Bioscience, Biotechnology, and Biochemistry
Online ISSN : 1347-6947
Print ISSN : 0916-8451
Volume 75 , Issue 1
Showing 1-36 articles out of 36 articles from the selected issue
Award Review
  • Kyoko KANAMARU
    2011 Volume 75 Issue 1 Pages 1-6
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    The His-Asp phosphorelay signal transduction system has been identified in most organisms, including bacteria, yeasts, fungi, and plants, except for animals. This system is important in adaptation to stress, control of cell growth, and induction of development in response to environmental changes. On the basis of genomic information, it has been found that Aspergillus nidulans, a model species of fungi, includes 15 histidine kinases (HKs), one histidine-containing phosphotransmitter protein (HPt), and four reponse regulators (RRs) as factors related to the signal transduction system. In this review, it is explain that the His-Asp phosphorelay system is important in controling cell growth (responses to fungicides, the induction of asexual and sexual development, and so on) under different growth conditions with reference to A. nidulans.
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Analytical Chemistry Communication
Organic Chemistry Regular Papers
  • Chiaki NAKANO, Takahiro OOTSUKA, Kazutoshi TAKAYAMA, Toshiaki MITSUI, ...
    2011 Volume 75 Issue 1 Pages 75-81
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    Supplementary material
    The Rv3377c and Rv3378c genes from Mycobacterium tuberculosis are specifically found in the virulent Mycobacterium species, but not in the avirulent species. The Rv3378c-encoded enzyme produced tuberculosinol 2 (5(6), 13(14)-halimadiene-15-ol), 13R-5a and 13S-isotuberculosinol 5b (5(6), 14(15)-halimadiene-13-ol) as its enzymatic products from tuberculosinyl diphosphate 3, indicating that the Rv3378c enzyme catalyzed the nucleophilic addition of a water molecule after the release of a diphosphate moiety. The three enzymatic products 2, 5a, and 5b were produced irrespective of the N- and C-terminal His-tagged Rv3378c enzymes, and of the maltose-binding protein fusion enzyme; the product distribution ratio was identical between the enzymes as 1:1 for 2:5, and 1:3 for 5a:5b. The successful separation of 5a and 5b by a chiral HPLC column provided the first complete assignments of 1H- and 13C-NMR data for 5a and 5b. The enzymatic mechanism for producing 2, 5a, and 5b is proposed here, and the optimal catalytic conditions and kinetic parameters, in addition to the divalent metal effects, are described. Site-directed mutagenesis of Asp into Asn, targeted at the DDXXD motif, resulted in significantly decreased enzymatic activity.
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  • Yoshinori SUGAI, Sho MIYAZAKI, Shinichiro MUKAI, Isamu YUMOTO, Masahir ...
    2011 Volume 75 Issue 1 Pages 128-135
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Supplementary material
    Natural terpenoids have elaborate structures and various bioactivities, making difficult their synthesis and labeling with isotopes. We report here the enzymatic total synthesis of plant hormone gibberellins (GAs) with recombinant biosynthetic enzymes from stable isotope-labeled acetate. Mevalonate (MVA) is a key intermediate for the terpenoid biosynthetic pathway. 13C-MVA was synthesized from 13C-acetate via acetyl-CoA, using four enzymes or fermentation with a MVA-secreted yeast. The diterpene hydrocarbon, ent-kaurene, was synthesized from 13C-acetate and 13C-MVA with ten and six recombinant enzymes in one test tube, respectively. Four recombinant enzymes, P450 monooxygenases and soluble dioxygenases involved in the GA4 biosynthesis from ent-kaurene via GA12 were prepared in yeast and Escherichia coli. All intermediates and the final product GA4 were uniformly labeled with 13C without dilution by natural abundance when [U-13C2] acetate was used. The 13C-NMR and MS data for [U-13C20] ent-kaurene confirmed 13C-13C coupling, and no dilution with the 12C atom was observed.
