centrosomes, cilia, and flagella in many eukaryotes. Centriole architecture is largely conserved across most organisms, however, individual centriolar features such as the central cartwheel or microtubule walls exhibit considerable variability when examined with finer resolution. Here, we review the ultrastructural characteristics of centrioles in commonly studied organisms, highlighting the subtle and not-so-subtle differences between specific structural components of these centrioles...
February 16, 2018: Journal of Biochemistry
Fengying Tang, Megan S Lord, William B Stallcup, John M Whitelock
Chondroitin sulfate proteoglycan 4 (CSPG4) is a cell surface proteoglycan highly expressed by tumor, perivascular and oligodendrocyte cells and known to be involved cell adhesion and migration. This study showed that CSPG4 was present as a proteoglycan on the cell surface of two melanoma cell lines, MM200 and Me1007, as well as shed into the conditioned medium. CSPG4 from the two melanoma cell lines differed in the amount of chondroitin sulfate (CS) decoration, as well as the way the protein core was fragmented...
February 15, 2018: Journal of Biochemistry
Daisuke Kato, Kei Eto, Junichi Nabekura, Hiroaki Wake
Electrical activity is essential for brain function. However, neurons, the electrically active cells, are less numerous than the non-electrical glial cells in the central nervous system. The non-electrical components modify the function of neural circuits, depending on the electrical neuronal activity, by wrapping synapses, myelinating axons, and phagocytozing the neuronal components. Moreover, recent evidence has suggested that they contribute to neurological and psychiatric disease by regulating neuronal circuits, ultimately affecting their behavior...
February 13, 2018: Journal of Biochemistry
Ziaur Rahman, Yuta Tsujimori, Megumi Maeda, Anowar Hossain, Takeshi Ishimizu, Yoshinobu Kimura
In a previous study, we molecular-characterized a tomato (Solanum lycopersicum) α1,3/4-fucosidase (α-Fuc'ase S1-1) encoded in a tomato gene (Solyc03g006980), indicating that α-Fuc'ase S1-1 is involved in the turnover of Lea epitope-containing N-glycans. In this study, we have characterized another tomato gene (Solyc11g069010) encoding α1,3/4-fucosidase (α-Fuc'ase S1-2), which is also active toward the complex type N-glycans containing Lea epitope(s). The baculovirus-insect cell expression system was used to express that α-Fuc'ase S1-2 with anti-FLAG tag, and the expression product (rFuc'ase Sl-2), was found as a 65 kDa protein using SDS-PAGE and has an optimum pH of around 5...
February 10, 2018: Journal of Biochemistry
Teisuke Takita, Jun Qian, Hongmin Geng, Zejian He, Sho Nemoto, Mariko Mori, Keisuke Tanaka, Shunji Hattori, Kenji Kojima, Kiyoshi Yasukawa
The collagenase produced by a gram-negative bacterium Grimontia hollisae strain 1706B (Ghcol) degrades collagen more efficiently than that produced by a gram-positive bacterium Clostridium histolyticum (Chcol), which is currently the most widely used collagenase in industry (Teramura et al. (2011) J. Bacteriol.193, 3049‒3056). Here, we compared the Ghcol and Chcol activities using two synthetic substrates. In the hydrolysis of (7-methoxycoumarin-4-yl)acetyl-L-Lys-L-Pro-L-Leu-Gly-L-Leu-[N3-(2,4-dinitrophen-yl)-L-2,3-diaminopropioyl]-L-Ala-L-Arg-NH2, Ghcol exhibited 350-fold higher activity than Chcol in the absence of CaCl2 and NaCl...
February 10, 2018: Journal of Biochemistry
Daisuke Saigusa, Norio Suzuki, Yotaro Matsumoto, Keiko Umeda, Yoshihisa Tomioka, Seizo Koshiba, Masayuki Yamamoto
Roxadustat (FG-4592, Rox) is a stabilizer for hypoxia-inducible transcription factors (HIFs), which induce production of the erythroid growth factor erythropoietin, and has been listed by the World Anti-Doping Agency as a prohibited substance for athletes since 2011. Although the detection technologies for Rox and its glucuronide-conjugated metabolite (Rox-Gluc) have been developed exploiting triple quadrupole mass spectrometry (MS/MS), the production of metabolites from Rox in the human body remains to be clarified...
February 9, 2018: Journal of Biochemistry
Kouki Tadai, Tatsumasa Shioiri, Jun Tsuchimoto, Naoko Nagai, Hideto Watanabe, Nobuo Sugiura
Receptor type of protein tyrosine phosphatase sigma (RPTPσ) functions as a glycosaminoglycan (GAG) receptor of neuronal cells in both the central and peripheral nervous systems. Both chondroitin sulfate (CS) and heparan sulfate (HS) are important constituents of GAG ligands for RPTPσ, although they have opposite effects on neuronal cells. CS inhibits neurite outgrowth and neural regeneration through RPTPσ, whereas HS enhances them. We prepared recombinant RPTPσ N-terminal fragment containing the GAG binding site and various types of biotin-conjugated GAG (CS and HS) with chemical modification and chemo-enzymatic synthesis...
February 6, 2018: Journal of Biochemistry
Mitsuhiro Itaya, Hiroko Kusakabe, Mitsuru Sato, Masaru Tomita, Rintaro Sato
Synechococcus elongatus PCC7942, a cyanobacterium that uses light and carbon dioxide to grow, has a high ability to incorporate DNA by transformation. To assess the effective delivery of large DNA in plasmid form, we cloned the endogenous plasmid pANL (46.4 kbp) into a BAC vector of Escherichia coli. The plasmid p38ANL (54.3 kbp) replaced the native plasmid. To assess the delivery of larger DNA into PCC7942, p38ANL was fused to the broad-host-range conjugal transfer plasmid pUB307IP (53.5 kbp). The resulting plasmid pUB307IP501 (107...
February 6, 2018: Journal of Biochemistry
Yuriko Egashira, Satoru Nagatoishi, Masato Kiyoshi, Akiko Ishii-Watabe, Kouhei Tsumoto
Silkworm-baculovirus expression systems are efficient means for production of recombinant proteins that provide high expression levels and post-translational modifications. Here, we characterized the stability, glycosylation pattern, and antibody-dependent cell-mediated cytotoxicity activity of anti-HER2 monoclonal antibodies containing native or glycoengineered mammalian-like N-glycans that were produced by using a silkworm-baculovirus expression system. Compared with a monoclonal antibody produced by using a Chinese hamster ovary cell expression system, the glycoengineered monoclonal antibody had comparable thermal stability and a higher antibody-dependent cell-mediated cytotoxicity activity...
February 5, 2018: Journal of Biochemistry
Takeshi Kaizuka, Toru Takumi
Synaptic connections are essential for neural circuits in order to convey brain functions. The postsynaptic density (PSD) is a huge protein complex associated with postsynaptic membranes of excitatory synapses. In mammals, the PSD is composed of more than 1,000 proteins including receptors, scaffold proteins, signaling enzymes, and cytoskeletal proteins. PSD proteins are crucial for synaptic transmission and plasticity. Proteomic studies have revealed the composition of PSD proteins in various species, brain regions, and specific physiological conditions...
February 5, 2018: Journal of Biochemistry
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