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  • Articles  (196)
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  • 1
    Publication Date: 2015-07-24
    Description: Bacteria secrete peptides and proteins to communicate, to poison competitors, and to manipulate host cells. Among the various protein-translocation machineries, the peptidase-containing ATP-binding cassette transporters (PCATs) are appealingly simple. Each PCAT contains two peptidase domains that cleave the secretion signal from the substrate, two transmembrane domains that form a translocation pathway, and two nucleotide-binding domains that hydrolyse ATP. In Gram-positive bacteria, PCATs function both as maturation proteases and exporters for quorum-sensing or antimicrobial polypeptides. In Gram-negative bacteria, PCATs interact with two other membrane proteins to form the type 1 secretion system. Here we present crystal structures of PCAT1 from Clostridium thermocellum in two different conformations. These structures, accompanied by biochemical data, show that the translocation pathway is a large alpha-helical barrel sufficient to accommodate small folded proteins. ATP binding alternates access to the transmembrane pathway and also regulates the protease activity, thereby coupling substrate processing to translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, David Yin-wei -- Huang, Shuo -- Chen, Jue -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jul 23;523(7561):425-30. doi: 10.1038/nature14623.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Laboratory of Membrane Biology and Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA [2] Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10065, USA. ; Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26201595" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphate/deficiency/metabolism ; Clostridium thermocellum/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Peptides/*metabolism/secretion ; Protein Binding ; Protein Multimerization ; Protein Structure, Tertiary ; Structure-Activity Relationship
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  • 2
    Publication Date: 2015-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Henry -- Horn, Rainer -- England -- Nature. 2015 Jan 29;517(7536):553. doi: 10.1038/517553d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China; and Pennsylvania State University, University Park, USA. ; Christian Albrechts University zu Kiel, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25631433" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; China ; Conservation of Natural Resources/*trends ; Goals ; *International Cooperation ; Soil/*chemistry ; *United Nations ; Water Supply/standards
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  • 3
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    Nature Publishing Group (NPG)
    Publication Date: 2015-03-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Mar 26;519(7544):S54-5. doi: 10.1038/519S54a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25806694" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/prevention & control ; Biomedical Research ; Chemistry/statistics & numerical data ; China ; Drug Industry ; Genome, Human/genetics ; Humans ; Investments ; Marine Biology ; Private Sector ; Publishing/statistics & numerical data ; Research/economics/*statistics & numerical data
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  • 4
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    Nature Publishing Group (NPG)
    Publication Date: 2015-09-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pain, Stephanie -- England -- Nature. 2015 Sep 24;525(7570):S10-1. doi: 10.1038/525S10a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26398731" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Canada ; Cannabinol/history ; *Cannabis/adverse effects/chemistry/classification/genetics ; China ; Dronabinol/adverse effects/history/pharmacology/therapeutic use ; Drug Approval/history ; Drug and Narcotic Control/*history ; Endocannabinoids/history/metabolism ; Herbal Medicine/*history ; History, 16th Century ; History, 17th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Medical Marijuana/adverse effects/history/pharmacology/therapeutic use ; Multiple Sclerosis/drug therapy/physiopathology ; New Orleans ; Phytotherapy/history ; Plant Extracts/therapeutic use ; Plants, Medicinal/adverse effects/chemistry/classification/genetics ; Receptors, Cannabinoid/history/metabolism
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  • 5
    Publication Date: 2015-02-20
    Description: Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage-specific behaviour of selected factors. In addition to the orchestrated remodelling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer, and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signalling effectors, and the epigenome during human embryonic stem cell differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499331/" 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/PMC4499331/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsankov, Alexander M -- Gu, Hongcang -- Akopian, Veronika -- Ziller, Michael J -- Donaghey, Julie -- Amit, Ido -- Gnirke, Andreas -- Meissner, Alexander -- 5F32DK095537/DK/NIDDK NIH HHS/ -- P01 GM099117/GM/NIGMS NIH HHS/ -- P01GM099117/GM/NIGMS NIH HHS/ -- P50HG006193/HG/NHGRI NIH HHS/ -- U01 ES017155/ES/NIEHS NIH HHS/ -- U01ES017155/ES/NIEHS NIH HHS/ -- England -- Nature. 2015 Feb 19;518(7539):344-9. doi: 10.1038/nature14233.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Immunology, Weizmann Institute, Rehovot, 76100 Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25693565" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Differentiation/genetics ; Cell Lineage ; Chromatin/chemistry/genetics/metabolism ; Chromatin Assembly and Disassembly/genetics ; DNA Methylation ; Embryonic Stem Cells/*cytology/*metabolism ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/genetics ; Epigenomics ; Genome, Human/genetics ; Germ Layers/cytology/metabolism ; Histones/chemistry/metabolism ; Humans ; Protein Binding ; Signal Transduction ; Transcription Factors/*metabolism ; Transcription, Genetic/genetics
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  • 6
    Publication Date: 2015-10-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2015 Oct 1;526(7571):13-4. doi: 10.1038/nature.2015.18440.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26432216" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/analysis/*economics/*supply & distribution ; China ; Environmental Policy/*economics/*trends ; *International Cooperation ; Renewable Energy/statistics & numerical data ; United Nations ; United States
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  • 7
    Publication Date: 2015-09-30
    Description: The battle for survival between bacteria and the viruses that infect them (phages) has led to the evolution of many bacterial defence systems and phage-encoded antagonists of these systems. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated (cas) genes comprise an adaptive immune system that is one of the most widespread means by which bacteria defend themselves against phages. We identified the first examples of proteins produced by phages that inhibit a CRISPR-Cas system. Here we performed biochemical and in vivo investigations of three of these anti-CRISPR proteins, and show that each inhibits CRISPR-Cas activity through a distinct mechanism. Two block the DNA-binding activity of the CRISPR-Cas complex, yet do this by interacting with different protein subunits, and using steric or non-steric modes of inhibition. The third anti-CRISPR protein operates by binding to the Cas3 helicase-nuclease and preventing its recruitment to the DNA-bound CRISPR-Cas complex. In vivo, this anti-CRISPR can convert the CRISPR-Cas system into a transcriptional repressor, providing the first example-to our knowledge-of modulation of CRISPR-Cas activity by a protein interactor. The diverse sequences and mechanisms of action of these anti-CRISPR proteins imply an independent evolution, and foreshadow the existence of other means by which proteins may alter CRISPR-Cas function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bondy-Denomy, Joseph -- Garcia, Bianca -- Strum, Scott -- Du, Mingjian -- Rollins, MaryClare F -- Hidalgo-Reyes, Yurima -- Wiedenheft, Blake -- Maxwell, Karen L -- Davidson, Alan R -- MOP-130482/Canadian Institutes of Health Research/Canada -- MOP-136845/Canadian Institutes of Health Research/Canada -- P20GM103500/GM/NIGMS NIH HHS/ -- R01GM108888/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Oct 1;526(7571):136-9. doi: 10.1038/nature15254. Epub 2015 Sep 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA. ; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26416740" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*metabolism/*virology ; Bacteriophages/*metabolism ; CRISPR-Associated Proteins/*antagonists & inhibitors/metabolism ; CRISPR-Cas Systems/genetics/*physiology ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Helicases/antagonists & inhibitors/metabolism ; DNA, Viral/metabolism ; DNA-Binding Proteins/antagonists & inhibitors/metabolism ; Endonucleases/antagonists & inhibitors/metabolism ; *Evolution, Molecular ; Protein Binding ; Protein Subunits/antagonists & inhibitors/metabolism ; Repressor Proteins/genetics/metabolism ; Substrate Specificity ; Viral Proteins/*metabolism
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  • 8
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2015 Dec 17;528(7582):S184-6. doi: 10.1038/528S184a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26673026" target="_blank"〉PubMed〈/a〉
    Keywords: Beijing ; China ; *Diffusion of Innovation ; Electronics ; Industry/economics/*statistics & numerical data ; Patents as Topic/statistics & numerical data ; Precision Medicine ; Public-Private Sector Partnerships ; Research/economics/organization & administration/*statistics & numerical data ; Technology Transfer ; Telecommunications
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  • 9
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    Nature Publishing Group (NPG)
    Publication Date: 2015-01-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gong, Zhaohui -- England -- Nature. 2015 Jan 8;517(7533):145. doi: 10.1038/517145c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ningbo University School of Medicine, Ningbo, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25567273" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/adverse effects/*prevention & control ; China ; Climate Change ; Congresses as Topic ; Humans ; Public Health ; Time Factors
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  • 10
    Publication Date: 2015-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Hong -- Thompson, Julian R -- Flower, Roger J -- England -- Nature. 2015 Sep 24;525(7570):455. doi: 10.1038/525455e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Oslo, Norway. ; University College London, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26399818" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Electric Power Supplies/utilization ; Rain ; *Seasons ; Snow ; *Snow Sports/economics ; Time Factors ; Water Supply/economics/*statistics & numerical data
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  • 11
    Publication Date: 2015-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Bo -- Davis, Wayne S -- England -- Nature. 2015 Nov 26;527(7579):446. doi: 10.1038/527446f.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Information Center, Ministry of Environmental Protection, Beijing, China. ; EPA, Washington DC, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26607534" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information ; China ; Environmental Pollutants/*analysis ; Internet/utilization ; United States ; *United States Environmental Protection Agency
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  • 12
    Publication Date: 2015-06-05