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Biochemistry & Molecular Biology Regular Papers
  • Beom-Su KIM, Yoon-Chul KIM, Homa ZADEH, Yoon-Jeong PARK, Sung-Hee PI, ...
    2011 Volume 75 Issue 1 Pages 13-19
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Dipsaci Radix is the dried root of Dipsacus asper Wall. It has been used in Korean herbal medicine to treat bone fractures. In this study, we examined the effect of the dichloromethane fraction of Dipsaci Radix (DRDM) on the osteoblastic differentiation of human alveolar bone marrow-derived MSCs (ABM-MSCs). The ABM-MSCs were isolated from healthy subjects and cultured in vitro, followed by phenotypic characterization. They showed a fibroblast-like morphology and expressed CD29, CD44, CD73, and CD105, but not CD34. Calcified nodules were generated in response to both dexamethasone (DEX) and DRDM. There was a significant increase in the alkaline phosphatase (ALP) activity and protein expression of bone sialoprotein (BSP) and osteocalcin (OC) in response to DEX and DRDM as compared to control. These results provide evidence for the osteogenic potential of cultured ABM-MSCs in response to DRDM. Also, an active single compound was additionally isolated from DRDM. The single compound (hederagenin 3-O-(2-O-acetyl)-α-L-arabinopyranoside) also significantly increased ALP activity and the level of protein expression of BSP and OC. These results highlight the possible clinical applications of DRDM and hederagenin 3-O-(2-O-acetyl)-α-L-arabinopyranoside in bone regeneration.
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  • Shigeru ITO, Masahiro SHIMIZU, Maki NAGATSUKA, Seiji KITAJIMA, Michiyo ...
    2011 Volume 75 Issue 1 Pages 20-25
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    Supplementary material
    To understand better the host defense mechanisms of mollusks against pathogens, we examined the anti-microbial activity of mucus from the giant African snail Achatina fulica. Hemagglutination activity of the mucus secreted by the integument of snails inoculated with Escherichia coli was observed to increase and to cause hemagglutination of rabbit red blood cells. Purification of the snail mucus lectin by sequential column chromatography revealed that the relative molecular mass of the lectin was 350 kDa. The hemagglutination activity of the lectin was Ca2+-dependent and was inhibited by galactose. Growth arrest tests showed that the lectin did not inhibit bacterial growth, but did induce agglutination of gram-positive and gram-negative bacteria. Tissue distribution analyses using a polyclonal antibody revealed that the lectin was expressed in the tissues of the mantle collar. The lectin isolated from the mucus of the snail appeared to contribute to its innate immunity.
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  • Tsuneo OHMORI, Hirokazu MORITA, Megumi TANAKA, Masanori TOMOI, Keisuke ...
    2011 Volume 75 Issue 1 Pages 26-33
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Rhodococcus jostii RHA1 is a polychlorinated biphenyl degrader. Multi-component biphenyl 2,3-dioxygenase (BphA) genes of RHA1 encode large and small subunits of oxygenase component and ferredoxin and reductase components. They did not express enzyme activity in Escherichia coli. To obtain BphA activity in E. coli, hybrid BphA gene derivatives were constructed by replacing ferredoxin and/or reductase component genes of RHA1 with those of Pseudomonas pseudoalcaligenes KF707. The results obtained indicate a lack of catalytic activity of the RHA1 ferredoxin component gene, bphAc in E. coli. To determine the cause of inability of RHA1 bphAc to express in E. coli, the bphAc gene was introduced into Rosetta (DE3) pLacI, which has extra tRNA genes for rare codons in E. coli. The resulting strain abundantly produced the bphAc product, and showed activity. These results suggest that codon usage bias is involved in inability of RHA1 bphAc to express its catalytic activity in E. coli.
