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Journal of Biochemistry

Sayaka Nagata, Motoo Yamasaki, Aya Kawano, Kazuo Kitamura
Human adrenomedullin (hAM) is a hypotensive peptide hormone that exerts powerful anti-inflammatory effects. However, treatment required continuous administration of hAM, as the half-life of native hAM is quite short in blood. To resolve this problem, we designed two kinds of human IgG1 Fc fusion proteins containing either full-length hAM (IgG1-AM) or hAM residues 6-52 [IgG1-AM (6-52)]. A DNA construct was constructed by connecting DNA sequences encoding hAM and the IgG1 Fc region with a DNA sequence encoding a (GGGGS)3 linker...
March 20, 2019: Journal of Biochemistry
Mohammed Abdelaziz, Yukihide Watanabe, Mitsuyasu Kato
PMEPA1/TMEPAI, a direct target and a negative regulator of TGF-β signaling, has an oncogenic role in many cancers. We observed that knockout (KO) of PMEPA1 in human breast cancer cell line MDA-MB-231 using a CRISPR-Cas9 system resulted in reduction of in vivo tumor growth and lung metastasis but not of in vitro monolayer growth capacity of these KO cell lines. This phenomenon was associated with PMEPA1 KO-mediated downregulation of the key proangiogenic factors VEGFA and IL8 that are essential for in vivo but not in vitro growing cells and are also substantial for initiation of lung metastasis...
March 14, 2019: Journal of Biochemistry
K F Houslay, B A Fertig, F Christian, A J Tibbo, J Ling, J E Findlay, M D Houslay, G S Baillie
Phosphodiesterases (PDEs) shape local cAMP gradients to underpin the specificity of receptor function. Key to this process is the highly defined nature of the intra-cellular location of PDEs in the cell. PDE4A5 is a PDE isoform that specifically degrades cAMP and is known to associate with the p75 neurotrophin receptor (p75NTR) where it modulates cAMP signalling cascades that regulate extracellular matrix remodelling in the lungs. Here we map and validate novel protein-protein interaction sites that are important for formation of the PDE4A5-p75NTR complex and show, for the first time, that phosphorylation of PDE4A5 by MAPKAPK2 enhances PDE4A5 interaction with p75NTR and that this, in turn, serves to attenuate fibrin degradation...
March 11, 2019: Journal of Biochemistry
Mazharul Islam, Ryuichi Nishinakamura
It is difficult to restore kidney function once it has become severely impaired. While kidney transplantation is a curative therapy, donor numbers remain limited. Thus, the generation of kidney organoids (mainly comprising glomeruli and renal tubules) from multipotent stem cells represents an important advance in regenerative medicine of the kidney. Recently, a protocol that can generate the higher-order structure of the mouse embryonic kidney was reported. Kidney organoids are now being used for disease modeling, and may eventually be applicable for clinical transplantation...
March 7, 2019: Journal of Biochemistry
Yulong Ma, Chunli Pan, Qihai Wang
The lipids containing cyclopropane fatty acid (CFA) protect bacteria from adverse conditions such as acidity, freeze-drying desiccation, and exposure to pollutants. CFA is synthesized when cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase, CFAS) transfers a methylene group from S-adenosylmethionine (SAM) across the cis double bonds of unsaturated fatty acyl chains. Here we reported a 2.7-Å crystal structure of CFAS from L. acidophilus. The enzyme is composed of N- and C-terminal domain, which belong to the sterol carrier protein and methyltransferase superfamily respectively...
March 4, 2019: Journal of Biochemistry
Akane Senga, Yoshiji Hantani, Gert-Jan Bekker, Narutoshi Kamiya, Yuki Kimura, Fusako Kawai, Masayuki Oda
A cutinase from Saccharomonospora viridis AHK190, Cut190, can hydrolyze polyethylene terephthalate and has a unique feature that the activity and stability are regulated by Ca2+ binding. Our recent structural and functional analyses showed three Ca2+ binding sites and their respective roles. Here, we analyzed the binding thermodynamics of Mn2+, Zn2+, and Mg2+ to Cut190 and their effects on the catalytic activity and thermal stability. The binding affinities of Mn2+ and Zn2+ were higher than that of Mg2+ and are all entropy driven with the binding stoichiometry of Zn2+, Mn2+, and Mg2+ were found to be three, one, and one, respectively...
March 2, 2019: Journal of Biochemistry
Yusuke Okamoto, James Hejna, Minoru Takata
Fanconi anemia (FA) is a devastating hereditary disorder with impaired genome stability resulting in physical abnormalities, gradual loss of hematopoietic stem cells, and development of tumors and leukemia. It has been suggested that functions of FA genes are required to maintain genome stability by counteracting endogenous metabolites, such as aldehydes, that damage DNA and stall replication forks. Recent studies have implicated co-transcriptional R-loops, consisting of a DNA:RNA hybrid and displaced single stranded DNA, as one of the potential endogenous sources that induce genome instability and the FA phenotype...
