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Journal of Biochemistry

Nicola Landi, Sara Ragucci, Rosita Russo, Paolo V Pedone, Angela Chambery, Antimo Di Maro
Here, we report the amino acid sequence of Ageritin, the first ribotoxin-like protein from basidiomycetes (Agrocybe aegerita). This protein consists of 135 amino acid residues with a theoretical molecular mass of 14801.80 Da (experimental mass 14802.84 Da, [M+H+]+). Unlike both the classic ribotoxins and homologous RNases T1 family from ascomycetes, Ageritin has a single free cysteinyl residue and does not show homology with known RNases endowed with the specific enzymatic activity on the universally conserved Sarcin Ricin Loop (SRL)...
December 12, 2018: Journal of Biochemistry
Hayase Mizukami, Jun-Dal Kim, Saori Tabara, Weizhe Lu, Chulwon Kwon, Misaki Nakashima, Akiyoshi Fukamizu
Males and females share the same genetic code, but gene expression profile often displays differences between two sexes. Mouse embryonic fibroblasts (MEFs) have been used to experiment as a useful tool to test gene function. They have also been characterized by gender-based differences in expressed genes such as Y-linked Sry or X-linked Hprt. However, there is no report on sex differences in global gene expression. Here, using the next-generation RNA sequencing, we compared the comprehensive transcriptome of MEFs derived from two sexes...
December 12, 2018: Journal of Biochemistry
Yong-Zhen Wang, Yan-Hua Wang, Xi-Lin Fu
Background: As is known, hepatic stellate cells (HSC) activation contributes to liver cirrhosis. This study aims to find out the acting mechanisms of miR-454 inhibiting the activation and proliferation of hepatic stellate cells. Methods: The expression of Col1A1, α-SMA and Wnt10a were determined by western blot, and the miR-454 level was determined by qRT-PCR in this study. We took two objects as experiment subjects, one was liver cirrhosis rats, and the other was TGF-β1-stimulated HSC-T6 cells...
December 7, 2018: Journal of Biochemistry
Yoshio Kimura, Hiroyuki Yamamoto, Shiori Kamatani
Adenylate kinase (Adk) plays a critical role in energy metabolism and adaptation of bacteria to environmental stresses. We have previously shown that Myxococcus xanthus expresses polyphosphate kinase 1 (Ppk1) that also has Adk activity in the absence of polyphosphates. In this study, we investigated the Adk activity of the other two M. xanthus enzymes, AdkA and AdkB. The activity of AdkA was increased by dithiothreitol (DTT), which also enhanced enzyme stability. Site-directed mutagenesis of three cysteine residues (C130, C150, and C153) present in the LID domain of AdkA revealed that the Adk activity and stability of C150S and C153S mutants were not affected by DTT addition, suggesting formation of a disulfide bond between C150 and C153 in AdkA...
December 7, 2018: Journal of Biochemistry
Zheng Jiang, Yan Guo, Lifeng Miao, Lizhang Han, Wei Zhang, Yuquan Jiang
Radiotherapy is the major treatment modality for malignant glioma. However, the treatment response of radiotherapy is suboptimal due to resistance. Here we aimed to explore the effect and mechanism of Mothers against decapentaplegic homolog (SMAD3) silencing in sensitizing malignant glioma to radiotherapy. Clonogenic assay was used to evaluate the sensitivity of glioma cells to increasing doses of radiation. Glioma cells were transfected with small-interfering RNAs (siRNAs) specific to SMAD3. Overexpression of SMAD3 was achieved by transfecting expression plasmid encoding SMAD3 cDNA...
December 6, 2018: Journal of Biochemistry
Youské Shimizu, Toru Togawa, Shigeru Chaen
The amino acid sequence of the motor domain of AnKinA, kinesin-1 from Aspergillus nidulans, growing optimally at 37°C, was compared with that of SbKin1, kinesin-1 from the snow mold Sclerotinia borealis. For cold-adaptation, some enzymes are thought to exhibit augmented protein structure flexibility, acquired most effectively by substituting a glycine residue for another amino acid residue. By the comparison described above, two glycine residues proximal to tightly-bound ADP were identified in the SbKin1 motor domain, of which the corresponding residues of AnKinA were non-glycine ones (P60 and S323)...