    Description: The endoplasmic reticulum (ER) is the largest intracellular endomembrane system, enabling protein and lipid synthesis, ion homeostasis, quality control of newly synthesized proteins and organelle communication. Constant ER turnover and modulation is needed to meet different cellular requirements and autophagy has an important role in this process. However, its underlying regulatory mechanisms remain unexplained. Here we show that members of the FAM134 reticulon protein family are ER-resident receptors that bind to autophagy modifiers LC3 and GABARAP, and facilitate ER degradation by autophagy ('ER-phagy'). Downregulation of FAM134B protein in human cells causes an expansion of the ER, while FAM134B overexpression results in ER fragmentation and lysosomal degradation. Mutant FAM134B proteins that cause sensory neuropathy in humans are unable to act as ER-phagy receptors. Consistently, disruption of Fam134b in mice causes expansion of the ER, inhibits ER turnover, sensitizes cells to stress-induced apoptotic cell death and leads to degeneration of sensory neurons. Therefore, selective ER-phagy via FAM134 proteins is indispensable for mammalian cell homeostasis and controls ER morphology and turnover in mice and humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khaminets, Aliaksandr -- Heinrich, Theresa -- Mari, Muriel -- Grumati, Paolo -- Huebner, Antje K -- Akutsu, Masato -- Liebmann, Lutz -- Stolz, Alexandra -- Nietzsche, Sandor -- Koch, Nicole -- Mauthe, Mario -- Katona, Istvan -- Qualmann, Britta -- Weis, Joachim -- Reggiori, Fulvio -- Kurth, Ingo -- Hubner, Christian A -- Dikic, Ivan -- England -- Nature. 2015 Jun 18;522(7556):354-8. doi: 10.1038/nature14498. Epub 2015 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany. ; Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Kollegiengasse 10, 07743 Jena, Germany. ; 1] Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands [2] Department of Cell Biology, University Medical Center Utrecht, University of Groningen, Antonious Deusinglaan 1, 3713 AV Groningen, The Netherlands. ; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany. ; Electron Microscopy Center, Jena University Hospital, Friedrich-Schiller-University Jena, Ziegelmuhlenweg 1, 07743 Jena, Germany. ; Institute for Biochemistry I, Jena University Hospital, Friedrich-Schiller-University Jena, 07743 Jena, Germany. ; Institute of Neuropathology, RWTH Aachen University Hospital, Pauwelsstr. 30, 52074 Aachen, Germany. ; 1] Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany [2] Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany [3] Institute of Immunology, School of Medicine University of Split, Mestrovicevo setaliste bb, 21 000 Split, Croatia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26040720" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Apoptosis ; Autophagy/*physiology ; Biomarkers/metabolism ; Cell Line ; Endoplasmic Reticulum/chemistry/*metabolism ; Female ; Gene Deletion ; Humans ; Lysosomes/metabolism ; Male ; Membrane Proteins/deficiency/genetics/*metabolism ; Mice ; Microtubule-Associated Proteins/metabolism ; Neoplasm Proteins/deficiency/genetics/*metabolism ; Phagosomes/metabolism ; Protein Binding ; Sensory Receptor Cells/metabolism/pathology
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  • 13
    Publication Date: 2015-08-11
    Description: G-protein-coupled receptors (GPCRs) constitute the largest family of membrane receptors in eukaryotes. Crystal structures have provided insight into GPCR interactions with ligands and G proteins, but our understanding of the conformational dynamics of activation is incomplete. Metabotropic glutamate receptors (mGluRs) are dimeric class C GPCRs that modulate neuronal excitability, synaptic plasticity, and serve as drug targets for neurological disorders. A 'clamshell' ligand-binding domain (LBD), which contains the ligand-binding site, is coupled to the transmembrane domain via a cysteine-rich domain, and LBD closure seems to be the first step in activation. Crystal structures of isolated mGluR LBD dimers led to the suggestion that activation also involves a reorientation of the dimer interface from a 'relaxed' to an 'active' state, but the relationship between ligand binding, LBD closure and dimer interface rearrangement in activation remains unclear. Here we use single-molecule fluorescence resonance energy transfer to probe the activation mechanism of full-length mammalian group II mGluRs. We show that the LBDs interconvert between three conformations: resting, activated and a short-lived intermediate state. Orthosteric agonists induce transitions between these conformational states, with efficacy determined by occupancy of the active conformation. Unlike mGluR2, mGluR3 displays basal dynamics, which are Ca(2+)-dependent and lead to basal protein activation. Our results support a general mechanism for the activation of mGluRs in which agonist binding induces closure of the LBDs, followed by dimer interface reorientation. Our experimental strategy should be widely applicable to study conformational dynamics in GPCRs and other membrane proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4597782/" 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/PMC4597782/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vafabakhsh, Reza -- Levitz, Joshua -- Isacoff, Ehud Y -- 2PN2EY018241/EY/NEI NIH HHS/ -- PN2 EY018241/EY/NEI NIH HHS/ -- England -- Nature. 2015 Aug 27;524(7566):497-501. doi: 10.1038/nature14679. Epub 2015 Aug 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA. ; Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA. ; Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26258295" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Drug Partial Agonism ; *Fluorescence Resonance Energy Transfer ; Humans ; Ligands ; Models, Biological ; Models, Molecular ; Protein Binding ; Protein Conformation ; Rats ; Receptors, Metabotropic Glutamate/*chemistry/*classification/genetics/metabolism
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  • 14
    Publication Date: 2015-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Jian -- Huang, Xiaolei -- England -- Nature. 2015 Apr 23;520(7548):436. doi: 10.1038/520436d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aarhus University, Denmark. ; Fujian Agriculture and Forestry University, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25903615" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/analysis ; Biodiversity ; China ; Crowdsourcing/economics/*instrumentation ; Environmental Monitoring/*instrumentation ; Mobile Applications/*supply & distribution/*utilization ; Organizations/economics/organization & administration
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  • 15
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    Nature Publishing Group (NPG)
    Publication Date: 2015-06-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gould, Julie -- England -- Nature. 2015 Jun 11;522(7555):245-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26065302" target="_blank"〉PubMed〈/a〉
    Keywords: Australia ; *Career Mobility ; Chile ; China ; Efficiency ; Emigrants and Immigrants/*statistics & numerical data ; Emigration and Immigration/*statistics & numerical data ; Europe ; *Internationality ; Research Personnel/*statistics & numerical data ; United States
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  • 16
    Publication Date: 2015-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Li -- England -- Nature. 2015 Nov 12;527(7577):135. doi: 10.1038/527135a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26560263" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Animals ; China ; Commerce/*legislation & jurisprudence ; Conservation of Natural Resources/*legislation & jurisprudence/*methods ; Crime/*legislation & jurisprudence ; *Elephants ; Endangered Species/*legislation & jurisprudence ; Horns/*chemistry ; United States
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 17
    Publication Date: 2015-02-18
    Description: The BCR-ABL1 fusion gene is a driver oncogene in chronic myeloid leukaemia and 30-50% of cases of adult acute lymphoblastic leukaemia. Introduction of ABL1 kinase inhibitors (for example, imatinib) has markedly improved patient survival, but acquired drug resistance remains a challenge. Point mutations in the ABL1 kinase domain weaken inhibitor binding and represent the most common clinical resistance mechanism. The BCR-ABL1 kinase domain gatekeeper mutation Thr315Ile (T315I) confers resistance to all approved ABL1 inhibitors except ponatinib, which has toxicity limitations. Here we combine comprehensive drug sensitivity and resistance profiling of patient cells ex vivo with structural analysis to establish the VEGFR tyrosine kinase inhibitor axitinib as a selective and effective inhibitor for T315I-mutant BCR-ABL1-driven leukaemia. Axitinib potently inhibited BCR-ABL1(T315I), at both biochemical and cellular levels, by binding to the active form of ABL1(T315I) in a mutation-selective binding mode. These findings suggest that the T315I mutation shifts the conformational equilibrium of the kinase in favour of an active (DFG-in) A-loop conformation, which has more optimal binding interactions with axitinib. Treatment of a T315I chronic myeloid leukaemia patient with axitinib resulted in a rapid reduction of T315I-positive cells from bone marrow. Taken together, our findings demonstrate an unexpected opportunity to repurpose axitinib, an anti-angiogenic drug approved for renal cancer, as an inhibitor for ABL1 gatekeeper mutant drug-resistant leukaemia patients. This study shows that wild-type proteins do not always sample the conformations available to disease-relevant mutant proteins and that comprehensive drug testing of patient-derived cells can identify unpredictable, clinically significant drug-repositioning opportunities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pemovska, Tea -- Johnson, Eric -- Kontro, Mika -- Repasky, Gretchen A -- Chen, Jeffrey -- Wells, Peter -- Cronin, Ciaran N -- McTigue, Michele -- Kallioniemi, Olli -- Porkka, Kimmo -- Murray, Brion W -- Wennerberg, Krister -- England -- Nature. 2015 Mar 5;519(7541):102-5. doi: 10.1038/nature14119. Epub 2015 Feb 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290 Helsinki, Finland. ; La Jolla Laboratories, Pfizer Worldwide Research &Development, San Diego, California 92121, USA. ; Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, 00290 Helsinki, Finland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25686603" target="_blank"〉PubMed〈/a〉
    Keywords: Angiogenesis Inhibitors/chemistry/pharmacology/therapeutic use ; Cell Line ; Cell Proliferation/drug effects ; Crystallization ; Crystallography, X-Ray ; Drug Repositioning ; Drug Resistance, Neoplasm/genetics ; Drug Screening Assays, Antitumor ; Fusion Proteins, bcr-abl/*antagonists & inhibitors/*chemistry/genetics/metabolism ; Humans ; Imidazoles/*chemistry/*pharmacology/therapeutic use ; Indazoles/*chemistry/*pharmacology/therapeutic use ; Kidney Neoplasms/drug therapy ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy/genetics/metabolism ; Models, Molecular ; Molecular Conformation ; Phosphorylation/drug effects ; Protein Binding ; Protein Kinase Inhibitors/chemistry/pharmacology/therapeutic use ; Proto-Oncogene Proteins c-abl/antagonists & ; inhibitors/chemistry/genetics/metabolism ; Vascular Endothelial Growth Factor Receptor-2/antagonists & ; inhibitors/chemistry/metabolism
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  • 18
    Publication Date: 2015-01-13
    Description: Evolutionarily conserved SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptors) proteins form a complex that drives membrane fusion in eukaryotes. The ATPase NSF (N-ethylmaleimide sensitive factor), together with SNAPs (soluble NSF attachment protein), disassembles the SNARE complex into its protein components, making individual SNAREs available for subsequent rounds of fusion. Here we report structures of ATP- and ADP-bound NSF, and the NSF/SNAP/SNARE (20S) supercomplex determined by single-particle electron cryomicroscopy at near-atomic to sub-nanometre resolution without imposing symmetry. Large, potentially force-generating, conformational differences exist between ATP- and ADP-bound NSF. The 20S supercomplex exhibits broken symmetry, transitioning from six-fold symmetry of the NSF ATPase domains to pseudo four-fold symmetry of the SNARE complex. SNAPs interact with the SNARE complex with an opposite structural twist, suggesting an unwinding mechanism. The interfaces between NSF, SNAPs, and SNAREs exhibit characteristic electrostatic patterns, suggesting how one NSF/SNAP species can act on many different SNARE complexes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320033/" 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/PMC4320033/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Minglei -- Wu, Shenping -- Zhou, Qiangjun -- Vivona, Sandro -- Cipriano, Daniel J -- Cheng, Yifan -- Brunger, Axel T -- 5-U01AI082051-05/AI/NIAID NIH HHS/ -- P50 GM082250/GM/NIGMS NIH HHS/ -- P50GM082250/GM/NIGMS NIH HHS/ -- R01 GM082893/GM/NIGMS NIH HHS/ -- R01 GM098672/GM/NIGMS NIH HHS/ -- R01GM082893/GM/NIGMS NIH HHS/ -- R01GM098672/GM/NIGMS NIH HHS/ -- R37 MH063105/MH/NIMH NIH HHS/ -- R37MH63105/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Feb 5;518(7537):61-7. doi: 10.1038/nature14148. Epub 2015 Jan 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA. ; Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA. ; 1] Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA [2] Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25581794" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Cricetulus ; Cryoelectron Microscopy ; Models, Molecular ; Multiprotein Complexes/*chemistry/*metabolism/ultrastructure ; N-Ethylmaleimide-Sensitive Proteins/chemistry/metabolism/ultrastructure ; Protein Binding ; Protein Structure, Tertiary ; Rats ; SNARE Proteins/*chemistry/*metabolism/ultrastructure ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment ; Proteins/chemistry/metabolism/ultrastructure
