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Journal of Biochemistry

Takashi Kida, Aoi Itoh, Akari Kimura, Hisatsugu Matsuoka, Hiroyuki Imai, Kentaro Kogure, Akira Tokumura, Tamotsu Tanaka
Previously, we detected an unknown sphingophospholipid in cabbage leaves and identified it as phytoceramide-1-phosphate (PC1P). We also found an enzyme activity that produces PC1P by glycosylinositol phosphoceramide (GIPC)-specific hydrolysis in cabbage leaves. To characterize the GIPC-specific phospholipase D (GIPC-PLD) activity, we investigated distributions of GIPC-PLD activity in 25 tissues of 10 plants. In most plants, the GIPC-PLD activity was the highest in roots. Young leaves of cabbage and Welsh onion had higher activities than corresponding aged outer leaves...
November 8, 2016: Journal of Biochemistry
Yusuke Kato, Kiyoshi Fukui
The G72 gene is one of the most susceptible genes to schizophrenia and is contained exclusively in the genomes of primates. The product of the G72 gene modulates the activity of D-amino acid oxidase (DAO) and is a small protein prone to aggregate, which hampers its structural studies. In addition, lack of a known structure of a homologue makes it difficult to use the homology modeling method for the prediction of the structure. Thus, we first developed a hybrid ab initio approach for small proteins prior to the prediction of the structure of G72...
November 3, 2016: Journal of Biochemistry
Ruriko Tatsumi, Yukio Ishimi
An MCM4 mutation detected in human cancer cells from endometrium was characterized. The mutation of G486D is located within MCM-box and the glycine at 486 in human MCM4 is conserved in Saccharomyces cerevisiae MCM4 and Sulfolobus solfataricus MCM. This MCM4 mutation affected human MCM4/6/7 complex formation, since the complex containing the mutant MCM4 protein is unstable and the mutant MCM4 protein is tend to be degraded. It is likely that the MCM4 mutation affects the interaction with MCM7 to destabilize the MCM4/6/7 complex...
October 29, 2016: Journal of Biochemistry
Akihiro Oguro, Asumi Yanagida, Yuta Fujieda, Ryo Amano, Maina Otsu, Taiichi Sakamoto, Gota Kawai, Senya Matsufuji
Though polyamines (putrescine, spermidine, and spermine) bind to the specific position in RNA molecules, interaction mechanisms are poorly understood. SELEX procedure has been used to isolate high-affinity oligoribonucleotides (aptamers) from randomized RNA libraries. Selected aptamers are useful in exploring sequences and/or structures in RNAs for binding molecules. In this study, to analyze the interaction mechanism of polyamine to RNA, we selected RNA aptamers targeted for spermine. Two spermine-binding aptamers (#5 and #24) were obtained and both of them had two stem-loop structures...
October 25, 2016: Journal of Biochemistry
Soo Huei Tan, Yahaya M Normi, Adam Thean Chor Leow, Abu Bakar Salleh, Abdul Munir Abdul Murad, Nor Muhammad Mahadi, Mohd Basyaruddin Abdul Rahman
The effectiveness of β-lactam antibiotics as chemotherapeutic agents to treat bacterial infections is gradually threatened with the emergence of antibiotic resistance mechanism among pathogenic bacteria through the production metallo-β-lactamase (MBL). In this study, we discovered a novel hypothetical protein (HP) termed Bleg1_2437 from the genome of alkaliphilic Bacillus lehensis G1 which exhibited MBL-like properties of B3 subclass; but evolutionary divergent from other circulating B3 MBLs. Domain and sequence analysis of HP Bleg1_2437 revealed that it contains highly conserved Zn(2+)-binding residues such as H54, H56, D58, H59, H131 and H191, important for catalysis, similar with the subclass B3 of MBL...
October 25, 2016: Journal of Biochemistry
Norihiro Takekawa, Seiji Kojima, Michio Homma
The bacterial flagellar motor is a rotary motor complex composed of various proteins. The motor contains a central rod, multiple ring-like structures and stators. The Na(+)-driven polar flagellar motor of the marine bacterium Vibrio alginolyticus has a specific ring, called the 'T-ring', which consists of two periplasmic proteins, MotX and MotY. The T-ring is essential for assembly of the torque-generating unit, the PomA/PomB stator complex, into the motor. To investigate the role of the T-ring for motor function, we performed random mutagenesis of the motX gene on a plasmid...
October 25, 2016: Journal of Biochemistry
Hiroshi Makuta, Keisuke Obara, Akio Kihara
Intracellular lipid amounts are regulated not only by metabolism but also by efflux. Yeast Rsb1 is the only known transporter/floppase of the sphingolipid components long-chain bases (LCBs). However, even fundamental knowledge about Rsb1, such as important amino acid residues for activity and substrate recognition, still remains unclear. Rsb1 belongs to the Rta1-like family. To date, it has not been determined whether all family members share a common ability to export LCBs. Here, we revealed that within the Rta1-like family, only Rsb1 suppressed the hypersensitivity of the mutant cells lacking LCB 1-phoshate-degrading enzymes, suggesting that LCB-exporting activity is specific to Rsb1...