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  • Hitomi KAJIWARA, Toshiki MINE, Tatsuo MIYAZAKI, Takeshi YAMAMOTO
    2011 Volume 75 Issue 1 Pages 47-53
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    Supplementary material
    A cytidine 5′-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac) synthetase was found in a crude extract prepared from Photobacterium leiognathi JT-SHIZ-145, a marine bacterium that also produces a β-galactoside α2,6-sialyltransferase. The CMP-Neu5Ac synthetase was purified from the crude extract of the cells by a combination of anion-exchange and gel filtration column chromatography. The purified enzyme migrated as a single band (60 kDa) on sodium dodecylsulfate–polyacrylamide gel electrophoresis. The activity of the enzyme was maximal at 35 °C at pH 9.0, and the synthetase required Mg2+ for activity. Although these properties are similar to those of other CMP-Neu5Ac synthetases isolated from bacteria, this synthetase produced not only CMP-Neu5Ac from cytidine triphosphate and Neu5Ac, but also CMP-N-glycolylneuraminic acid from cytidine triphosphate and N-glycolylneuraminic acid, unlike CMP-Neu5Ac synthetase purified from Escherichia coli.
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  • Jing YAO, Yuxiang WANG, Weishi WANG, Ning WANG, Hui LI
    2011 Volume 75 Issue 1 Pages 54-61
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in a variety of biological processes. Studies of miRNAs in mammals suggest that many are involved in lipid metabolism and adipocyte differentiation, but little is known about miRNA expression profiles during chicken adipogenesis. In this study, the Solexa sequencing approach was used to sequence a small RNA library prepared from Arbor Acres broiler pre-adipocytes, and more than 106 short sequence reads were obtained. From these, 159 known chicken miRNAs and 63 novel miRNAs were identified using a bioinformatics approach. Fifty-nine of these miRNA genes were further organized into 27 compact miRNA genomic clusters, and 34 new chicken mirtrons were also discovered, among which there were 27 mirtron candidates. These findings should serve as a foundation for future research on the functional roles of miRNAs in chicken adipocyte differentiation.
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  • Beatrice LYIMO, Fumio YAGI, Yuji MINAMI
    2011 Volume 75 Issue 1 Pages 62-69
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    A new galectin was characterized in the Amethyst deceiver mushroom Laccaria amethystina. The complete amino acid (AA) sequence of the lectin, which exhibited β-galactoside specificity, was deduced from its peptide sequences. The AA sequence of L. amethystina galectin (LAG) showed high homology with those of the same genus, at 75.6% identity to Laccaria bicolor, and 35.5–65.0% to galectins of Agrocybe spp. and Coprinopsis cinerea. The AA sequence of LAG contained all but one conserved residue known to be involved in β-galactoside binding, with His at the position 57 residue replaced by Thr in LAG. Analysis of binding specificity by hemagglutination inhibition assay and enzyme-linked lectin-sorbent assay revealed high specificity of LAG towards O-glycoproteins.
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  • Flávio Couto CORDEIRO, Claudete SANTA-CATARINA, Vanildo SILVEIR ...
    2011 Volume 75 Issue 1 Pages 70-74
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Humic acids (HAs) have positive effects on plant physiology, but the molecular mechanisms underlying these events are only partially understood. The induction of root growth and emission of lateral roots (LRs) promoted by exogenous auxin is a natural phenomenon. Exogenous auxins are also associated with HA. Gas nitric oxide (NO) is a secondary messenger produced endogenously in plants. It is associated with metabolic events dependent on auxin. With the application of auxin, NO production is significantly increased, resulting in positive effects on plant physiology. Thus it is possible to evaluate the beneficial effects of the application of HA as an effect of auxin. To investigate the effects of HA the parameters of root growth, Zea mays was studied by evaluating the application of 3 mM C L−1 of HA extracted from Oxisol and 100 μM SNP (sodium nitroprusside) and the NO donor, subject to two N–NO3, high dose (5.0 mM N–NO3) and low dose (5.0 mM N–NO3). Treatments with HA and NO were positively increased, regardless of the N–NO3 taken, as assessed by fresh weight and dry root, issue of LRs. The effects were more pronounced in the treatment with a lower dose of N–NO3. Detection of reactive oxygen species (ROS) in vivo and catalase activity were evaluated; these tests were associated with root growth. Under application of the bioactive substances tested, detection of ROS and catalase activity increased, especially in treatments with lower doses of N–NO3. The results of this experiment indicate that the effects of HA are dependent on ROS generation, which act as a messenger that induces root growth and the emission of LRs.