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  • 19
    Publication Date: 2015-02-18
    Description: Autophagy, an important catabolic pathway implicated in a broad spectrum of human diseases, begins by forming double membrane autophagosomes that engulf cytosolic cargo and ends by fusing autophagosomes with lysosomes for degradation. Membrane fusion activity is required for early biogenesis of autophagosomes and late degradation in lysosomes. However, the key regulatory mechanisms of autophagic membrane tethering and fusion remain largely unknown. Here we report that ATG14 (also known as beclin-1-associated autophagy-related key regulator (Barkor) or ATG14L), an essential autophagy-specific regulator of the class III phosphatidylinositol 3-kinase complex, promotes membrane tethering of protein-free liposomes, and enhances hemifusion and full fusion of proteoliposomes reconstituted with the target (t)-SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) syntaxin 17 (STX17) and SNAP29, and the vesicle (v)-SNARE VAMP8 (vesicle-associated membrane protein 8). ATG14 binds to the SNARE core domain of STX17 through its coiled-coil domain, and stabilizes the STX17-SNAP29 binary t-SNARE complex on autophagosomes. The STX17 binding, membrane tethering and fusion-enhancing activities of ATG14 require its homo-oligomerization by cysteine repeats. In ATG14 homo-oligomerization-defective cells, autophagosomes still efficiently form but their fusion with endolysosomes is blocked. Recombinant ATG14 homo-oligomerization mutants also completely lose their ability to promote membrane tethering and to enhance SNARE-mediated fusion in vitro. Taken together, our data suggest an autophagy-specific membrane fusion mechanism in which oligomeric ATG14 directly binds to STX17-SNAP29 binary t-SNARE complex on autophagosomes and primes it for VAMP8 interaction to promote autophagosome-endolysosome fusion.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4442024/" 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/PMC4442024/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diao, Jiajie -- Liu, Rong -- Rong, Yueguang -- Zhao, Minglei -- Zhang, Jing -- Lai, Ying -- Zhou, Qiangjun -- Wilz, Livia M -- Li, Jianxu -- Vivona, Sandro -- Pfuetzner, Richard A -- Brunger, Axel T -- Zhong, Qing -- 5P30CA142543/CA/NCI NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- R01 CA133228/CA/NCI NIH HHS/ -- R01 R37-MH63105/MH/NIMH NIH HHS/ -- R37 MH063105/MH/NIMH NIH HHS/ -- T32 GM007232/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Apr 23;520(7548):563-6. doi: 10.1038/nature14147. Epub 2015 Feb 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA [2] Department of Structural Biology, Stanford University, Stanford, California 94305, USA [3] Department of Photon Science, Stanford University, Stanford, California 94305, USA [4] Department of Neurology and Neurological Sciences, Stanford University, Stanford, California 94305, USA [5] Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA. ; 1] Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [3] College of Food Science &Nutritional Engineering, China Agricultural University, Beijing 100083, China. ; 1] Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25686604" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport/*chemistry/*metabolism ; *Autophagy ; Endosomes/*metabolism ; HEK293 Cells ; HeLa Cells ; Humans ; Lysosomes/*metabolism ; *Membrane Fusion ; Phagosomes/chemistry/*metabolism ; Protein Binding ; Protein Multimerization ; Protein Structure, Tertiary ; Qa-SNARE Proteins/metabolism ; Qb-SNARE Proteins/metabolism ; Qc-SNARE Proteins/metabolism ; R-SNARE Proteins/metabolism ; SNARE Proteins/chemistry/metabolism
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  • 20
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grayson, Michelle -- England -- Nature. 2015 Apr 30;520(7549):S10-2. doi: 10.1038/520S10a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924192" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/standards ; China ; Commerce/economics ; Evaluation Studies as Topic ; Great Britain ; Humans ; Research/economics/manpower/*standards/trends ; Research Personnel/standards ; Social Change
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  • 21
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grayson, Michelle -- England -- Nature. 2015 Apr 30;520(7549):S1. doi: 10.1038/520S1a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924191" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes ; Age Factors ; China ; Research Personnel ; Science/economics/manpower/*standards
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  • 22
    Publication Date: 2015-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zheng, Xiaoyan -- Lv, Yibing -- England -- Nature. 2015 Jul 16;523(7560):290. doi: 10.1038/523290e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉China National Environmental Monitoring Center, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26178953" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Cities ; Environmental Monitoring/*instrumentation ; Environmental Policy/*legislation & jurisprudence ; Environmental Pollution/*analysis/statistics & numerical data
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  • 23
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    Nature Publishing Group (NPG)
    Publication Date: 2015-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grayson, Michelle -- Pincock, Stephen -- England -- Nature. 2015 Nov 12;527(7577):S49. doi: 10.1038/527S49a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉custom publishing and Nature Index.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26560450" target="_blank"〉PubMed〈/a〉
    Keywords: *Bibliometrics ; China ; *Cooperative Behavior ; Geographic Mapping ; International Cooperation ; Periodicals as Topic/*statistics & numerical data ; Research/manpower/*organization & administration/*statistics & numerical data
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  • 24
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kogleck, Larissa -- England -- Nature. 2015 Dec 17;528(7582):S166-7. doi: 10.1038/528S166a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26673022" target="_blank"〉PubMed〈/a〉
    Keywords: *Bibliometrics ; China ; Cities/economics/statistics & numerical data ; Research/*statistics & numerical data
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  • 25
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Yingying -- England -- Nature. 2015 Dec 17;528(7582):S170-3. doi: 10.1038/528S170a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26673023" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Science Disciplines ; Chemistry ; China ; Diffusion of Innovation ; Ecology ; Economic Recession ; Humans ; International Cooperation ; Nobel Prize ; Physics ; Research/economics/manpower/standards/*statistics & numerical data ; Research Personnel/education/standards/supply & distribution ; Time Factors
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  • 26
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    Nature Publishing Group (NPG)
    Publication Date: 2015-09-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Zhao-Min -- England -- Nature. 2015 Sep 10;525(7568):187. doi: 10.1038/525187a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yunnan Public Security Bureau for Forests, Kunming, Yunnan, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26354475" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Wild/classification ; China ; *Classification ; Conservation of Natural Resources/*legislation & jurisprudence ; Endangered Species/*legislation & jurisprudence/*statistics & numerical data ; Plants/classification
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  • 27
    Publication Date: 2015-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Zhao-Min -- England -- Nature. 2015 Feb 19;518(7539):303. doi: 10.1038/518303c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yunnan Public Security Bureau for Forests, Kunming, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25693554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; China ; Conservation of Natural Resources/economics/*legislation & jurisprudence ; Crime/economics/*legislation & jurisprudence ; Endangered Species/economics/*legislation & jurisprudence ; *Horns ; Medicine, Chinese Traditional/economics
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  • 28
    Publication Date: 2015-09-04
    Description: TP53 (which encodes p53 protein) is the most frequently mutated gene among all human cancers. Prevalent p53 missense mutations abrogate its tumour suppressive function and lead to a 'gain-of-function' (GOF) that promotes cancer. Here we show that p53 GOF mutants bind to and upregulate chromatin regulatory genes, including the methyltransferases MLL1 (also known as KMT2A), MLL2 (also known as KMT2D), and acetyltransferase MOZ (also known as KAT6A or MYST3), resulting in genome-wide increases of histone methylation and acetylation. Analysis of The Cancer Genome Atlas shows specific upregulation of MLL1, MLL2, and MOZ in p53 GOF patient-derived tumours, but not in wild-type p53 or p53 null tumours. Cancer cell proliferation is markedly lowered by genetic knockdown of MLL1 or by pharmacological inhibition of the MLL1 methyltransferase complex. Our study reveals a novel chromatin mechanism underlying the progression of tumours with GOF p53, and suggests new possibilities for designing combinatorial chromatin-based therapies for treating individual cancers driven by prevalent GOF p53 mutations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568559/" 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/PMC4568559/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Jiajun -- Sammons, Morgan A -- Donahue, Greg -- Dou, Zhixun -- Vedadi, Masoud -- Getlik, Matthaus -- Barsyte-Lovejoy, Dalia -- Al-awar, Rima -- Katona, Bryson W -- Shilatifard, Ali -- Huang, Jing -- Hua, Xianxin -- Arrowsmith, Cheryl H -- Berger, Shelley L -- 092809/Z/10/Z/Wellcome Trust/United Kingdom -- P30 ES013508/ES/NIEHS NIH HHS/ -- R01 CA078831/CA/NCI NIH HHS/ -- R01 GM069905/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Sep 10;525(7568):206-11. doi: 10.1038/nature15251. Epub 2015 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada. ; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada. ; Abramson Family Cancer Research Institute, Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, Illinois 60611, USA. ; Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA. ; Princess Margaret Cancer Centre, and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2C4, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26331536" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cell Line, Tumor ; Cell Proliferation/genetics ; Chromatin/chemistry/*genetics/*metabolism ; Female ; Genes, Tumor Suppressor ; Genome, Human/genetics ; Histone Acetyltransferases/metabolism ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/chemistry/metabolism ; Humans ; Male ; Mice ; Mutant Proteins/genetics/metabolism ; Mutation/*genetics ; Myeloid-Lymphoid Leukemia Protein/metabolism ; Neoplasms/*genetics/metabolism/*pathology ; Phenotype ; Protein Binding ; Protein Processing, Post-Translational ; Tumor Suppressor Protein p53/*genetics/*metabolism
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  • 29
    Publication Date: 2015-12-18
