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FEBS Journal

Cover image for Vol. 278 Issue 21

November 2011

Volume 278, Issue 21

Pages 3953–4167

  1. Review Articles

    1. Top of page
    2. Review Articles
    3. Original Articles
    4. Corrigendum
    5. Author Index
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      Genome walking in eukaryotes (pages 3953–3977)

      Claudia Leoni, Mariateresa Volpicella, Francesca De Leo, Raffaele Gallerani and Luigi R. Ceci

      Article first published online: 15 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08307.x

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      The identification of nucleotide sequences flanking already characterized genome regions can be pursued by several genome walking (GW) strategies. Several GW methods have been developed in the last 20 years, including the recent coupling with Next Generation Sequencing technologies. This review focuses on the use of GW strategies in several aspects of the study of eukaryotic genomes

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      The AMPK/SNF1/SnRK1 fuel gauge and energy regulator: structure, function and regulation (pages 3978–3990)

      Ruben Ghillebert, Erwin Swinnen, Jing Wen, Lies Vandesteene, Matthew Ramon, Koen Norga, Filip Rolland and Joris Winderickx

      Article first published online: 26 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08315.x

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      The AMPK/SNF1/SnRK1-mediated responses across species show remarkable similarities, indicating that the cross-species structural conservation of the kinase complex reflects the remarkable functional conservation. Although intensive research has already been performed on the AMPK/SNF1/SnRK1 kinase complexes, several fundamental issues still await to be clarified. In this review, we highlight these issues and focus on the structure, function and regulation

  2. Original Articles

    1. Top of page
    2. Review Articles
    3. Original Articles
    4. Corrigendum
    5. Author Index
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      Chitin oligosaccharide binding to a family GH19 chitinase from the moss Bryum coronatum (pages 3991–4001)

      Takayuki Ohnuma, Morten Sørlie, Tatsuya Fukuda, Noriko Kawamoto, Toki Taira and Tamo Fukamizo

      Article first published online: 27 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08301.x

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      From ITC analysis, chitin oligosaccharide binding to a family GH19 chitinase from Bryum coronatum was found to be driven by favorable enthalpy changes with unfavorable entropy changes. The longer the chain length of the oligosaccharide tested (3–6), the larger the negative values of the binding free energy changes. The analysis provided new insight into the binding mode of GH19 enzymes

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      The prion protein binds thiamine (pages 4002–4014)

      Rolando Perez-Pineiro, Trent C. Bjorndahl, Mark V. Berjanskii, David Hau, Li Li, Alan Huang, Rose Lee, Ebrima Gibbs, Carol Ladner, Ying Wei Dong, Ashenafi Abera, Neil R. Cashman and David S. Wishart

      Article first published online: 15 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08304.x

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      To identify a possible biological role of the prion protein, we performed a protein-binding screen of naturally occurring metabolites. Using a combination of NMR, fluorescence and SPR we identified thiamine as a specific prion ligand (KD∼ 60 μm). This is one of the first endogenous prion ligands to be identified and may suggest a new physiological function for this protein

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      Induction of a stress response in Lactococcus lactis is associated with a resistance to ribosomally active antibiotics (pages 4015–4024)

      James M. Dorrian, Deborah A. Briggs, Michael L. Ridley, Robert Layfield and Ian D. Kerr

      Article first published online: 15 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08305.x

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      Expression of an ATP binding cassette protein, LmrC, in Lactococcus lactis led to an increase in resistance to ribosomally active antibiotics. However, LmrC function did not cause this resistance. Rather, a cellular stress response induced by the expression of LmrC was responsible. A model in which the induction of cellular stress responses leads to antibiotic resistance is presented

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      Increased expression of nonmuscle myosin IIs is associated with 3MC-induced mouse tumor (pages 4025–4034)

      Shekhar Saha, Sumit K. Dey, Provas Das and Siddhartha S. Jana

      Article first published online: 19 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08306.x