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  • Yuri MUKAI, Masao YOSHIZAWA, Takanori SASAKI, Masami IKEDA, Kentaro TO ...
    2011 Volume 75 Issue 1 Pages 82-88
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    Membrane proteins in the Golgi apparatus play important roles in biological functions, predominantly as catalysts related to post-translational modification of protein oligosaccharides. We succeeded in extracting the characteristics of Golgi type II membrane proteins computationally by comparison with those of Golgi no retention proteins, which are mainly localized in the plasma membrane. Golgi type II membrane proteins were detected by combining hydropathy alignment and a position-specific score matrix of the amino acid propensities around the transmembrane region. We achieved 96.2% sensitivity, 93.5% specificity, and a 0.949 success rate in a self-consistency test. In a 5-fold cross-validation test, 88.0% sensitivity, 85.5% specificity, and a 0.867 success rate were achieved.
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  • Masako NISHIZAWA, Yoshiyasu YABUSAKI, Masaharu KANAOKA
    2011 Volume 75 Issue 1 Pages 89-94
    Published: January 23, 2011
    Released: January 23, 2011
    JOURNALS FREE ACCESS
    The role of amino acid residues in the enzymatic activity of carboxylesterase from Arthrobacter globiformis was analyzed by diisopropyl fluorophosphate (DFP) labeling and site-directed mutagenesis. The electrospray ionization mass spectrometric (ESI-MS) analysis of the esterase, covalently labeled by DFP, showed stoichiometric incorporation of the inhibitor into the enzyme. The further comparison of endopeptidase-digested fragments between native and DFP-labeled esterase by fast atom bombardment mass spectrometric (FAB-MS) analysis as well as site-directed mutagenesis indicated that Ser59 in the consensus sequence Ser-X-X-Lys, which is conserved exclusively in penicillin-binding proteins and some esterases, served as a catalytic nucleophile. In addition, the results obtained from analysis of the mutants at position 62 suggested the importance of the basic amino acid side chain at this position, and suggested the significance of this residue acting directly as a general base rather than its involvement in the maintenance of the optimum hydrogen-bonding network at the active site.
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  • Bo Eng CHEONG, Tomoya TAKEMURA, Kayo YOSHIMATSU, Fumihiko SATO
    2011 Volume 75 Issue 1 Pages 107-113
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Carapichea ipecacuanha produces various emetine-type alkaloids, known as ipecac alkaloids, which have long been used as expectorants, emetics, and amebicides. In this study, we isolated an O-methyltransferase cDNA from this medicinal plant. The encoded protein (CiOMT1) showed 98% sequence identity to IpeOMT2, which catalyzes the 7′-O-methylation of 7′-O-demethylcephaeline to form cephaeline at the penultimate step of emetine biosynthesis (Nomura and Kutchan, J. Biol. Chem., 285, 7722–7738 (2010)). Recombinant CiOMT1 showed both 7′-O-methylation and 6′-O-methylation activities at the last two steps of emetine biosynthesis. This indicates that small differences in amino acid residues are responsible for distinct regional methylation specificities between IpeOMT2 and CiOMT1, and that CiOMT1 might contribute to two sequential O-methylation steps from 7′-O-demethylcephaeline to emetine.
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  • Yukari MUTO, Shoji SEGAMI, Hidehiro HAYASHI, Junko SAKURAI, Mari MURAI ...