    Description: Eukaryotic transcription factors (TFs) are key determinants of gene activity, yet they bind only a fraction of their corresponding DNA sequence motifs in any given cell type. Chromatin has the potential to restrict accessibility of binding sites; however, in which context chromatin states are instructive for TF binding remains mainly unknown. To explore the contribution of DNA methylation to constrained TF binding, we mapped DNase-I-hypersensitive sites in murine stem cells in the presence and absence of DNA methylation. Methylation-restricted sites are enriched for TF motifs containing CpGs, especially for those of NRF1. In fact, the TF NRF1 occupies several thousand additional sites in the unmethylated genome, resulting in increased transcription. Restoring de novo methyltransferase activity initiates remethylation at these sites and outcompetes NRF1 binding. This suggests that binding of DNA-methylation-sensitive TFs relies on additional determinants to induce local hypomethylation. In support of this model, removal of neighbouring motifs in cis or of a TF in trans causes local hypermethylation and subsequent loss of NRF1 binding. This competition between DNA methylation and TFs in vivo reveals a case of cooperativity between TFs that acts indirectly via DNA methylation. Methylation removal by methylation-insensitive factors enables occupancy of methylation-sensitive factors, a principle that rationalizes hypomethylation of regulatory regions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Domcke, Silvia -- Bardet, Anais Flore -- Adrian Ginno, Paul -- Hartl, Dominik -- Burger, Lukas -- Schubeler, Dirk -- England -- Nature. 2015 Dec 24;528(7583):575-9. doi: 10.1038/nature16462. Epub 2015 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland. ; University of Basel, Faculty of Sciences, Petersplatz 1, CH 4003 Basel, Switzerland. ; Swiss Institute of Bioinformatics, Maulbeerstrasse 66, CH 4058 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26675734" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Binding, Competitive ; Cells, Cultured ; Chromatin/chemistry/genetics/*metabolism ; *DNA Methylation ; Deoxyribonuclease I/metabolism ; Genome/genetics ; Humans ; Mice ; Mouse Embryonic Stem Cells/metabolism ; Nuclear Respiratory Factor 1/*metabolism ; Protein Binding ; Transcription Factors/*metabolism
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  • 30
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong-Yan, Jin -- Cheung, Felix -- England -- Nature. 2015 Apr 30;520(7549):S37. doi: 10.1038/520S37a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924200" target="_blank"〉PubMed〈/a〉
    Keywords: Bibliometrics ; China ; Hong Kong ; *Internationality ; Peer Review, Research/*methods/*standards ; *Personnel Selection ; Research Personnel/*standards ; United States ; Universities
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  • 31
    Publication Date: 2015-02-25
    Description: Plants and plant pathogens are subject to continuous co-evolutionary pressure for dominance, and the outcomes of these interactions can substantially impact agriculture and food security. In virus-plant interactions, one of the major mechanisms for plant antiviral immunity relies on RNA silencing, which is often suppressed by co-evolving virus suppressors, thus enhancing viral pathogenicity in susceptible hosts. In addition, plants use the nucleotide-binding and leucine-rich repeat (NB-LRR) domain-containing resistance proteins, which recognize viral effectors to activate effector-triggered immunity in a defence mechanism similar to that employed in non-viral infections. Unlike most eukaryotic organisms, plants are not known to activate mechanisms of host global translation suppression to fight viruses. Here we demonstrate in Arabidopsis that the constitutive activation of NIK1, a leucine-rich repeat receptor-like kinase (LRR-RLK) identified as a virulence target of the begomovirus nuclear shuttle protein (NSP), leads to global translation suppression and translocation of the downstream component RPL10 to the nucleus, where it interacts with a newly identified MYB-like protein, L10-INTERACTING MYB DOMAIN-CONTAINING PROTEIN (LIMYB), to downregulate translational machinery genes fully. LIMYB overexpression represses ribosomal protein genes at the transcriptional level, resulting in protein synthesis inhibition, decreased viral messenger RNA association with polysome fractions and enhanced tolerance to begomovirus. By contrast, the loss of LIMYB function releases the repression of translation-related genes and increases susceptibility to virus infection. Therefore, LIMYB links immune receptor LRR-RLK activation to global translation suppression as an antiviral immunity strategy in plants.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779052/" 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/PMC4779052/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zorzatto, Cristiane -- Machado, Joao Paulo B -- Lopes, Kenia V G -- Nascimento, Kelly J T -- Pereira, Welison A -- Brustolini, Otavio J B -- Reis, Pedro A B -- Calil, Iara P -- Deguchi, Michihito -- Sachetto-Martins, Gilberto -- Gouveia, Bianca C -- Loriato, Virgilio A P -- Silva, Marcos A C -- Silva, Fabyano F -- Santos, Anesia A -- Chory, Joanne -- Fontes, Elizabeth P B -- 5R01-GM94428/GM/NIGMS NIH HHS/ -- R01 GM094428/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Apr 30;520(7549):679-82. doi: 10.1038/nature14171. Epub 2015 Feb 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Departamento de Bioquimica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Vicosa, 36570.000 Vicosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Vicosa, 36570.000 Vicosa, Minas Gerais, Brazil. ; 1] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Vicosa, 36570.000 Vicosa, Minas Gerais, Brazil [2] Departamento de Genetica, Universidade Federal do Rio de Janeiro, 21944.970 Rio de Janeiro, Brazil. ; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Vicosa, 36570.000 Vicosa, Minas Gerais, Brazil. ; Departamento de Zootecnia, Universidade Federal de Vicosa, 36570.000 Vicosa, Minas Gerais, Brazil. ; 1] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Vicosa, 36570.000 Vicosa, Minas Gerais, Brazil [2] Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25707794" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Arabidopsis/*immunology/*virology ; Arabidopsis Proteins/*metabolism ; Begomovirus/*immunology ; Cell Nucleus/metabolism ; Down-Regulation ; Gene Expression Regulation, Plant ; Immune Tolerance ; *Immunity, Innate ; *Plant Immunity ; Protein Binding ; Protein Biosynthesis/genetics/*immunology ; Protein-Serine-Threonine Kinases/*metabolism ; Ribosomal Proteins/metabolism ; Transcription Factors/metabolism
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  • 32
    Publication Date: 2015-11-03
    Description: Macroautophagy (hereafter referred to as autophagy) is a catabolic membrane trafficking process that degrades a variety of cellular constituents and is associated with human diseases. Although extensive studies have focused on autophagic turnover of cytoplasmic materials, little is known about the role of autophagy in degrading nuclear components. Here we report that the autophagy machinery mediates degradation of nuclear lamina components in mammals. The autophagy protein LC3/Atg8, which is involved in autophagy membrane trafficking and substrate delivery, is present in the nucleus and directly interacts with the nuclear lamina protein lamin B1, and binds to lamin-associated domains on chromatin. This LC3-lamin B1 interaction does not downregulate lamin B1 during starvation, but mediates its degradation upon oncogenic insults, such as by activated RAS. Lamin B1 degradation is achieved by nucleus-to-cytoplasm transport that delivers lamin B1 to the lysosome. Inhibiting autophagy or the LC3-lamin B1 interaction prevents activated RAS-induced lamin B1 loss and attenuates oncogene-induced senescence in primary human cells. Our study suggests that this new function of autophagy acts as a guarding mechanism protecting cells from tumorigenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dou, Zhixun -- Xu, Caiyue -- Donahue, Greg -- Shimi, Takeshi -- Pan, Ji-An -- Zhu, Jiajun -- Ivanov, Andrejs -- Capell, Brian C -- Drake, Adam M -- Shah, Parisha P -- Catanzaro, Joseph M -- Ricketts, M Daniel -- Lamark, Trond -- Adam, Stephen A -- Marmorstein, Ronen -- Zong, Wei-Xing -- Johansen, Terje -- Goldman, Robert D -- Adams, Peter D -- Berger, Shelley L -- P01AG031862/AG/NIA NIH HHS/ -- R01 CA078831/CA/NCI NIH HHS/ -- R01 GM106023/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Nov 5;527(7576):105-9. doi: 10.1038/nature15548. Epub 2015 Oct 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA. ; Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA. ; Institute of Cancer Sciences, University of Glasgow and Beatson Institute for Cancer Research, Glasgow G61 1BD, UK. ; Department of Biochemistry &Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Molecular Cancer Research Group, Institute of Medical Biology, University of Tromso - The Arctic University of Norway, 9037 Tromso, Norway. ; Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26524528" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Animals ; *Autophagy ; Cell Aging ; Cell Transformation, Neoplastic ; Cells, Cultured ; Chromatin/chemistry/metabolism ; Cytoplasm/metabolism ; Fibroblasts ; HEK293 Cells ; Humans ; Lamin Type B/genetics/metabolism ; Lysosomes/metabolism ; Mice ; Microfilament Proteins/metabolism ; Microtubule-Associated Proteins/metabolism ; Nuclear Lamina/*metabolism ; Oncogene Protein p21(ras)/metabolism ; Protein Binding ; Proteolysis
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 33
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doudna, Jennifer -- England -- Nature. 2015 Dec 3;528(7580):S6. doi: 10.1038/528S6a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Berkeley.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26630598" target="_blank"〉PubMed〈/a〉
    Keywords: *CRISPR-Cas Systems ; China ; Congresses as Topic ; Embryo Research/*ethics/*legislation & jurisprudence ; Genetic Engineering/*ethics/*legislation & jurisprudence/standards ; *Genome ; Germ-Line Mutation/*ethics ; Great Britain ; Humans ; Safety/legislation & jurisprudence/standards ; United States
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 34
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    Nature Publishing Group (NPG)
    Publication Date: 2015-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adams, Jonathan -- Loach, Tamar -- England -- Nature. 2015 Nov 12;527(7577):S58-9. doi: 10.1038/527S58a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Digital Science and visiting professor at The Policy Institute, King's College, London.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26560452" target="_blank"〉PubMed〈/a〉
    Keywords: Bibliometrics ; China ; *Cooperative Behavior ; Geographic Mapping ; *International Cooperation ; Periodicals as Topic/statistics & numerical data ; Research/manpower/*organization & administration/*statistics & numerical data
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  • 35
    Publication Date: 2015-03-25
    Description: Cell migration is a stepwise process that coordinates multiple molecular machineries. Using in vitro angiogenesis screens with short interfering RNA and chemical inhibitors, we define here a MAP4K4-moesin-talin-beta1-integrin molecular pathway that promotes efficient plasma membrane retraction during endothelial cell migration. Loss of MAP4K4 decreased membrane dynamics, slowed endothelial cell migration, and impaired angiogenesis in vitro and in vivo. In migrating endothelial cells, MAP4K4 phosphorylates moesin in retracting membranes at sites of focal adhesion disassembly. Epistasis analyses indicated that moesin functions downstream of MAP4K4 to inactivate integrin by competing with talin for binding to beta1-integrin intracellular domain. Consequently, loss of moesin (encoded by the MSN gene) or MAP4K4 reduced adhesion disassembly rate in endothelial cells. Additionally, alpha5beta1-integrin blockade reversed the membrane retraction defects associated with loss of Map4k4 in vitro and in vivo. Our study uncovers a novel aspect of endothelial cell migration. Finally, loss of MAP4K4 function suppressed pathological angiogenesis in disease models, identifying MAP4K4 as a potential therapeutic target.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vitorino, Philip -- Yeung, Stacey -- Crow, Ailey -- Bakke, Jesse -- Smyczek, Tanya -- West, Kristina -- McNamara, Erin -- Eastham-Anderson, Jeffrey -- Gould, Stephen -- Harris, Seth F -- Ndubaku, Chudi -- Ye, Weilan -- England -- Nature. 2015 Mar 26;519(7544):425-30. doi: 10.1038/nature14323. Epub 2015 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Department, Genentech, Inc., South San Francisco, California 94080, USA. ; Chemical Biology and Therapeutics Department, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA. ; Translational Oncology Department, Genentech, Inc., South San Francisco, California 94080, USA. ; Pathology Department, Genentech, Inc., South San Francisco, California 94080, USA. ; Structural Biology Department, Genentech, Inc., South San Francisco, California 94080, USA. ; Discovery Chemistry Department, Genentech, Inc., South San Francisco, California 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25799996" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Antigens, CD29/chemistry/drug effects/metabolism ; Cell Membrane/drug effects/metabolism ; *Cell Movement ; Cell Shape/drug effects ; Endothelial Cells/*cytology/drug effects/*metabolism ; Epistasis, Genetic ; Focal Adhesions/metabolism ; Humans ; Integrin alpha1/drug effects/metabolism ; Integrins/drug effects/*metabolism ; Intracellular Signaling Peptides and Proteins/antagonists & ; inhibitors/deficiency/genetics/*metabolism ; Male ; Mice ; Microfilament Proteins/deficiency/genetics/metabolism ; Neovascularization, Pathologic ; Phosphorylation ; Protein Binding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/antagonists & ; inhibitors/deficiency/genetics/*metabolism ; Talin/chemistry/metabolism