October 22, 2016: Journal of Biochemistry
Biji Chatterjee, Krishna Ghosh, Nitin Yadav, Santosh R Kanade
Lectins are omnipresent in almost all life forms, being the proteins which specifically bind to carbohydrate moieties on the cell surface; they have been explored for their anti-tumour activities. In this study, we purified a fucose specific-lectin (IFL) from Fenneropenaeus indicus hemolymph using fucose-affinity column and characterized for its hemagglutination activity, carbohydrate specificity, dependency on cations and cytotoxicity against cancer cells. The lectin showed non-specificity against human erythrocytes...
October 13, 2016: Journal of Biochemistry
Yan Zhang, Chunyu Yang, Andrew Dancis, Eiko Nakamaru-Ogiso
Yeast Dre2 (anamorsin or CIAPIN1) is an essential component for cytosolic Fe/S cluster biosynthesis. The C-terminal domain contains eight evolutionarily conserved cysteine residues, and we previously demonstrated that the yeast Dre2 overexpressed in Escherichia coli contains one binuclear ([2Fe-2S]) cluster and one tetranuclear ([4Fe-4S]) cluster. In this study, we replaced each conserved cysteine with alanine and analyzed the effects by Electron Paramagnetic Resonance. Although the C311A mutant lacked both signals, our data clearly suggest that the [2Fe-2S] cluster is ligated to Cys252, Cys263, Cys266 and Cys268, whereas the [4Fe-4S] cluster is ligated to Cys311, Cys314, Cys322 and Cys325...
September 26, 2016: Journal of Biochemistry
Yuki Kawakami, Mai Kinoshita, Yoshiko Mori, Shuji Okochi, Shiori Hirano, Ichika Shimoda, Keita Kanzaki, Toshiko Suzuki-Yamamoto, Masumi Kimoto, Mitsuaki Sugahara, Tetsuya Hori, Hiromichi Saino, Masashi Miyano, Shozo Yamamoto, Yoshitaka Takahashi
The X-ray crystal structure of an anti-leukotriene (LT) C4 monoclonal antibody (mAbLTC) in complex with LTC4 was determined, however, crystallographic studies alone are not enough to fully understand the structures of the antigen-binding site. To elucidate the individual contribution of Tyr-54 and Asn-58 in the light chain of mAbLTC, both of which formed a hydrogen bond with glutamic acid of LTC4, we examined whether substitution of the residues affects the antigen binding affinity and specificity using an anti-LTC4 single chain variable fragment (scFvLTC)...
September 20, 2016: Journal of Biochemistry
Ami Sotokawauchi, Miyuki Kato-Murayama, Kazutaka Murayama, Toshiaki Hosaka, Iori Maeda, Michio Onjo, Noboru Ohsawa, Dai-Ichiro Kato, Kazunari Arima, Mikako Shirouzu
Cucumisin [EC], a subtilisin-like serine endopeptidase, was isolated from melon fruit, Cucumis melo L. Mature cucumisin (67 kDa, 621 residues) is produced by removal of the propeptide (10 kDa, 88 residues) from the cucumisin precursor by subsequence processing. It is reported that cucumisin is inhibited by its own propeptide. The crystal structure of mature cucumisin is reported to be composed of three domains: the subtilisin-like catalytic domain, the protease-associated domain, and the C-terminal fibronectin-III-like domain...
September 10, 2016: Journal of Biochemistry
Masayasu Kojima, Akie Hamamoto, Takahiro Sato
In the gastric peptide hormone ghrelin, serine 3 (threonine 3 in frogs) is modified, primarily by n-octanoic acid; this modification is essential for ghrelin's activity. The enzyme that transfers n-octanoic acid to Ser3 of ghrelin is ghrelin O-acyltransferase (GOAT). GOAT, the only enzyme known to catalyze acyl modification of ghrelin, specifically modifies serine (or threonine) at the third position and does not modify other serine residues in ghrelin peptides. GOAT prefers n-hexanoyl-CoA over n-octanoyl-CoA as the acyl donor, although in the stomach the n-octanoyl form is the predominant form of acyl-modified ghrelin...
