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  • 1
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    Active-site models for complexes of quinolinate synthase with substrates and intermediates (2013)
    Wiley-Blackwell
    Details
    Publication Date: 2013-09-26
    Description: Quinolinate synthase (QS) catalyzes the condensation of iminoaspartate and dihydroxyacetone phosphate to form quinolinate, the universal precursor for the de novo biosynthesis of nicotinamide adenine dinucleotide. QS has been difficult to characterize owing either to instability or lack of activity when it is overexpressed and purified. Here, the structure of QS from Pyrococcus furiosus has been determined at 2.8 Å resolution. The structure is a homodimer consisting of three domains per protomer. Each domain shows the same topology with a four-stranded parallel β-sheet flanked by four α-helices, suggesting that the domains are the result of gene triplication. Biochemical studies of QS indicate that the enzyme requires a [4Fe–4S] cluster, which is lacking in this crystal structure, for full activity. The organization of domains in the protomer is distinctly different from that of a monomeric structure of QS from P. horikoshii [Sakuraba et al. (2005), J. Biol. Chem. 280 , 26645–26648]. The domain arrangement in P. furiosus QS may be related to protection of cysteine side chains, which are required to chelate the [4Fe–4S] cluster, prior to cluster assembly.
    Print ISSN: 0907-4449
    Electronic ISSN: 1399-0047
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley-Blackwell on behalf of International Union of Crystallography (IUCr).
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  • 2
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    Cell metabolism: autophagy transcribed (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-11-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Settembre, Carmine -- Ballabio, Andrea -- England -- Nature. 2014 Dec 4;516(7529):40-1. doi: 10.1038/nature13939. Epub 2014 Nov 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Telethon Institute of Genetics and Medicine, Naples 80078, Italy; in the Department of Translational Medicine, Federico II University, Naples; and in the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25383529" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autophagy/*genetics ; Cyclic AMP Response Element-Binding Protein/metabolism ; Fatty Acids/metabolism ; *Gene Expression Regulation ; Liver/cytology/*metabolism ; PPAR alpha/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Receptors, Cytoplasmic and Nuclear/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-09-16
    Description: Article Cytomegalovirus is a danger to individuals with compromised immune systems and neonates infected in utero . Here the authors show the structure of a neutralizing antibody-bound viral fusion protein glycoprotein B, supporting the development of therapeutic antibodies and vaccines. Nature Communications doi: 10.1038/ncomms9176 Authors: Sumana Chandramouli, Claudio Ciferri, Pavel A. Nikitin, Stefano Caló, Rachel Gerrein, Kara Balabanis, James Monroe, Christy Hebner, Anders E. Lilja, Ethan C. Settembre, Andrea Carfi
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain (2016)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2016-12-07
    Description: Nature Medicine 22, 1465 (2016). doi:10.1038/nm.4223 Authors: Donald D Raymond, Shaun M Stewart, Jiwon Lee, Jack Ferdman, Goran Bajic, Khoi T Do, Michael J Ernandes, Pirada Suphaphiphat, Ethan C Settembre, Philip R Dormitzer, Giuseppe Del Giudice, Oretta Finco, Tae Hyun Kang, Gregory C Ippolito, George Georgiou, Thomas B Kepler, Barton F Haynes, M Anthony Moody, Hua-Xin Liao, Aaron G Schmidt & Stephen C Harrison For broad protection against infection by viruses such as influenza or HIV, vaccines should elicit antibodies that bind conserved viral epitopes, such as the receptor-binding site (RBS). RBS-directed antibodies have been described for both HIV and influenza virus, and the design of immunogens to elicit them is a goal of vaccine research in both fields. Residues in the RBS of influenza virus hemagglutinin (HA) determine a preference for the avian or human receptor, α-2,3-linked sialic acid and α-2,6-linked sialic acid, respectively. Transmission of an avian-origin virus between humans generally requires one or more mutations in the sequences encoding the influenza virus RBS to change the preferred receptor from avian to human, but passage of a human-derived vaccine candidate in chicken eggs can select for reversion to avian receptor preference. For example, the X-181 strain of the 2009 new pandemic H1N1 influenza virus, derived from the A/California/07/2009 isolate and used in essentially all vaccines since 2009, has arginine at position 226, a residue known to confer preference for an α-2,3 linkage in H1 subtype viruses; the wild-type A/California/07/2009 isolate, like most circulating human H1N1 viruses, has glutamine at position 226. We describe, from three different individuals, RBS-directed antibodies that recognize the avian-adapted H1 strain in current influenza vaccines but not the circulating new pandemic 2009 virus; Arg226 in the vaccine-strain RBS accounts for the restriction. The polyclonal sera of the three donors also reflect this preference. Therefore, when vaccines produced from strains that are never passaged in avian cells become widely available, they may prove more capable of eliciting RBS-directed, broadly neutralizing antibodies than those produced from egg-adapted viruses, extending the established benefits of current seasonal influenza immunizations.