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  • 36
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kun, Huang -- England -- Nature. 2015 Apr 30;520(7549):S18-20. doi: 10.1038/520S18a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924194" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/organization & administration/*standards ; Bibliometrics ; China ; Research/*standards ; Research Personnel/*standards ; Social Change
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  • 37
    Publication Date: 2015-07-30
    Description: DNA replication in eukaryotes is strictly regulated by several mechanisms. A central step in this replication is the assembly of the heterohexameric minichromosome maintenance (MCM2-7) helicase complex at replication origins during G1 phase as an inactive double hexamer. Here, using cryo-electron microscopy, we report a near-atomic structure of the MCM2-7 double hexamer purified from yeast G1 chromatin. Our structure shows that two single hexamers, arranged in a tilted and twisted fashion through interdigitated amino-terminal domain interactions, form a kinked central channel. Four constricted rings consisting of conserved interior beta-hairpins from the two single hexamers create a narrow passageway that tightly fits duplex DNA. This narrow passageway, reinforced by the offset of the two single hexamers at the double hexamer interface, is flanked by two pairs of gate-forming subunits, MCM2 and MCM5. These unusual features of the twisted and tilted single hexamers suggest a concerted mechanism for the melting of origin DNA that requires structural deformation of the intervening DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Ningning -- Zhai, Yuanliang -- Zhang, Yixiao -- Li, Wanqiu -- Yang, Maojun -- Lei, Jianlin -- Tye, Bik-Kwoon -- Gao, Ning -- England -- Nature. 2015 Aug 13;524(7564):186-91. doi: 10.1038/nature14685. Epub 2015 Jul 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China. ; 1] Division of Life Science, Hong Kong Universityof Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China [2] Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. ; 1] Division of Life Science, Hong Kong Universityof Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China [2] Department of Molecular Biology and Genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26222030" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Cycle Proteins/chemistry/metabolism/ultrastructure ; Chromatin/chemistry ; Conserved Sequence ; *Cryoelectron Microscopy ; DNA/chemistry/metabolism/ultrastructure ; DNA-Directed DNA Polymerase/chemistry/ultrastructure ; G1 Phase ; Minichromosome Maintenance Proteins/*chemistry/metabolism/*ultrastructure ; Models, Biological ; Models, Molecular ; Multienzyme Complexes/chemistry/ultrastructure ; Nucleic Acid Denaturation ; Protein Binding ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Subunits/*chemistry/metabolism ; Replication Origin ; Saccharomyces cerevisiae/*chemistry/*ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/metabolism/ultrastructure
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  • 38
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-25
    Description: China's economic slowdown could bring a windfall for basic science. Cosmic evolution, the structure of matter, the origins of life, and understanding how the brain works all deserve strengthened support, according to China's latest 5-year development plan, which could triple funding for basic research by 2020. An outline of the plan, which covers 2016 through 2020, received pro forma approval by the National People's Congress on 16 March at its closing session. Though details are still scarce, one expectation is that funding for basic research will rise to 10% of total R&D spending by 2020, up from less than 5% now. If the 10% goal is achieved, investment in basic research could hit 225 billion yuan, or about $34.5 billion, in 2020, compared with last year's $10 billion. Author: Hao Xin
    Keywords: China
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 39
    Publication Date: 2015-02-25
    Description: Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their associated (Cas) proteins provide adaptive immunity against viral infection in prokaryotes. Upon infection, short phage sequences known as spacers integrate between CRISPR repeats and are transcribed into small RNA molecules that guide the Cas9 nuclease to the viral targets (protospacers). Streptococcus pyogenes Cas9 cleavage of the viral genome requires the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) sequence immediately downstream of the viral target. It is not known whether and how viral sequences flanked by the correct PAM are chosen as new spacers. Here we show that Cas9 selects functional spacers by recognizing their PAM during spacer acquisition. The replacement of cas9 with alleles that lack the PAM recognition motif or recognize an NGGNG PAM eliminated or changed PAM specificity during spacer acquisition, respectively. Cas9 associates with other proteins of the acquisition machinery (Cas1, Cas2 and Csn2), presumably to provide PAM-specificity to this process. These results establish a new function for Cas9 in the genesis of prokaryotic immunological memory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385744/" 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/PMC4385744/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heler, Robert -- Samai, Poulami -- Modell, Joshua W -- Weiner, Catherine -- Goldberg, Gregory W -- Bikard, David -- Marraffini, Luciano A -- 1DP2AI104556-01/AI/NIAID NIH HHS/ -- DP2 AI104556/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Mar 12;519(7542):199-202. doi: 10.1038/nature14245. Epub 2015 Feb 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA. ; 1] Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA [2] Synthetic Biology Group, Institut Pasteur, 28 Rue du Dr. Roux, 75015 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25707807" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; CRISPR-Associated Proteins/*metabolism ; *CRISPR-Cas Systems/immunology ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics/immunology ; DNA, Viral/*genetics/immunology/metabolism ; Molecular Sequence Data ; Nucleotide Motifs ; Protein Binding ; Protein Structure, Tertiary ; Staphylococcus aureus ; Streptococcus pyogenes/*enzymology/*genetics/immunology/virology ; Substrate Specificity
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  • 40
    Publication Date: 2015-08-08
    Description: micro-Opioid receptors (microORs) are G-protein-coupled receptors that are activated by a structurally diverse spectrum of natural and synthetic agonists including endogenous endorphin peptides, morphine and methadone. The recent structures of the muOR in inactive and agonist-induced active states (Huang et al., ref. 2) provide snapshots of the receptor at the beginning and end of a signalling event, but little is known about the dynamic sequence of events that span these two states. Here we use solution-state NMR to examine the process of muOR activation using a purified receptor (mouse sequence) preparation in an amphiphile membrane-like environment. We obtain spectra of the muOR in the absence of ligand, and in the presence of the high-affinity agonist BU72 alone, or with BU72 and a G protein mimetic nanobody. Our results show that conformational changes in transmembrane segments 5 and 6 (TM5 and TM6), which are required for the full engagement of a G protein, are almost completely dependent on the presence of both the agonist and the G protein mimetic nanobody, revealing a weak allosteric coupling between the agonist-binding pocket and the G-protein-coupling interface (TM5 and TM6), similar to that observed for the beta2-adrenergic receptor. Unexpectedly, in the presence of agonist alone, we find larger spectral changes involving intracellular loop 1 and helix 8 compared to changes in TM5 and TM6. These results suggest that one or both of these domains may play a role in the initial interaction with the G protein, and that TM5 and TM6 are only engaged later in the process of complex formation. The initial interactions between the G protein and intracellular loop 1 and/or helix 8 may be involved in G-protein coupling specificity, as has been suggested for other family A G-protein-coupled receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sounier, Remy -- Mas, Camille -- Steyaert, Jan -- Laeremans, Toon -- Manglik, Aashish -- Huang, Weijiao -- Kobilka, Brian K -- Demene, Helene -- Granier, Sebastien -- DA036246/DA/NIDA NIH HHS/ -- R37 DA036246/DA/NIDA NIH HHS/ -- T32 GM008294/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Aug 20;524(7565):375-8. doi: 10.1038/nature14680. Epub 2015 Aug 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Genomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, F-34000 Montpellier, France. ; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. ; Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium. ; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA. ; Centre de Biochimie Structurale, CNRS UMR 5048-INSERM 1054- University of Montpellier, 29 rue de Navacelles, 34090 Montpellier Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26245377" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Animals ; Binding Sites ; Heterotrimeric GTP-Binding Proteins/metabolism ; Lysine/metabolism ; Mice ; Models, Molecular ; Morphinans/chemistry/metabolism/pharmacology ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation/drug effects ; Pyrroles/chemistry/metabolism/pharmacology ; Receptors, Adrenergic, beta-2/chemistry ; Receptors, Opioid, mu/*chemistry/*metabolism ; Single-Chain Antibodies/chemistry/metabolism/pharmacology ; Structure-Activity Relationship ; Substrate Specificity
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 41
    Publication Date: 2015-12-10