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      Nonmuscle myosin IIs (NM IIs) are known to be involved in cell migration, division and adhesion. We report that expression of NM IIs is increased in 3-methylcholanthrene (3MC) induced mouse tumor. Treatment of 3MC initiates dedifferentiation of C2C12-myotube in our in vitro study. Dedifferentiation of muscle fibers along with fibroblast transformation could be cellular pathways for 3MC induced tumor formation in mice

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      Role of HoxE subunit in Synechocystis PCC6803 hydrogenase (pages 4035–4043)

      Emeline Aubert-Jousset, Melissa Cano, Geneviève Guedeney, Pierre Richaud and Laurent Cournac

      Article first published online: 15 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08308.x

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      Cyanobacterial NAD(P)-reducing reversible hydrogenases comprise five subunits (HoxE/F/U/Y/H). Upon hoxE deletion, the Synechocystis PCC6803 hydrogenase became unable to catalyze H2 production or uptake in interaction with NADH/NAD+. However, activation of the electron transfer-independent H+/D exchange reaction by NADPH was still observed, whereas activation by NADH was lost. These data suggest different mechanisms for diaphorase-mediated electron transfer and catalytic site activation

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      Homology-modelled structure of the βB2B3-crystallin heterodimer studied by ion mobility and radical probe MS (pages 4044–4054)

      Kevin M. Downard, Yuichi Kokabu, Mitsunori Ikeguchi and Satoko Akashi

      Article first published online: 15 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08309.x

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      Homology modelled structure of the βB2B3-crystallin heterodimer based on data obtained by ion mobility and radical probe mass spectrometry

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      A kinetic model linking protein conformational motions, interflavin electron transfer and electron flux through a dual-flavin enzyme – simulating the reductase activity of the endothelial and neuronal nitric oxide synthase flavoprotein domains (pages 4055–4069)

      Mohammad M. Haque, Claire Kenney, Jesús Tejero and Dennis J. Stuehr

      Article first published online: 15 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08310.x

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      Kinetic model for electron flux through a dual-flavin enzyme. Computer simulations of the kinetic model, along with experimentally-determined measures of the KAhq and the cytochrome c (Cyt c) reductase activity, provide rate estimates for the protein conformational opening and closing steps (k1,k3, k−1, k−3) and the interflavin electron transfer step (k2) that enable catalysis by dual-flavin enzymes

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      Extensive post-translational processing of potato tuber storage proteins and vacuolar targeting (pages 4070–4087)

      Malene Jørgensen, Allan Stensballe and Karen Gjesing Welinder

      Article first published online: 22 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08311.x

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      Potato tuber storage proteins were obtained from vacuoles isolated from field-grown starch potato tubers cv. Kuras. Proteome analysis demonstrated an abundance of molecular forms of six abundant super families, Kunitz and carboxy protease inhibitors, protease inhibitors 1 and 2, patatins and lipoxygenases

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      Multiple NF-Y-binding CCAAT boxes are essential for transcriptional regulation of the human C7orf24 gene, a novel tumor-associated gene (pages 4088–4099)

      Yuji Ohno, Akira Hattori, Masamichi Ueda, Susumu Kageyama, Tatsuhiro Yoshiki and Hideaki Kakeya

      Article first published online: 26 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08314.x

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      We characterized the promoter region of the human chromosome 7 open reading frame 24 gene (C7orf24) to explore its transcriptional regulatory mechanism. A luciferase reporter gene assay demonstrated that the three proximal CCAAT boxes are essential for C7orf24 gene transcription. Moreover, we revealed that NF-Ys bind to the three CCAAT boxes and play a central role in C7orf24 gene expression

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      Biological characteristics of two lysines on human serum albumin in the high-affinity binding of 4Z,15Z-bilirubin-IXα revealed by phage display (pages 4100–4111)

      Ai Minomo, Yu Ishima, Ulrich Kragh-Hansen, Victor T. G. Chuang, Makiyo Uchida, Kazuaki Taguchi, Hiroshi Watanabe, Toru Maruyama, Hiroshi Morioka and Masaki Otagiri

      Article first published online: 23 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08316.x