    Print ISSN: 1078-8956
    Electronic ISSN: 1546-170X
    Topics: Biology , Medicine
    Published by Nature Publishing Group (NPG)
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  • 5
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    Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody [Immunology and Inflammation] (2018)
    National Academy of Sciences
    Details
    Publication Date: 2018-01-03
    Description: Circulating influenza viruses evade neutralization in their human hosts by acquiring escape mutations at epitopes of prevalent antibodies. A goal for next-generation influenza vaccines is to reduce escape likelihood by selectively eliciting antibodies recognizing conserved surfaces on the viral hemagglutinin (HA). The receptor-binding site (RBS) on the HA “head” and...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    TFEB links autophagy to lysosomal biogenesis (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-28
    Description: Autophagy is a cellular catabolic process that relies on the cooperation of autophagosomes and lysosomes. During starvation, the cell expands both compartments to enhance degradation processes. We found that starvation activates a transcriptional program that controls major steps of the autophagic pathway, including autophagosome formation, autophagosome-lysosome fusion, and substrate degradation. The transcription factor EB (TFEB), a master gene for lysosomal biogenesis, coordinated this program by driving expression of autophagy and lysosomal genes. Nuclear localization and activity of TFEB were regulated by serine phosphorylation mediated by the extracellular signal-regulated kinase 2, whose activity was tuned by the levels of extracellular nutrients. Thus, a mitogen-activated protein kinase-dependent mechanism regulates autophagy by controlling the biogenesis and partnership of two distinct cellular organelles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638014/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638014/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Settembre, Carmine -- Di Malta, Chiara -- Polito, Vinicia Assunta -- Garcia Arencibia, Moises -- Vetrini, Francesco -- Erdin, Serkan -- Erdin, Serpil Uckac -- Huynh, Tuong -- Medina, Diego -- Colella, Pasqualina -- Sardiello, Marco -- Rubinsztein, David C -- Ballabio, Andrea -- 250154/European Research Council/International -- 5 P30 HD024064/HD/NICHD NIH HHS/ -- G0600194/Medical Research Council/United Kingdom -- P30 HD024064/HD/NICHD NIH HHS/ -- R01 NS078072/NS/NINDS NIH HHS/ -- TGM11CB6/Telethon/Italy -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Jun 17;332(6036):1429-33. doi: 10.1126/science.1204592. Epub 2011 May 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, 80131 Naples, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21617040" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Animals ; *Autophagy ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics/*metabolism ; COS Cells ; Cell Nucleus/*metabolism ; Cells, Cultured ; Cercopithecus aethiops ; Cytoplasm/metabolism ; Gene Expression Regulation ; HeLa Cells ; Humans ; Liver/metabolism ; Lysosomes/*metabolism ; MAP Kinase Signaling System ; Mice ; Mice, Transgenic ; Microtubule-Associated Proteins/metabolism ; Mitogen-Activated Protein Kinase 1/metabolism ; Phagosomes/metabolism ; Phosphorylation ; RNA Interference ; Transcription, Genetic ; Up-Regulation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Insulin granules. Insulin secretory granules control autophagy in pancreatic beta cells (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-02-24