    Description: Inactivation of the TNFAIP3 gene, encoding the A20 protein, is associated with critical inflammatory diseases including multiple sclerosis, rheumatoid arthritis and Crohn's disease. However, the role of A20 in attenuating inflammatory signalling is unclear owing to paradoxical in vitro and in vivo findings. Here we utilize genetically engineered mice bearing mutations in the A20 ovarian tumour (OTU)-type deubiquitinase domain or in the zinc finger-4 (ZnF4) ubiquitin-binding motif to investigate these discrepancies. We find that phosphorylation of A20 promotes cleavage of Lys63-linked polyubiquitin chains by the OTU domain and enhances ZnF4-mediated substrate ubiquitination. Additionally, levels of linear ubiquitination dictate whether A20-deficient cells die in response to tumour necrosis factor. Mechanistically, linear ubiquitin chains preserve the architecture of the TNFR1 signalling complex by blocking A20-mediated disassembly of Lys63-linked polyubiquitin scaffolds. Collectively, our studies reveal molecular mechanisms whereby A20 deubiquitinase activity and ubiquitin binding, linear ubiquitination, and cellular kinases cooperate to regulate inflammation and cell death.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wertz, Ingrid E -- Newton, Kim -- Seshasayee, Dhaya -- Kusam, Saritha -- Lam, Cynthia -- Zhang, Juan -- Popovych, Nataliya -- Helgason, Elizabeth -- Schoeffler, Allyn -- Jeet, Surinder -- Ramamoorthi, Nandhini -- Kategaya, Lorna -- Newman, Robert J -- Horikawa, Keisuke -- Dugger, Debra -- Sandoval, Wendy -- Mukund, Susmith -- Zindal, Anuradha -- Martin, Flavius -- Quan, Clifford -- Tom, Jeffrey -- Fairbrother, Wayne J -- Townsend, Michael -- Warming, Soren -- DeVoss, Jason -- Liu, Jinfeng -- Dueber, Erin -- Caplazi, Patrick -- Lee, Wyne P -- Goodnow, Christopher C -- Balazs, Mercedesz -- Yu, Kebing -- Kolumam, Ganesh -- Dixit, Vishva M -- England -- Nature. 2015 Dec 17;528(7582):370-5. doi: 10.1038/nature16165. Epub 2015 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Discovery Oncology, Genentech, South San Francisco, California 94080, USA. ; Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA. ; Physiological Chemistry, Genentech, South San Francisco, California 94080, USA. ; Immunology, Genentech, South San Francisco, California 94080, USA. ; Molecular Biology, Genentech, South San Francisco, California 94080, USA. ; Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia. ; Protein Chemistry, Genentech, South San Francisco, California 94080, USA. ; Structural Biology, Genentech, South San Francisco, California 94080, USA. ; Bioinformatics, Genentech, South San Francisco, California 94080, USA. ; Pathology, Genentech, South San Francisco, California 94080, USA. ; Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Sydney, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26649818" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Death ; Cysteine Endopeptidases/chemistry/genetics/*metabolism ; Female ; Inflammation/genetics/*metabolism/pathology ; Intracellular Signaling Peptides and Proteins/chemistry/genetics/*metabolism ; Lysine/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mutation ; Phosphorylation ; Polyubiquitin/chemistry/metabolism ; Protein Binding ; Protein Kinases/metabolism ; Signal Transduction ; Tumor Necrosis Factor-alpha/metabolism ; Ubiquitin/*chemistry/*metabolism ; Ubiquitination
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  • 42
    Publication Date: 2015-11-10
    Description: One of the most important questions in biology is how transcription factors (TFs) and cofactors control enhancer function and thus gene expression. Enhancer activation usually requires combinations of several TFs, indicating that TFs function synergistically and combinatorially. However, while TF binding has been extensively studied, little is known about how combinations of TFs and cofactors control enhancer function once they are bound. It is typically unclear which TFs participate in combinatorial enhancer activation, whether different TFs form functionally distinct groups, or if certain TFs might substitute for each other in defined enhancer contexts. Here we assess the potential regulatory contributions of TFs and cofactors to combinatorial enhancer control with enhancer complementation assays. We recruited GAL4-DNA-binding-domain fusions of 812 Drosophila TFs and cofactors to 24 enhancer contexts and measured enhancer activities by 82,752 luciferase assays in S2 cells. Most factors were functional in at least one context, yet their contributions differed between contexts and varied from repression to activation (up to 289-fold) for individual factors. Based on functional similarities across contexts, we define 15 groups of TFs that differ in developmental functions and protein sequence features. Similar TFs can substitute for each other, enabling enhancer re-engineering by exchanging TF motifs, and TF-cofactor pairs cooperate during enhancer control and interact physically. Overall, we show that activators and repressors can have diverse regulatory functions that typically depend on the enhancer context. The systematic functional characterization of TFs and cofactors should further our understanding of combinatorial enhancer control and gene regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stampfel, Gerald -- Kazmar, Tomas -- Frank, Olga -- Wienerroither, Sebastian -- Reiter, Franziska -- Stark, Alexander -- England -- Nature. 2015 Dec 3;528(7580):147-51. doi: 10.1038/nature15545. Epub 2015 Nov 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26550828" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Cell Line ; DNA/genetics/metabolism ; Down-Regulation/genetics ; Drosophila melanogaster/genetics ; Enhancer Elements, Genetic/*genetics ; *Gene Expression Regulation/genetics ; Genes, Reporter/genetics ; Genetic Complementation Test ; Luciferases/genetics/metabolism ; Protein Binding ; Transcription Factors/*metabolism ; *Transcription, Genetic/genetics ; Up-Regulation/genetics
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  • 43
    Publication Date: 2015-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reardon, Sara -- England -- Nature. 2015 Dec 10;528(7581):173. doi: 10.1038/528173a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26659159" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Congresses as Topic ; Embryo Research/*ethics ; Genetic Engineering/*ethics/legislation & jurisprudence/standards/trends ; Great Britain ; Humans ; United States
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  • 44
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cifelli, Richard L -- England -- Nature. 2015 Apr 9;520(7546):158. doi: 10.1038/520158a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sam Noble Museum, Norman, Oklahoma, USA. He collaborated extensively with Zofia Kielan-Jaworowska from 1998 onwards.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25855448" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; China ; Fossils ; History, 20th Century ; History, 21st Century ; Paleontology/*history ; Poland ; Zoology/*history
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  • 45
    Publication Date: 2015-11-03
    Description: DNA methylation is an important epigenetic modification. Ten-eleven translocation (TET) proteins are involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Here we show that human TET1 and TET2 are more active on 5mC-DNA than 5hmC/5fC-DNA substrates. We determine the crystal structures of TET2-5hmC-DNA and TET2-5fC-DNA complexes at 1.80 A and 1.97 A resolution, respectively. The cytosine portion of 5hmC/5fC is specifically recognized by TET2 in a manner similar to that of 5mC in the TET2-5mC-DNA structure, and the pyrimidine base of 5mC/5hmC/5fC adopts an almost identical conformation within the catalytic cavity. However, the hydroxyl group of 5hmC and carbonyl group of 5fC face towards the opposite direction because the hydroxymethyl group of 5hmC and formyl group of 5fC adopt restrained conformations through forming hydrogen bonds with the 1-carboxylate of NOG and N4 exocyclic nitrogen of cytosine, respectively. Biochemical analyses indicate that the substrate preference of TET2 results from the different efficiencies of hydrogen abstraction in TET2-mediated oxidation. The restrained conformation of 5hmC and 5fC within the catalytic cavity may prevent their abstractable hydrogen(s) adopting a favourable orientation for hydrogen abstraction and thus result in low catalytic efficiency. Our studies demonstrate that the substrate preference of TET2 results from the intrinsic value of its substrates at their 5mC derivative groups and suggest that 5hmC is relatively stable and less prone to further oxidation by TET proteins. Therefore, TET proteins are evolutionarily tuned to be less reactive towards 5hmC and facilitate the generation of 5hmC as a potentially stable mark for regulatory functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Lulu -- Lu, Junyan -- Cheng, Jingdong -- Rao, Qinhui -- Li, Ze -- Hou, Haifeng -- Lou, Zhiyong -- Zhang, Lei -- Li, Wei -- Gong, Wei -- Liu, Mengjie -- Sun, Chang -- Yin, Xiaotong -- Li, Jie -- Tan, Xiangshi -- Wang, Pengcheng -- Wang, Yinsheng -- Fang, Dong -- Cui, Qiang -- Yang, Pengyuan -- He, Chuan -- Jiang, Hualiang -- Luo, Cheng -- Xu, Yanhui -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Nov 5;527(7576):118-22. doi: 10.1038/nature15713. Epub 2015 Oct 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China. ; Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China. ; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China. ; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. ; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China. ; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China. ; MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China. ; Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, USA. ; Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA. ; Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA. ; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26524525" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methylcytosine/metabolism ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Cytosine/analogs & derivatives/metabolism ; DNA/*chemistry/*metabolism ; DNA Methylation ; DNA-Binding Proteins/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Oxidation-Reduction ; Protein Binding ; Proto-Oncogene Proteins/*chemistry/*metabolism ; Substrate Specificity
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  • 46
    Publication Date: 2015-12-18
    Description: T helper 17 (TH17) lymphocytes protect mucosal barriers from infections, but also contribute to multiple chronic inflammatory diseases. Their differentiation is controlled by RORgammat, a ligand-regulated nuclear receptor. Here we identify the RNA helicase DEAD-box protein 5 (DDX5) as a RORgammat partner that coordinates transcription of selective TH17 genes, and is required for TH17-mediated inflammatory pathologies. Surprisingly, the ability of DDX5 to interact with RORgammat and coactivate its targets depends on intrinsic RNA helicase activity and binding of a conserved nuclear long noncoding RNA (lncRNA), Rmrp, which is mutated in patients with cartilage-hair hypoplasia. A targeted Rmrp gene mutation in mice, corresponding to a gene mutation in cartilage-hair hypoplasia patients, altered lncRNA chromatin occupancy, and reduced the DDX5-RORgammat interaction and RORgammat target gene transcription. Elucidation of the link between Rmrp and the DDX5-RORgammat complex reveals a role for RNA helicases and lncRNAs in tissue-specific transcriptional regulation, and provides new opportunities for therapeutic intervention in TH17-dependent diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762670/" 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/PMC4762670/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Wendy -- Thomas, Benjamin -- Flynn, Ryan A -- Gavzy, Samuel J -- Wu, Lin -- Kim, Sangwon V -- Hall, Jason A -- Miraldi, Emily R -- Ng, Charles P -- Rigo, Frank W -- Meadows, Sarah -- Montoya, Nina R -- Herrera, Natalia G -- Domingos, Ana I -- Rastinejad, Fraydoon -- Myers, Richard M -- Fuller-Pace, Frances V -- Bonneau, Richard -- Chang, Howard Y -- Acuto, Oreste -- Littman, Dan R -- 1F30CA189514-01/CA/NCI NIH HHS/ -- F30 CA189514/CA/NCI NIH HHS/ -- P50 HG007735/HG/NHGRI NIH HHS/ -- P50-HG007735/HG/NHGRI NIH HHS/ -- R01 AI080885/AI/NIAID NIH HHS/ -- R01 AI121436/AI/NIAID NIH HHS/ -- R01 DK103358/DK/NIDDK NIH HHS/ -- R01 HG004361/HG/NHGRI NIH HHS/ -- R01AI080885/AI/NIAID NIH HHS/ -- R01DK103358/DK/NIDDK NIH HHS/ -- R01HG004361/HG/NHGRI NIH HHS/ -- T32 AI100853/AI/NIAID NIH HHS/ -- T32 CA009161/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Dec 24;528(7583):517-22. doi: 10.1038/nature16193. Epub 2015 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA. ; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK. ; Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA. ; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA. ; Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10012, USA. ; Simons Center for Data Analysis, Simons Foundation, New York, New York 10010, USA. ; Isis Pharmaceuticals, Carlsbad, California 92010, USA. ; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA. ; Instituto Gulbenkian de Ciencia, Oeiras 2780-156, Portugal. ; Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827, USA. ; Division of Cancer Research, University of Dundee, Dundee DD1 9SY, UK. ; Howard Hughes Medical Institute, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26675721" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/genetics/metabolism ; DEAD-box RNA Helicases/genetics/*metabolism ; Female ; Gene Expression Regulation/genetics ; Hair/abnormalities ; Hirschsprung Disease/genetics ; Humans ; Immunologic Deficiency Syndromes/genetics ; Inflammation/immunology/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Mutation/genetics ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Organ Specificity ; Osteochondrodysplasias/congenital/genetics ; Protein Binding ; RNA, Long Noncoding/genetics/*metabolism ; Th17 Cells/*immunology/*metabolism ; Transcription, Genetic/genetics