December 5, 2018: Journal of Biochemistry
Wataru Kobiayashi, Enwei Liu, Hajime Ishii, Sachihiro Matsunaga, Peter Schlögelhofer, Hitoshi Kurumizaka
In eukaryotes, homologous recombination plays a pivotal role in both genome maintenance and generation of genetic diversity. Eukaryotic RecA homologues, RAD51 and DMC1, are key proteins in homologous recombination that promote pairing between homologous DNA sequences. Arabidopsis thaliana is a prominent model plant for studying eukaryotic homologous recombination. However, A. thaliana RAD51 and DMC1 have not been biochemically characterized. In the present study, we purified A. thaliana RAD51 (AtRAD51) and DMC1 (AtDMC1)...
December 5, 2018: Journal of Biochemistry
Smriti Sultana Binte Mustafiz, Toru Uyama, Zahir Hussain, Katsuhisa Kawai, Kazuhito Tsuboi, Nobukazu Araki, Natsuo Ueda
N-Acyl-phosphatidylethanolamines (NAPEs) represent a class of glycerophospholipids and serve as the precursors of bioactive N-acylethanolamines, including arachidonoylethanolamide (anandamide), palmitoylethanolamide and oleoylethanolamide. NAPEs are produced in mammals by N-acyltransferases, the enzymes which transfer an acyl chain of glycerophospholipids to the amino group of phosphatidylethanolamine. Recently, the ε isoform of cytosolic phospholipase A2 (cPLA2ε, also called PLA2G4E) was identified as Ca2+-dependent N-acyltransferase...
December 4, 2018: Journal of Biochemistry
Hideki Nishitoh
Organelles are intracellular compartments that are delineated by lipid bilayers and play specific roles in regulating various cellular events. Organelle dysfunction contributes to the pathological mechanisms of various diseases. The development and prevalence of super-resolved fluorescence microscopy have enabled the characterization of various functional regions and organellar dynamics by a number of cell biologists. These local functional organelle regions are named "zones", and three review articles in this issue summarize three different organelle zones, namely, the "Response zone", "Communication zone" and "Sorting zone"...
November 29, 2018: Journal of Biochemistry
Yan Li, Hengke Jiang, Xin Sun, Ahsan Asghar Muhammad, Jiang Liu, Weiguo Liu, Kai Shu, Jing Shang, Feng Yang, Xiaoling Wu, Taiwen Yong, Xiaochun Wang, Liang Yu, Chunyan Liu, Wenyu Yang, Junbo Du
Soybean-based intercropping is important for sustainable agricultural practice on a regional and global scale. However, most soybean varieties use shade avoidance strategy to acquire more light absorption when suffered in canopy shade in intercropping systems, thus reduced the yield of the whole population on a farmland. The mechanisms underlying early response of soybean in shade avoidance is still largely unknown. Here we report our identification of differentially accumulated proteins in shade-sensitive soybean seedlings by global quantitative proteome analysis under white light and shade conditions...
November 29, 2018: Journal of Biochemistry
Motoki Tsukiashi, Misato Baba, Kenji Kojima, Kohei Himeda, Teisuke Takita, Kiyoshi Yasukawa
Ribonuclease H (RNase H) specifically hydrolyzes the 5'-phosphodiester bonds of the RNA of RNA/DNA hybrid. Both type 1 and 2 RNases H act on the RNA strand of the hybrid, while only type 2 acts on the single ribonucleotide embedded in DNA duplex. In this study, to explore the role of mammalian type 2 RNase H (RNase H2) in cells, we constructed the RNase H2 knockout NIH3T3 cells (KO cells) by CRISPR/Cas9 system. KO cells hydrolyzed RNA strands in RNA/DNA hybrid, but not single ribonucleotides in DNA duplex, while wild-type NIH3T3 cells (WT cells) hydrolyzed both...