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      We identified key amino acid residues of HSA involved in 4Z,15Z-bilirubin-IXα (4Z,15Z-BR) binding using phage display analysis and point mutation techniques. From various binding assays and photoconversion experiments, whilst both Lys195 and Lys199 in subdomain IIA are important for the high affinity binding of 4Z,15Z-BR, Lys199 plays a more prominent role in the elimination of 4Z,15Z-BR

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      Selenodiglutathione uptake by the Saccharomyces cerevisiae vacuolar ATP-binding cassette transporter Ycf1p (pages 4112–4121)

      Myriam Lazard, Nguyet-Thanh Ha-Duong, Stéphanie Mounié, Romary Perrin, Pierre Plateau and Sylvain Blanquet

      Article first published online: 29 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08318.x

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      The Saccharomyces cerevisiae vacuolar ABC-transporter Ycf1p is involved in selenite toxicity. Using secretory vesicles isolated from a sec6-4 mutant, we establish that the glutathione-conjugate selenodiglutathione is a high-affinity substrate of this ABC-transporter and that oxidized glutathione is also efficiently transported. Finally, we show that the presence of Ycf1p impairs the GSH/GSSG ratio of cells subjected to a selenite stress

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      Characterization of the PLP-dependent aminotransferase NikK from Streptomyces tendae and its putative role in nikkomycin biosynthesis (pages 4122–4135)

      Alexandra Binter, Gustav Oberdorfer, Sebastian Hofzumahaus, Stefanie Nerstheimer, Georg Altenbacher, Karl Gruber and Peter Macheroux

      Article first published online: 28 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08319.x

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      As inhibitors of chitin synthase, nikkomycins have attracted interest as potential antibiotics. However, information on the biosynthetic reactions leading to these peptide nucleosides is still very limited. In order to elucidate the last step of the biosynthesis of the aminohexuronic building block of nikkomycins, we have identified a pyridoxal-5-phosphate dependent aminotransferase

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      Crystal structure of Onconase at 1.1 Å resolution – insights into substrate binding and collective motion (pages 4136–4149)

      Daniel E. Holloway, Umesh P. Singh, Kuslima Shogen and K. Ravi Acharya

      Article first published online: 28 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08320.x

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      Onconase, an antitumoral ribonuclease, is a much poorer catalyst than its relative, ribonuclease A. We determine a low-temperature, atomic-resolution crystal structure that clarifies deficiencies in its active site. Peptide backbone displacements, anisotropic atomic displacement parameters and an elastic network model reveal collective motion that had previously eluded detection. Differences in conformational equilibria could contribute to onconase’s reduced ribonucleolytic activity

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      Insights into the mechanism of enhanced mobilization of hematopoietic progenitor cells and release of CXCL12 by a combination of AMD3100 and aminoglycoside–polyarginine conjugates (pages 4150–4165)

      Alexander Berchanski, Alexander Kalinkovich, Aya Ludin, Tsvee Lapidot and Aviva Lapidot

      Article first published online: 4 OCT 2011 | DOI: 10.1111/j.1742-4658.2011.08348.x

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      Mobilization of hematopoietic stem and progenitor cells (HSPCs) from the bone marrow to the peripheral blood is utilized in clinical HSPC transplantation protocols. Aminoglycoside-polyarginine conjugates (APACs) induce mobilization of white blood cells and preferentially immature hematopoietic progenitor cells in mice. Administration of AMD3100 with each one of the APACs revealed additional HPC mobilization, accompanied by a significant elevation in plasma CXCL12 levels

  3. Corrigendum

    1. Top of page
    2. Review Articles
    3. Original Articles
    4. Corrigendum
    5. Author Index
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      Corrigendum (page 4166)

      Article first published online: 26 SEP 2011 | DOI: 10.1111/j.1742-4658.2011.08255.x

      This article corrects:
  4. Author Index

    1. Top of page
    2. Review Articles
    3. Original Articles
    4. Corrigendum
    5. Author Index
    1. You have free access to this content
      Author index (page 4167)

      Article first published online: 21 OCT 2011 | DOI: 10.1111/j.1742-4658.2011.07857.x

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