    2011 Volume 75 Issue 1 Pages 114-122
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    Supplementary material
    Rapid growth of the submerged shoots of deepwater rice is essential for survival during the rainy season. We investigated changes in the expression of vacuolar H+-ATPase (V-ATPase), H+-pyrophosphatase (V-PPase), and aquaporins under submerged conditions. The amounts of vacuolar proton pumps, which support the active transport of ions into the vacuoles, were maintained on a membrane protein basis in the developing vacuoles. Among the six isogenes of V-PPase, OsVHP1;3 was markedly enhanced by submersion. The gene expression of efficient water channels, OsTIP1;1, OsTIP2;2, OsPIP1;1, OsPIP2;1, and OsPIP2;2, was markedly enhanced by submersion. The increase in aquaporin expression might support quick elongation of internodes. The mRNA levels of OsNIP2;2 and OsNIP3;1, which transport silicic and boric acids respectively, clearly decreased. The present study indicates that internodes of deepwater rice upregulate vacuolar proton pumps and water channel aquaporins and downregulate aquaporins that allow permeation of the substrates that suppress internode growth.
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Biochemistry & Molecular Biology Notes
Food & Nutrition Science Regular Papers
  • Yuichiro TAKANAMI, Tsutomu NAKAYAMA
    2011 Volume 75 Issue 1 Pages 34-39
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    The reactive oxygen species generated by an aqueous extract of the particulate phase of cigarette smoke were evaluated by an electron spin resonance (ESR) analysis, using spin-trapping agents, and by comparing with model reaction systems. The ESR signals of DMPO-OH were detected from the extract by using 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). These signals were eliminated by adding superoxide dismutase, but hardly by catalase. These responses of the ESR signals to the scavengers were similar to those of a hypoxanthine-xanthine oxidase system. The results indicate that the signals of DMPO-OH from the extract were derived from a reaction product of DMPO with superoxide anion radicals and clarify the mechanism by which the extract generated superoxide anion radicals.
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  • Kosuke NISHI, Ai KONDO, Takeaki OKAMOTO, Hiroyuki NAKANO, Miho DAIFUKU ...
    2011 Volume 75 Issue 1 Pages 40-46
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    The water-soluble fraction of kale (Brassica oleracea L. var. acephala DC.) had immunoglobulin (Ig) production stimulating activity in human hybridoma HB4C5 cells and human peripheral blood lymphocytes. The biochemical and physical properties of the main active substance in kale were found to be a heat-stable protein with a molecular weight higher than 50 kDa. The Ig production-stimulating factors were assumed to act on the translational and/or secreting processes of Igs. This Ig production-stimulating effect was also observed in lymphocytes from the mesenteric lymph node and Peyer’s patches of mice that had been administered with the kale extract for 14 d. The partially purified kale extract was analyzed by LC-ESI-MS/MS, the result indicating ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) as an active substance. Rubisco from spinach indeed exhibited Ig production-stimulating activity in HB4C5 cells. These findings provide another beneficial aspect of kale as a health-promoting foodstuff.
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  • Satoshi HARAMIZU, Fuminori KAWABATA, Yoriko MASUDA, Koichiro OHNUKI, T ...
    2011 Volume 75 Issue 1 Pages 95-99
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Enhancing energy expenditure and reducing energy intake are both crucial for weight control. Capsinoids, which are non-pungent capsaicin analogs, are known to suppress body fat accumulation and reduce body weight by enhancing energy expenditure in both mice and humans. However, it is poorly understood whether the suppression of body fat accumulation by capsinoids has an advantage over dietary restriction. This study shows that the oxygen consumption was increased in mice administered with capsinoids but not in dietary-restricted mice, although there was a similar suppression of body fat accumulation in both groups. The weight rebound was more notable in the dietary-restricted mice than in the mice administered with capsinoids. These results indicate that suppressing body fat accumulation by capsinoids was more beneficial than a restricted diet for maintaining body weight.