November 27, 2018: Journal of Biochemistry
Yosuke Funato, Hiroaki Miki
Cyclin M (CNNM) family proteins are evolutionarily conserved Mg2+ transporters. They extrude Mg2+ from cells and maintain intracellular Mg2+ levels within the normal range. Moreover, they play an important role in Mg2+ (re)absorption in the intestine and kidney by mediating the directional transport of Mg2+ across epithelial tissue from the tubular lumen to the body inside. Mg2+ efflux is suppressed by the direct binding with phosphatase of regenerating liver (PRL), and the formation of the complex is dynamically regulated by cysteine phosphorylation of PRL...
November 22, 2018: Journal of Biochemistry
Mariko Takahara, Masataka Kunii, Kentaro Nakamura, Akihiro Harada, Tomoaki Hirano, Yohei Katoh, Kazuhisa Nakayama
Cilia are organelles that serve as cellular antennae. Intraflagellar transport (IFT) particles containing the IFT-A and IFT-B complexes mediate bidirectional trafficking of ciliary proteins. Particularly, in concert with the BBSome complex, IFT particles play an essential role in trafficking of ciliary G-protein-coupled receptors. Therefore, proteins interacting with the IFT components are potential regulators of ciliary protein trafficking. We here revealed that an uncharacterized protein, C11ORF74, interacts with the IFT-A complex via the IFT122 subunit and is accumulated at the distal tip in the absence of an IFT-A subunit IFT139, suggesting that at least a fraction of C11ORF74 molecules can be transported toward the ciliary tip by associating with the IFT-A complex, although its majority might be out of cilia at steady state...
November 22, 2018: Journal of Biochemistry
Paul R Sanders, Benjamin K Dickerman, Sarah C Charnaud, Paul A Ramsland, Brendan S Crabb, Paul R Gilson
In order to facilitate a number of processes including nutrient acquisition and immune evasion, malaria parasites extensively remodel their host erythrocyte. This remodeling is to a large extent accomplished through protein export, a crucial process mediated by the PTEX translocon which is comprised of three core components, HSP101, PTEX150 and EXP2. EXP2 has been structurally and electrophysiologically shown to form the pore that spans the vacuole membrane enveloping the parasite. Here, we biochemically investigate the structure and function of EXP2...
November 22, 2018: Journal of Biochemistry
Jun Yasuda, Kengo Kinoshita, Fumiki Katsuoka, Inaho Danjoh, Mika Sakurai-Yageta, Ikuko N Motoike, Yoko Kuroki, Sakae Saito, Kaname Kojima, Matsuyuki Shirota, Daisuke Saigusa, Akihito Otsuki, Junko Kawashima, Yumi Yamaguchi-Kabata, Shu Tadaka, Yuichi Aoki, Takahiro Mimori, Kazuki Kumada, Jin Inoue, Satoshi Makino, Miho Kuriki, Nobuo Fuse, Seizo Koshiba, Osamu Tanabe, Masao Nagasaki, Gen Tamiya, Ritsuko Shimizu, Takako Takai-Igarashi, Soichi Ogishima, Atsushi Hozawa, Shinichi Kuriyama, Junichi Sugawara, Akio Tsuboi, Hideyasu Kiyomoto, Tadashi Ishii, Hiroaki Tomita, Naoko Minegishi, Yoichi Suzuki, Kichiya Suzuki, Hiroshi Kawame, Hiroshi Tanaka, Yasuyuki Taki, Nobuo Yaegashi, Shigeo Kure, Fuji Nagami, Kenjiro Kosaki, Yoichi Sutoh, Tsuyoshi Hachiya, Atsushi Shimizu, Makoto Sasaki, Masayuki Yamamoto
Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics, and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM-CommCohort (adult general population) and a TMM-BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts...