October 2016: Journal of Biochemistry
Madhavan Narayanan, Joseph A Sakyiama, Mahmoud M Elguindy, Eiko Nakamaru-Ogiso
Respiratory complex I has an L-shaped structure formed by the hydrophilic arm responsible for electron transfer and the membrane arm that contains protons pumping machinery. Here, to gain mechanistic insights into the role of subunit NuoL, we investigated the effects of Mg(2+), Zn(2+) and the Na(+)/H(+) antiporter inhibitor 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) on proton pumping activities of various isolated NuoL mutant complex I after reconstitution into Escherichia coli double knockout (DKO) membrane vesicles lacking complex I and the NADH dehydrogenase type 2...
October 2016: Journal of Biochemistry
Jing Liu, Xiangdong Sun, Hongcheng Zhu, Qin Qin, Xi Yang, Xinchen Sun
Oesophageal carcinoma is one of the most lethal cancer types in the world, especially in some part of China. Oesophageal squamous cell carcinoma (OSCC) is a major subtype, which has been shown to be associated with unhealthy diet habit, smoking, environmental carcinogens etc. The OSCC often progress slowly, however, it is often diagnosed at an advanced stage. Thus it is imperative to elucidate the molecular mechanisms involved in the initiation and progression of OSCC. Long noncoding RNAs (lncRNA) has emerged as a novel functional player transcribed from the genome...
October 2016: Journal of Biochemistry
(no author information available yet)
No abstract text is available yet for this article.
September 2016: Journal of Biochemistry
Takashi Aoi
In 2006, induced pluripotent stem (iPS) cells were generated by Yamanaka and Takahashi for the first time from a mouse fibroblast culture by introducing four factors. In the 10 years since then, this breakthrough discovery has been making waves in the fields of biology and medical science. For example, various technologies for generating iPS cells have been developed, and we have cultivated a better understanding of the mechanisms involved in reprogramming. In addition, many researchers have explored the applications of iPS cells, such as drug discovery, the study of disease mechanisms and regenerative medicine, and the development of advanced technologies for the differentiation and qualification of the cells...
September 2016: Journal of Biochemistry
Saki Inuzuka, Kei-Ichiro Nishimura, Hitoshi Kakizawa, Yuki Fujita, Hiroyuki Furuta, Shigeyoshi Matsumura, Yoshiya Ikawa
The Vc2 riboswitch possesses an aptamer domain belonging to the class-I c-di-GMP riboswitch family. This domain has been analysed and the molecular mechanism by which it recognizes the c-di-GMP ligand has been elucidated. On the other hand, the regulatory mechanism of the full-length Vc2 riboswitch to control its downstream open reading frame (ORF) remains largely unknown. In this study, we performed in vivo reporter assays and in vitro biochemical analyses of the full-length riboswitch and its aptamer domain...
September 2016: Journal of Biochemistry
Rupali Yadav, Kuldeep Verma, Mintu Chandra, Madhumita Mukherjee, Sunando Datta
Entamoeba histolytica, an enteric parasite expresses a Gal/GalNAc-specific lectin that contributes to its virulence by establishing adhesion to host cell. In this study, carbohydrate recognition domain of Hgl (EhCRD) was purified and biophysical studies were conducted to understand the thermodynamic basis of its binding to carbohydrate and Ca(++) Here, we show that carbohydrate recognition domain (CRD) of the lectin binds to calcium through DPN motif. To decipher the role of calcium in carbohydrate binding and host cell adhesion, biophysical and cell-based studies were carried out...
September 2016: Journal of Biochemistry
Priyabrata Das, Soma Mukhopadhyay, Nirmal Kumar Sarkar, Suvra Mandal, Manoj Kar, Ashis Mukhopadhyay
Iron chelation therapies are required for the treatment of iron overloaded patients; nonetheless, their side effects are also well known. We have evaluated iron-chelating activity of wheat grass extract (WHE) and its purified compound, mugineic acid in murine model with phenylhydrazine (PHZ) and dextran induced acute and chronic iron overload conditions. PHZ and dextran treatment induced acute and chronic iron overload condition in mice, respectively, as indicated by increased serum and tissue iron in both cases...
September 2016: Journal of Biochemistry
Rubi Figueroa-Teran, Heidi Pak, Gary J Blomquist, Claus Tittiger
Ips spp. bark beetles use ipsdienol, ipsenol, ipsdienone and ipsenone as aggregation pheromone components and pheromone precursors. For Ips pini, the short-chain oxidoreductase ipsdienol dehydrogenase (IDOLDH) converts (-)-ipsdienol to ipsdienone, and thus likely plays a role in determining pheromone composition. In order to further understand the role of IDOLDH in pheromone biosynthesis, we compared IDOLDH to its nearest functionally characterized ortholog with a solved structure: human L-3-hydroxyacyl-CoA dehydrogenase type II/ amyloid-β binding alcohol dehydrogenase (hHADH II/ABAD), and conducted functional assays of recombinant IDOLDH to determine substrate and product ranges and structural characteristics...
September 2016: Journal of Biochemistry
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