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  • Takeshi ISHII, Tatsuya ICHIKAWA, Kanako MINODA, Koji KUSAKA, Sohei ITO ...
    2011 Volume 75 Issue 1 Pages 100-106
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Human serum albumin (HSA) contributes to the stabilization of (−)-epigallocatechin gallate (EGCg) in serum. We characterize in the present study the mechanisms for preventing EGCg oxidation by HSA. EGCg was stable in human serum or buffers with HSA, but (−)-epigallocatechin (EGC) was unstable. We show by comparing EGCg and EGC in a neutral buffer that EGCg had a higher binding affinity than EGC. This indicates that the galloyl moiety participated in the interaction of EGCg with HSA and that this interaction was of critical importance in preventing EGCg oxidation. The binding affinity of EGCg for HSA and protein carbonyl formation in HSA were enhanced in an alkaline buffer. These results suggest the reversible covalent modification of EGCg via Schiff-base formation, and that the immobilization of EGCg to HSA, through the formation of a stable complex, prevented the polymerization and decomposition of EGCg in human serum.
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Food & Nutrition Science Notes
Microbiology & Fermentation Technology Regular Papers
  • Kimiko WATANABE, Satsuki TOMIOKA, Kiyoko TANIMURA, Hisae OKU, Koichiro ...
    2011 Volume 75 Issue 1 Pages 7-12
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
    JOURNALS FREE ACCESS
    The uptake activity ratio for AMP, ADP, and ATP in mutant (T-1) cells of Escherichia coli W, deficient in de novo purine biosynthesis at a point between IMP and 5-aminoimidazole-4-carboxiamide-1-β-D-ribofuranoside (AICAR), was 1:0.43:0.19. This ratio was approximately equal to the 5′-nucleotidase activity ratio in E. coli W cells. The order of inhibitory effect on [2-3H]ADP uptake by T-1 cells was adenine > adenosine > AMP > ATP. About 2-fold more radioactive purine bases than purine nucleosides were detected in the cytoplasm after 5 min in an experiment with [8-14C]AMP and T-1 cells. Uptake of [2-3H]adenosine in T-1 cells was inhibited by inosine, but not in mutant (Ad-3) cells of E. coli W, which lacked adenosine deaminase and adenylosuccinate lyase. These experiments suggest that AMP, ADP, and ATP are converted mainly to adenine and hypoxanthine via adenosine and inosine before uptake into the cytoplasm by E. coli W cells.
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  • Nobuyuki YOSHIDA, Takuya HAYASAKI, Hiroshi TAKAGI
    2011 Volume 75 Issue 1 Pages 123-127
    Published: January 23, 2011
    Released: January 23, 2011
    [Advance publication] Released: January 07, 2011
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    Rhodococcus erythropolis N9T-4 shows extremely oligotrophic growth requiring atmospheric CO2 without any additional carbon or energy source. We performed a gene expression analysis of the oxidoreductases, which are involved in methanol metabolism, under various growth and induction conditions in N9T-4. A real-time PCR analysis revealed that the genes encoding NAD-dependent formaldehyde dehydrogenase (nFADH) and N,N′-dimethyl-4-nitrosoaniline-dependent methanol dehydrogenase (MDH) were strongly expressed under the oligotrophic conditions at levels of 20–100 fold those under heterotrophic conditions, in which n-tetradecane was used as the sole carbon source, while glucose did not affect the gene expression pattern in a minimum medium. The genes encoding mycothiol-dependent formaldehyde dehydrogenase (mFADH) and formate dehydrogenase were not induced under oligotrophic conditions, although mFADH expression was observed when formaldehyde was added to the induction medium. These results suggest that N9T-4 had three distinct formaldehyde oxidation systems, and that MDH and nFADH were the key enzymes in its oligotrophic growth.
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Microbiology & Fermentation Technology Notes
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