November 19, 2018: Journal of Biochemistry
Eun-Ji Hong, Haeri Jeong, Dong-Seok Lee, Younhee Kim, Heung-Shick Lee
In this study, we analyzed the ahpD gene from Corynebacterium glutamicum, which may function in a H2O2-mediated stress responses. Cells overexpressing C. glutamicum ahpD (P180-ahpD) showed increased sensitivity to H2O2 when exposed to the latter in concentrations of 8 mM or greater while showing reduced expression of katA, which encodes catalase. On the other hand, cells that lack ahpD (ΔahpD) displayed increased sensitivity when exposed to low levels of H2O2 while showing katA transcription that was comparable to the level in the wild-type strain...
November 15, 2018: Journal of Biochemistry
Kotarosumitomo Nakayama, Kana Wakamatsu, Hironobu Fujii, Shinichiro Shinzaki, Shinji Takamatsu, Shinobu Kitazume, Yoshihiro Kamada, Tetsuo Takehara, Naoyuki Taniguchi, Eiji Miyoshi
Core fucosylation, catalyzed by α-1,6 fucosyltransferase (FUT8), regulates growth factor receptors in immune function. Although core fucose regulates many immune cell types, few reports confront the association between core fucose activity and an innate immune reaction. Here, we have investigated the function of core fucose in macrophages in vivo and in vitro using Fut8-deficient mice and cells. Following lipopolysaccharide (LPS) stimulation, inflammatory cytokine production in Fut8-deficient (Fut8-/-) macrophages was suppressed in both in vivo and in vitro experiments...
November 15, 2018: Journal of Biochemistry
Shota Akai, Hiroko Ikushiro, Taiki Sawai, Takato Yano, Nobuo Kamiya, Ikuko Miyahara
Homoserine dehydrogenase from Thermus thermophilus (TtHSD) is a key enzyme in the aspartate pathway that catalyzes the reversible conversion of L-aspartate-β-semialdehyde to L-homoserine (L-Hse) with NAD(P)H. We determined the crystal structures of unliganded TtHSD, TtHSD complexed with L-Hse and NADPH, and Lys99Ala and Lys195Ala mutant TtHSDs, which have no enzymatic activity, complexed with L-Hse and NADP+ at 1.83, 2.00, 1.87, and 1.93 Å resolutions, respectively. Binding of L-Hse and NADPH induced the conformational changes of TtHSD from an open to a closed form: The mobile loop containing Glu180 approached to fix L-Hse and NADPH, and both Lys99 and Lys195 could make hydrogen bonds with the hydroxy group of L-Hse...
November 13, 2018: Journal of Biochemistry
Usama M Hegazy, Mohamed I El-Khonezy, Abeer Shokeer, Somaia S Abdel-Ghany, Roqaya I Bassuny, Amal Z Barakat, Walaa H Salama, Rasha A M Azouz, Afaf S Fahmy
Xylan saccharification is a key step in many important biotechnological applications. Xylose is the main product of xylan degradation and is a major xylanase inhibitor in a bioreactor; however, xylose-binding site of xylanase is not discovered yet. Evolving of xylose-tolerant xylanase variants will reduce the cost of xylanases in industry. Glycoside hydrolase family-10 thermostable Geobacillus stearothermophilus xylanase XT6 is non-competitively inhibited by xylose with inhibition constant ki equals to 12.2 mM...
November 8, 2018: Journal of Biochemistry
Mateen A Khan
Interactions of phosphorylated eIFiso4E binding to VPg as a function of temperature and ionic strength were assessed employing fluorescence spectroscopic. Phosphorylation increased the binding affinity ∼3.5-fold between VPg and eIFiso4E under equilibrium conditions. Binding affinity of VPg for eIFiso4Ep correlates with the ability to enhance in vitro protein synthesis. Addition of VPg and eIFiso4Ep together to Dep WGE enhances the translation for both uncapped and capped mRNA. However, capped mRNA translation was inhibited with addition of eIFiso4Ep alone in dep WGE, suggesting that phosphorylation prevents the cap binding and favors the VPg binding to promotes translation...
October 29, 2018: Journal of Biochemistry
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