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  • 47
    Publication Date: 2015-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miao, Xin -- Tang, Yanhong -- Wong, Christina W Y -- England -- Nature. 2015 Feb 26;518(7540):483. doi: 10.1038/518483d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harbin Institute of Technology, Harbin, China. ; Northeast Agricultural University, Harbin, China. ; The Hong Kong Polytechnic University, Kowloon, Hong Kong.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25719657" target="_blank"〉PubMed〈/a〉
    Keywords: China ; *Ecosystem ; Environmental Policy/economics/*legislation & jurisprudence ; Environmental Pollution/*analysis/economics/*legislation & ; jurisprudence/prevention & control ; Human Migration ; Industrial Waste/analysis/economics/legislation & jurisprudence ; Industry/*legislation & jurisprudence/trends ; *Poverty
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  • 48
    Publication Date: 2015-10-28
    Description: Negative-sense RNA viruses, such as influenza, encode large, multidomain RNA-dependent RNA polymerases that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase (FluPol) is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching. Replication occurs through de novo initiation and involves a complementary RNA intermediate. Currently available structures of the influenza A and B virus polymerases include promoter RNA (the 5' and 3' termini of viral genome segments), showing FluPol in transcription pre-initiation states. Here we report the structure of apo-FluPol from an influenza C virus, solved by X-ray crystallography to 3.9 A, revealing a new 'closed' conformation. The apo-FluPol forms a compact particle with PB1 at its centre, capped on one face by PB2 and clamped between the two globular domains of P3. Notably, this structure is radically different from those of promoter-bound FluPols. The endonuclease domain of P3 and the domains within the carboxy-terminal two-thirds of PB2 are completely rearranged. The cap-binding site is occluded by PB2, resulting in a conformation that is incompatible with transcription initiation. Thus, our structure captures FluPol in a closed, transcription pre-activation state. This reveals the conformation of newly made apo-FluPol in an infected cell, but may also apply to FluPol in the context of a non-transcribing ribonucleoprotein complex. Comparison of the apo-FluPol structure with those of promoter-bound FluPols allows us to propose a mechanism for FluPol activation. Our study demonstrates the remarkable flexibility of influenza virus RNA polymerase, and aids our understanding of the mechanisms controlling transcription and genome replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hengrung, Narin -- El Omari, Kamel -- Serna Martin, Itziar -- Vreede, Frank T -- Cusack, Stephen -- Rambo, Robert P -- Vonrhein, Clemens -- Bricogne, Gerard -- Stuart, David I -- Grimes, Jonathan M -- Fodor, Ervin -- 075491/Z/04/Wellcome Trust/United Kingdom -- 092931/Z/10/Z/Wellcome Trust/United Kingdom -- G1000099/Medical Research Council/United Kingdom -- G1100138/Medical Research Council/United Kingdom -- MR/K000241/1/Medical Research Council/United Kingdom -- England -- Nature. 2015 Nov 5;527(7576):114-7. doi: 10.1038/nature15525. Epub 2015 Oct 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. ; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK. ; European Molecular Biology Laboratory, Grenoble Outstation and University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France. ; Diamond Light Source Ltd, Harwell Science &Innovation Campus, Didcot OX11 0DE, UK. ; Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26503046" target="_blank"〉PubMed〈/a〉
    Keywords: Apoenzymes/chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Endonucleases/chemistry/metabolism ; Enzyme Activation ; Influenzavirus C/*enzymology ; Models, Molecular ; Peptide Chain Initiation, Translational ; Promoter Regions, Genetic/genetics ; Protein Binding ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; RNA Caps/metabolism ; RNA Replicase/*chemistry/metabolism ; RNA, Viral/biosynthesis/metabolism ; Ribonucleoproteins/chemistry
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  • 49
    Publication Date: 2015-06-11
    Description: Gram-negative bacteria inhabit a broad range of ecological niches. For Escherichia coli, this includes river water as well as humans and animals, where it can be both a commensal and a pathogen. Intricate regulatory mechanisms ensure that bacteria have the right complement of beta-barrel outer membrane proteins (OMPs) to enable adaptation to a particular habitat. Yet no mechanism is known for replacing OMPs in the outer membrane, an issue that is further confounded by the lack of an energy source and the high stability and abundance of OMPs. Here we uncover the process underpinning OMP turnover in E. coli and show it to be passive and binary in nature, in which old OMPs are displaced to the poles of growing cells as new OMPs take their place. Using fluorescent colicins as OMP-specific probes, in combination with ensemble and single-molecule fluorescence microscopy in vivo and in vitro, as well as molecular dynamics simulations, we established the mechanism for binary OMP partitioning. OMPs clustered to form approximately 0.5-mum diameter islands, where their diffusion is restricted by promiscuous interactions with other OMPs. OMP islands were distributed throughout the cell and contained the Bam complex, which catalyses the insertion of OMPs in the outer membrane. However, OMP biogenesis occurred as a gradient that was highest at mid-cell but largely absent at cell poles. The cumulative effect is to push old OMP islands towards the poles of growing cells, leading to a binary distribution when cells divide. Hence, the outer membrane of a Gram-negative bacterium is a spatially and temporally organized structure, and this organization lies at the heart of how OMPs are turned over in the membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rassam, Patrice -- Copeland, Nikki A -- Birkholz, Oliver -- Toth, Csaba -- Chavent, Matthieu -- Duncan, Anna L -- Cross, Stephen J -- Housden, Nicholas G -- Kaminska, Renata -- Seger, Urban -- Quinn, Diana M -- Garrod, Tamsin J -- Sansom, Mark S P -- Piehler, Jacob -- Baumann, Christoph G -- Kleanthous, Colin -- BB/G020671/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/L002558/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- WT092970MA/Wellcome Trust/United Kingdom -- England -- Nature. 2015 Jul 16;523(7560):333-6. doi: 10.1038/nature14461. Epub 2015 Jun 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK [2] Department of Biology, University of York, York YO10 5DD, UK. ; Department of Biology, University of York, York YO10 5DD, UK. ; Department of Biology, University of Osnabruck, Barbarastrasse 11, 49076 Osnabruck, Germany. ; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26061769" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/*metabolism ; Cell Polarity ; Diffusion ; Escherichia coli/chemistry/*cytology/genetics/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Lipid-Linked Proteins/metabolism ; Microscopy, Confocal ; Microscopy, Fluorescence ; Molecular Dynamics Simulation ; Multiprotein Complexes/metabolism ; Protein Binding ; Protein Transport
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  • 50
    Publication Date: 2015-06-05
    Description: Macroautophagy (hereafter referred to as autophagy) degrades various intracellular constituents to regulate a wide range of cellular functions, and is also closely linked to several human diseases. In selective autophagy, receptor proteins recognize degradation targets and direct their sequestration by double-membrane vesicles called autophagosomes, which transport them into lysosomes or vacuoles. Although recent studies have shown that selective autophagy is involved in quality/quantity control of some organelles, including mitochondria and peroxisomes, it remains unclear how extensively it contributes to cellular organelle homeostasis. Here we describe selective autophagy of the endoplasmic reticulum (ER) and nucleus in the yeast Saccharomyces cerevisiae. We identify two novel proteins, Atg39 and Atg40, as receptors specific to these pathways. Atg39 localizes to the perinuclear ER (or the nuclear envelope) and induces autophagic sequestration of part of the nucleus. Atg40 is enriched in the cortical and cytoplasmic ER, and loads these ER subdomains into autophagosomes. Atg39-dependent autophagy of the perinuclear ER/nucleus is required for cell survival under nitrogen-deprivation conditions. Atg40 is probably the functional counterpart of FAM134B, an autophagy receptor for the ER in mammals that has been implicated in sensory neuropathy. Our results provide fundamental insight into the pathophysiological roles and mechanisms of 'ER-phagy' and 'nucleophagy' in other organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mochida, Keisuke -- Oikawa, Yu -- Kimura, Yayoi -- Kirisako, Hiromi -- Hirano, Hisashi -- Ohsumi, Yoshinori -- Nakatogawa, Hitoshi -- England -- Nature. 2015 Jun 18;522(7556):359-62. doi: 10.1038/nature14506. Epub 2015 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan. ; Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan. ; Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan. ; 1] Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan [2] CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26040717" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Autophagy ; Cell Nucleus/*metabolism ; Endoplasmic Reticulum/*metabolism ; Microbial Viability ; Microtubule-Associated Proteins/metabolism ; Neoplasm Proteins/metabolism ; Nitrogen/deficiency/metabolism ; Nuclear Envelope/metabolism ; Phenotype ; Protein Binding ; Receptors, Cytoplasmic and Nuclear/chemistry/deficiency/genetics/*metabolism ; Saccharomyces cerevisiae/*cytology/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Vesicular Transport Proteins/metabolism
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  • 51
    Publication Date: 2015-07-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hsu, Angel -- Xu, Kaiyang -- Moffat, Andrew -- England -- Nature. 2015 Jul 9;523(7559):158. doi: 10.1038/523158d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yale School of Forestry and Environmental Studies, New Haven, Connecticut, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26156362" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollutants/*standards ; *Carbon Dioxide ; China ; *Climate Change/statistics & numerical data ; Environmental Monitoring/standards
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  • 52
    Publication Date: 2015-11-26
    Description: Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. Here we present the cryo-electron microscopy structures of the Saccharomyces cerevisiae Pol III elongating complex at 3.9 A resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 A resolution, respectively, which allow the building of a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82-C34-C31 heterotrimer in close proximity to the stalk. The C53-C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681132/" 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/PMC4681132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoffmann, Niklas A -- Jakobi, Arjen J -- Moreno-Morcillo, Maria -- Glatt, Sebastian -- Kosinski, Jan -- Hagen, Wim J H -- Sachse, Carsten -- Muller, Christoph W -- England -- Nature. 2015 Dec 10;528(7581):231-6. doi: 10.1038/nature16143. Epub 2015 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26605533" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; *Models, Molecular ; Protein Binding ; Protein Structure, Tertiary ; RNA Polymerase III/*chemistry ; Saccharomyces cerevisiae/*enzymology ; Saccharomyces cerevisiae Proteins/*chemistry
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  • 53
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2015-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheetham, Anthony -- Fleming, Nic -- England -- Nature. 2015 Apr 30;520(7549):S34-5. doi: 10.1038/520S34a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924198" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/organization & administration ; Chemistry/statistics & numerical data ; China ; Efficiency ; Peer Review, Research/standards ; Personnel Selection ; Research/economics/*manpower/*organization & administration ; Research Personnel/economics/standards ; Research Support as Topic