    Description: Pancreatic beta cells lower insulin release in response to nutrient depletion. The question of whether starved beta cells induce macroautophagy, a predominant mechanism maintaining energy homeostasis, remains poorly explored. We found that, in contrast to many mammalian cells, macroautophagy in pancreatic beta cells was suppressed upon starvation. Instead, starved beta cells induced lysosomal degradation of nascent secretory insulin granules, which was controlled by protein kinase D (PKD), a key player in secretory granule biogenesis. Starvation-induced nascent granule degradation triggered lysosomal recruitment and activation of mechanistic target of rapamycin that suppressed macroautophagy. Switching from macroautophagy to insulin granule degradation was important to keep insulin secretion low upon fasting. Thus, beta cells use a PKD-dependent mechanism to adapt to nutrient availability and couple autophagy flux to secretory function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goginashvili, Alexander -- Zhang, Zhirong -- Erbs, Eric -- Spiegelhalter, Coralie -- Kessler, Pascal -- Mihlan, Michael -- Pasquier, Adrien -- Krupina, Ksenia -- Schieber, Nicole -- Cinque, Laura -- Morvan, Joelle -- Sumara, Izabela -- Schwab, Yannick -- Settembre, Carmine -- Ricci, Romeo -- New York, N.Y. -- Science. 2015 Feb 20;347(6224):878-82. doi: 10.1126/science.aaa2628.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM, CNRS, Universite de Strasbourg, 67404 Illkirch, France. ; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany. ; Dulbecco Telethon Institute and Telethon Institute of Genetics and Medicine (TIGEM), 80131 Naples, Italy. ; Dulbecco Telethon Institute and Telethon Institute of Genetics and Medicine (TIGEM), 80131 Naples, Italy. Medical Genetics, Department of Medical and Translational Science Unit, Federico II University, Via Pansini 5, 80131 Naples, Italy. ; Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM, CNRS, Universite de Strasbourg, 67404 Illkirch, France. Nouvel Hopital Civil, Laboratoire de Biochimie et de Biologie Moleculaire, Universite de Strasbourg, 67091 Strasbourg, France. romeo.ricci@igbmc.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700520" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Autophagy ; Cells, Cultured ; Fasting ; Humans ; Insulin/*secretion ; Insulin-Secreting Cells/*physiology/secretion/ultrastructure ; Mice ; Mice, Mutant Strains ; Mice, Transgenic ; Mitogen-Activated Protein Kinase 13/genetics ; Protein Kinase C/physiology ; Secretory Vesicles/*physiology/secretion
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    FGF signalling regulates bone growth through autophagy (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-11-26
    Description: Skeletal growth relies on both biosynthetic and catabolic processes. While the role of the former is clearly established, how the latter contributes to growth-promoting pathways is less understood. Macroautophagy, hereafter referred to as autophagy, is a catabolic process that plays a fundamental part in tissue homeostasis. We investigated the role of autophagy during bone growth, which is mediated by chondrocyte rate of proliferation, hypertrophic differentiation and extracellular matrix (ECM) deposition in growth plates. Here we show that autophagy is induced in growth-plate chondrocytes during post-natal development and regulates the secretion of type II collagen (Col2), the major component of cartilage ECM. Mice lacking the autophagy related gene 7 (Atg7) in chondrocytes experience endoplasmic reticulum storage of type II procollagen (PC2) and defective formation of the Col2 fibrillary network in the ECM. Surprisingly, post-natal induction of chondrocyte autophagy is mediated by the growth factor FGF18 through FGFR4 and JNK-dependent activation of the autophagy initiation complex VPS34-beclin-1. Autophagy is completely suppressed in growth plates from Fgf18(-/-) embryos, while Fgf18(+/-) heterozygous and Fgfr4(-/-) mice fail to induce autophagy during post-natal development and show decreased Col2 levels in the growth plate. Strikingly, the