March 1, 2019: Journal of Biochemistry
Tomoki Himiyama, Maki Oshima, Koichi Uegaki, Tsutomu Nakamura
Peroxiredoxins from Pyrococcus horikoshii (PhPrx) and Thermococcus kodakaraensis (TkPrx) are highly homologous proteins sharing 196 of the 216 residues. We previously reported a pentagonal ring-type decameric structure of PhPrx. Here, we present the crystal structure of TkPrx. Despite their homology, unlike PhPrx, the quaternary structure of TkPrx was found to be a dodecamer comprised of six homodimers arranged in a hexagonal ring-type assembly. The possibility of the redox-dependent conversion of the molecular assembly, which had been observed in PhPrx, was excluded for TkPrx based on the crystal structure of a mutant in which all of the cysteine residues were substituted with serine...
February 22, 2019: Journal of Biochemistry
Koutarou Nakamura, Takashi Shichita
Cerebral inflammation is a promising therapeutic target for ischemic stroke. After ischemic stroke, inflammatogenic self molecules, which originate from damaged brain tissue due to ischemia, activate infiltrating immune cells (neutrophils, macrophages, and lymphocytes) and thereby trigger sterile inflammation. Innate immunity plays the central role in sterile inflammation at the acute phase of brain ischemia, although immune response by T lymphocytes (innate or acquired immunity) is also implicated in inflammation at the subacute phase, which sustains ischemic brain damage...
February 22, 2019: Journal of Biochemistry
Tomisin Happy Ogunwa, Kenichi Taii, Kei Sadakane, Yuka Kawata, Shinsaku Maruta, Takayuki Miyanishi
Among forty plant-derived biflavonoids with inhibitory potential against Eg5, morelloflavone from Garcinia dulcis leaves was selected for further testing based on in silico analysis of binding modes, molecular interactions, binding energies, and functional groups that interact with Eg5. Computational models predicted that morelloflavone binds the putative allosteric pocket of Eg5, within the cavity surrounded by amino acid residues of Ile-136, Glu-116, Glu-118, Trp-127, Gly-117, Ala-133, Glu-215, Leu-214, and Tyr-211...
February 20, 2019: Journal of Biochemistry
Seiji Kojima, Takuro Yoneda, Wakako Morimoto, Michio Homma
YcgR, a c-di-GMP binding protein expressed in Escherichia coli, brakes flagellar rotation by binding to the motor in a c-di-GMP dependent manner and has been implicated in triggering biofilm formation. Vibrio alginolyticus has a single polar flagellum and encodes YcgR homolog, PlzD. When PlzD or PlzD-GFP were highly over-produced in nutrient-poor condition, the polar flagellar motility of V. alginolyticus was reduced. This inhibitory effect is c-di-GMP independent since mutants substituting putative c-di-GMP binding residues retain the effect...
February 18, 2019: Journal of Biochemistry
Jan M Klenk, Max-Philipp Fischer, Paulina Dubiel, Mahima Sharma, Benjamin Rowlinson, Gideon Grogan, Bernhard Hauer
Cytochrome P450 monooxygenases (P450s) play crucial roles in the cell metabolism and provide an unsurpassed diversity of catalyzed reactions. Here, we report the identification and biochemical characterization of two P450s from Arthrobacter sp., a gram-positive organism known to degrade the opium alkaloid papaverine. Combining phylogenetic and genomic analysis suggested physiological roles for P450s in metabolism, and revealed potential gene clusters with redox partners facilitating the reconstitution of the P450 activities in vitro...
February 13, 2019: Journal of Biochemistry
Shin-Ichiro Horigane, Yukihiro Ozawa, Hirokazu Yamada, Sayaka Takemoto-Kimura
Neuronal migration is a crucial event in neuronal development for the construction of brain architecture and neuronal networks. Newborn neurons proliferate in the germinal zone and start migration toward their final destination. Migrating neurons adopt different routes, cell shapes, and migratory modes depending on extracellular factors and outer physical substrates. Intracellular Ca2+ is an essential second messenger that regulates diverse cellular functions by activating Ca2+-dependent signaling molecules that underlie Ca2+-responsive cellular functions...
February 12, 2019: Journal of Biochemistry
Kosuke Kamemura, Takahiro Chihara
VAP (VAMP-associated protein) is a type Ⅱ integral membrane protein of the endoplasmic reticulum (ER), and its N-terminal MSP domain faces the cytoplasmic side. VAP functions as a tethering molecule at the membrane contact sites between the ER and intracellular organelles and regulates a wide variety of cellular functions, including lipid transport, membrane trafficking, microtubule reorganization, and unfolded protein response. VAP-point mutations in human vapb are strongly associated with amyotrophic lateral sclerosis (ALS)...
February 6, 2019: Journal of Biochemistry
Daiki Hayashi, Ryosuke Tsumagari, Ke Liu, Shuji Ueda, Minoru Yamanoue, Fumio Sakane, Yasuhito Shirai
Diacylglycerol kinase (DGK) is a lipid kinase that converts diacylglycerol (DG) into phosphatidic acid (PA). DG and PA function as lipid messengers contributing to various signaling pathways. Thus, DGK plays a pivotal role in the signaling pathways by maintaining DG and PA levels. For example, DGKδ is involved in diabetes and DGKβ is important for higher brain function including memory and emotion. Recently, we also revealed that the activation of DGKα ameliorated diabetic nephropathy (DN) in mice, suggesting that DGK can be therapeutic target...
February 4, 2019: Journal of Biochemistry
Daiju Doubayashi, Masaya Oki, Bunzo Mikami, Hiroyuki Uchida
Aspergillus oryzae RIB40 formate oxidase has Arg87 and Arg554 near the formyl group and O(4) atom of 8-formyl-flavin adenine dinucleotide (FAD), respectively, with Asp396 neighboring Arg554. Herein, we probed the roles of these three residues in modification of FAD to 8-formyl-FAD. Replacement of Arg87 or Arg554 with Lys or Ala decreased and abolished the modification, respectively. Replacement of Asp396 with Ala or Asn lowered the modification rate. The observation of unusual effects of maintaining pH 7.0 on the modification in R87K, R554K, and D396 variants indicates initial and subsequent processes with different pH dependencies...
February 1, 2019: Journal of Biochemistry
Wenhui Tu, Yonghong Yang, Yulong Song, Weijun Zhu
Objective: This study investigated the underlying mechanism of long noncoding RNA (lncRNA) small nucleolar RNA host gene 20 (SNHG20) in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Materials and methods: LncRNA SNHG20 and PTEN expression levels were detected by qRT-PCR and western blot. The proliferation of HCC cells was measured by MTT assay, and the apoptosis of HCC cells was measured by flow cytometry analysis. Results: SNHG20 expression level and HBx protein level were upregulated in HBV(+) group than that of HBV(-) group, whereas PTEN protein level was downregulated in HBV(+) group...
January 25, 2019: Journal of Biochemistry
Akihiro Murashima, Keiko Shinjo, Keisuke Katsushima, Tetsuo Onuki, Yasumitsu Kondoh, Hiroyuki Osada, Noritaka Kagaya, Kazuo Shinya, Hiroshi Kimura, Minoru Yoshida, Shingo Murakami, Yutaka Kondo
Dysregulation of enhancer of zeste homolog 2 (EZH2), a methyltransferase component of polycomb repressive complex 2 (PRC2), is found in many types of cancers especially those that are highly progressive and aggressive. Specific catalytic inhibitors of EZH2 have high anti-tumor activity, particularly in lymphomas with EZH2 activating mutations. However, the clinical benefits of EZH2 catalytic inhibitors in tumors overexpressing EZH2 are still limited. Here, we identified NPD13668, a novel modulator of EZH2-mediated gene silencing, from 329,049 small chemical compounds using a cell-based high-throughput screening assay...
January 25, 2019: Journal of Biochemistry
Tsuyoshi Kadomatsu, Yuichi Oike
Various types of stem cells reside in the body and self-renew thoughout an organism's lifetime. Such self-renewal is essential for maintenance of tissue homeostasis and is coordinately regulated by stem cell-intrinsic signals and signals from stem cell niche. Angiopoietin is a niche-derived signaling molecule well known to contribute to maintenance of hematopoietic stem cells. Angiopoietin-like proteins (ANGPTLs) are structurally similar to angiopoietin, and recent studies reveal that they function in angiogenesis, lipid and energy metabolism, and regulation of inflammation...
January 23, 2019: Journal of Biochemistry
Juan C Cifuentes-Goches, Lizbeth Hernández-Ancheyta, Gabriel Guarneros, N Oviedo, Javier Hernández-Sánchez
S1, a multi-domain ribosomal protein associated with the 30S subunit, is essential for translation initiation. S1 binds with high affinity to single-stranded mRNA containing AU-rich patches upstream of the start codon. It was previously reported that domains 1-3 of S1 protein play a role in the docking and unfolding of structured mRNAs to the ribosome. Moreover, S1-deficient 30S subunits are still able to bind to low structured mRNAs. However, mRNAs containing AU-rich patches in the early base positions after start codon enhance protein synthesis and mRNA binding to the ribosome, which suggests that S1 is also able to interact with these AU-rich regions...
January 21, 2019: Journal of Biochemistry
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