Fgf18(+/-) and Fgfr4(-/-) phenotypes can be rescued in vivo by pharmacological activation of autophagy, pointing to autophagy as a novel effector of FGF signalling in bone. These data demonstrate that autophagy is a developmentally regulated process necessary for bone growth, and identify FGF signalling as a crucial regulator of autophagy in chondrocytes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cinque, Laura -- Forrester, Alison -- Bartolomeo, Rosa -- Svelto, Maria -- Venditti, Rossella -- Montefusco, Sandro -- Polishchuk, Elena -- Nusco, Edoardo -- Rossi, Antonio -- Medina, Diego L -- Polishchuk, Roman -- De Matteis, Maria Antonietta -- Settembre, Carmine -- England -- Nature. 2015 Dec 10;528(7581):272-5. doi: 10.1038/nature16063. Epub 2015 Nov 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078 Pozzuoli (NA), Italy. ; Dulbecco Telethon Institute, Via Campi Flegrei, 34, 80078 Pozzuoli (NA), Italy. ; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy. ; Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26595272" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autophagy/genetics/*physiology ; Bone Development/genetics/*physiology ; Cell Differentiation ; Cell Proliferation ; Cells, Cultured ; Chondrocytes/cytology/metabolism ; Collagen Type II/secretion ; Embryo, Mammalian ; Extracellular Matrix/genetics ; Fibroblast Growth Factors/*genetics/metabolism ; Growth Plate/cytology/metabolism ; MAP Kinase Signaling System ; Mice ; Microtubule-Associated Proteins/genetics/metabolism ; Receptor, Fibroblast Growth Factor, Type 4/genetics/metabolism ; *Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Astrocyte dysfunction and neurodegeneration in LSD [Genetics] (2012)
    National Academy of Sciences
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    Publication Date: 2012-08-29
    Description: The role of astrocytes in neurodegenerative processes is increasingly appreciated. Here we investigated the contribution of astrocytes to neurodegeneration in multiple sulfatase deficiency (MSD), a severe lysosomal storage disorder caused by mutations in the sulfatase modifying factor 1 (SUMF1) gene. Using Cre/Lox mouse models, we found that astrocyte-specific deletion of...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    A RANKL-PKC{beta}-TFEB signaling cascade is necessary for lysosomal biogenesis in osteoclasts [Research Papers] (2013)
    Cold Spring Harbor Laboratory Press
    Details
    Publication Date: 2013-04-30
    Description: Bone resorption by osteoclasts requires a large number of lysosomes that release proteases in the resorption lacuna. Whether lysosomal biogenesis is a consequence of the action of transcriptional regulators of osteoclast differentiation or is under the control of a different and specific transcriptional pathway remains unknown. We show here, through cell-based assays and cell-specific gene deletion experiments in mice, that the osteoclast differentiation factor RANKL promotes lysosomal biogenesis once osteoclasts are differentiated through the selective activation of TFEB, a member of the MITF/TFE family of transcription factors. This occurs following PKCβ phosphorylation of TFEB on three serine residues located in its last 15 amino acids. This post-translational modification stabilizes and increases the activity of this transcription factor. Supporting these biochemical observations, mice lacking in osteoclasts—either TFEB or PKCβ—show decreased lysosomal gene expression and increased bone mass. Altogether, these results uncover a RANKL-dependent signaling pathway taking place in differentiated osteoclasts and culminating in the activation of TFEB to enhance lysosomal biogenesis—a necessary step for proper bone resorption.
    Print ISSN: 0890-9369
    Topics: Biology
    Published by Cold Spring Harbor Laboratory Press
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