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  • 54
    Publication Date: 2015-07-23
    Description: Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times. Rice paddies are the largest anthropogenic methane source and produce 7-17% of atmospheric methane. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25-100-million tonnes. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades. There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement. Despite proposed strategies to increase rice productivity and reduce methane emissions, no high-starch low-methane-emission rice has been developed. Here we show that the addition of a single transcription factor gene, barley SUSIBA2 (refs 7, 8), conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates. Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased methane emissions from paddies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, J -- Hu, C -- Yan, X -- Jin, Y -- Chen, Z -- Guan, Q -- Wang, Y -- Zhong, D -- Jansson, C -- Wang, F -- Schnurer, A -- Sun, C -- England -- Nature. 2015 Jul 30;523(7562):602-6. doi: 10.1038/nature14673. Epub 2015 Jul 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China [2] Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, SE-75007 Uppsala, Sweden. ; Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, SE-75007 Uppsala, Sweden. ; 1] Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, SE-75007 Uppsala, Sweden [2] Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China. ; Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China. ; The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, PO Box 999, K8-93 Richland, Washington 99352, USA. ; Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26200336" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/methods/trends ; Atmosphere/chemistry ; Biomass ; Carbon Cycle ; China ; Conservation of Natural Resources/methods ; Food Supply/methods ; Genotype ; Global Warming/prevention & control ; Greenhouse Effect/*prevention & control ; Hordeum/*genetics ; Methane/biosynthesis/*metabolism ; Molecular Sequence Data ; Oryza/genetics/growth & development/*metabolism ; Phenotype ; Photosynthesis ; Plant Components, Aerial/metabolism ; Plant Proteins/genetics/*metabolism ; Plant Roots/metabolism ; Plants, Genetically Modified ; Rhizosphere ; Seeds/metabolism ; Starch/biosynthesis/*metabolism ; Transcription Factors/genetics/*metabolism
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  • 55
    Publication Date: 2015-06-18
    Description: The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the mitotic checkpoint complex and interphase early mitotic inhibitor 1 (Emi1) ensures the correct order and timing of distinct cell-cycle transitions. Here we use cryo-electron microscopy to determine atomic structures of APC/C-coactivator complexes with either Emi1 or a UbcH10-ubiquitin conjugate. These structures define the architecture of all APC/C subunits, the position of the catalytic module and explain how Emi1 mediates inhibition of the two E2s UbcH10 and Ube2S. Definition of Cdh1 interactions with the APC/C indicates how they are antagonized by Cdh1 phosphorylation. The structure of the APC/C with UbcH10-ubiquitin reveals insights into the initiating ubiquitination reaction. Our results provide a quantitative framework for the design of future experiments to investigate APC/C functions in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608048/" 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/PMC4608048/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Leifu -- Zhang, Ziguo -- Yang, Jing -- McLaughlin, Stephen H -- Barford, David -- A8022/Cancer Research UK/United Kingdom -- MC_UP_1201/6/Medical Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- England -- Nature. 2015 Jun 25;522(7557):450-4. doi: 10.1038/nature14471. Epub 2015 Jun 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26083744" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase-Promoting Complex-Cyclosome/chemistry/*metabolism/*ultrastructure ; Apc1 Subunit, Anaphase-Promoting ; Complex-Cyclosome/chemistry/metabolism/ultrastructure ; Apc10 Subunit, Anaphase-Promoting ; Complex-Cyclosome/chemistry/metabolism/ultrastructure ; Apc11 Subunit, Anaphase-Promoting Complex-Cyclosome/chemistry/metabolism ; Apc3 Subunit, Anaphase-Promoting Complex-Cyclosome/chemistry/metabolism ; Apc8 Subunit, Anaphase-Promoting ; Complex-Cyclosome/chemistry/metabolism/ultrastructure ; Cadherins/chemistry/metabolism/ultrastructure ; Catalytic Domain ; Cell Cycle Proteins/chemistry/metabolism/ultrastructure ; Cryoelectron Microscopy ; Cytoskeletal Proteins/chemistry/metabolism ; F-Box Proteins/chemistry/metabolism/ultrastructure ; Humans ; Lysine/metabolism ; Models, Molecular ; Phosphorylation ; Protein Binding ; Protein Subunits/chemistry/metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Ubiquitin/chemistry/metabolism/ultrastructure ; Ubiquitin-Conjugating Enzymes/chemistry/metabolism/ultrastructure ; *Ubiquitination
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  • 56
    Publication Date: 2015-07-15
    Description: The E3 ubiquitin ligase PARKIN (encoded by PARK2) and the protein kinase PINK1 (encoded by PARK6) are mutated in autosomal-recessive juvenile Parkinsonism (AR-JP) and work together in the disposal of damaged mitochondria by mitophagy. PINK1 is stabilized on the outside of depolarized mitochondria and phosphorylates polyubiquitin as well as the PARKIN ubiquitin-like (Ubl) domain. These phosphorylation events lead to PARKIN recruitment to mitochondria, and activation by an unknown allosteric mechanism. Here we present the crystal structure of Pediculus humanus PARKIN in complex with Ser65-phosphorylated ubiquitin (phosphoUb), revealing the molecular basis for PARKIN recruitment and activation. The phosphoUb binding site on PARKIN comprises a conserved phosphate pocket and harbours residues mutated in patients with AR-JP. PhosphoUb binding leads to straightening of a helix in the RING1 domain, and the resulting conformational changes release the Ubl domain from the PARKIN core; this activates PARKIN. Moreover, phosphoUb-mediated Ubl release enhances Ubl phosphorylation by PINK1, leading to conformational changes within the Ubl domain and stabilization of an open, active conformation of PARKIN. We redefine the role of the Ubl domain not only as an inhibitory but also as an activating element that is restrained in inactive PARKIN and released by phosphoUb. Our work opens up new avenues to identify small-molecule PARKIN activators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wauer, Tobias -- Simicek, Michal -- Schubert, Alexander -- Komander, David -- U105192732/Medical Research Council/United Kingdom -- England -- Nature. 2015 Aug 20;524(7565):370-4. doi: 10.1038/nature14879. Epub 2015 Jul 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26161729" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites/genetics ; Conserved Sequence/genetics ; Crystallography, X-Ray ; Enzyme Activation ; Humans ; Models, Molecular ; Mutation/genetics ; Parkinsonian Disorders/genetics ; Pediculus/*chemistry ; Phosphates/metabolism ; Phosphoproteins/chemistry/metabolism ; Phosphorylation ; Protein Binding ; Protein Kinases/metabolism ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Ubiquitin/*chemistry/*metabolism ; Ubiquitin-Protein Ligases/*chemistry/genetics/*metabolism
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  • 57
    Publication Date: 2015-01-28
    Description: The origin of mutations is central to understanding evolution and of key relevance to health. Variation occurs non-randomly across the genome, and mechanisms for this remain to be defined. Here we report that the 5' ends of Okazaki fragments have significantly increased levels of nucleotide substitution, indicating a replicative origin for such mutations. Using a novel method, emRiboSeq, we map the genome-wide contribution of polymerases, and show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-alpha (Pol-alpha) is retained in vivo, comprising approximately 1.5% of the mature genome. We propose that DNA-binding proteins that rapidly re-associate post-replication act as partial barriers to Pol-delta-mediated displacement of Pol-alpha-synthesized DNA, resulting in incorporation of such Pol-alpha tracts and increased mutation rates at specific sites. We observe a mutational cost to chromatin and regulatory protein binding, resulting in mutation hotspots at regulatory elements, with signatures of this process detectable in both yeast and humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374164/" 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/PMC4374164/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reijns, Martin A M -- Kemp, Harriet -- Ding, James -- de Proce, Sophie Marion -- Jackson, Andrew P -- Taylor, Martin S -- MC_PC_U127580972/Medical Research Council/United Kingdom -- MC_PC_U127597124/Medical Research Council/United Kingdom -- MC_U127597124/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2015 Feb 26;518(7540):502-6. doi: 10.1038/nature14183. Epub 2015 Jan 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical and Developmental Genetics, MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK. ; Biomedical Systems Analysis, MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25624100" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromatin/chemistry/metabolism ; Conserved Sequence/genetics ; DNA/*biosynthesis/*genetics ; DNA Polymerase I/metabolism ; DNA Polymerase III/metabolism ; DNA Replication/*genetics ; DNA-Binding Proteins/metabolism ; Evolution, Molecular ; Genome, Human/*genetics ; Humans ; Models, Biological ; Mutagenesis/genetics ; Mutation/*genetics ; Protein Binding ; Saccharomyces cerevisiae/genetics ; Transcription Factors/metabolism
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  • 58
    Publication Date: 2015-01-22
    Description: DNA methylation is an epigenetic modification associated with transcriptional repression of promoters and is essential for mammalian development. Establishment of DNA methylation is mediated by the de novo DNA methyltransferases DNMT3A and DNMT3B, whereas DNMT1 ensures maintenance of methylation through replication. Absence of these enzymes is lethal, and somatic mutations in these genes have been associated with several human diseases. How genomic DNA methylation patterns are regulated remains poorly understood, as the mechanisms that guide recruitment and activity of DNMTs in vivo are largely unknown. To gain insights into this matter we determined genomic binding and site-specific activity of the mammalian de novo DNA methyltransferases DNMT3A and DNMT3B. We show that both enzymes localize to methylated, CpG-dense regions in mouse stem cells, yet are excluded from active promoters and enhancers. By specifically measuring sites of de novo methylation, we observe that enzymatic activity reflects binding. De novo methylation increases with CpG density, yet is excluded from nucleosomes. Notably, we observed selective binding of DNMT3B to the bodies of transcribed genes, which leads to their preferential methylation. This targeting to transcribed sequences requires SETD2-mediated methylation of lysine 36 on histone H3 and a functional PWWP domain of DNMT3B. Together these findings reveal how sequence and chromatin cues guide de novo methyltransferase activity to ensure methylome integrity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baubec, Tuncay -- Colombo, Daniele F -- Wirbelauer, Christiane -- Schmidt, Juliane -- Burger, Lukas -- Krebs, Arnaud R -- Akalin, Altuna -- Schubeler, Dirk -- England -- Nature. 2015 Apr 9;520(7546):243-7. doi: 10.1038/nature14176. Epub 2015 Jan 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland. ; 1] Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland [2] Swiss Institute of Bioinformatics. Maulbeerstrasse 66, CH-4058 Basel, Switzerland. ; 1] Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland [2] University of Basel, Faculty of Sciences, Petersplatz 1, CH-4001 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25607372" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Chromatin/chemistry/genetics/metabolism ; CpG Islands/genetics ; DNA (Cytosine-5-)-Methyltransferase/chemistry/*metabolism ; DNA Methylation/*genetics ; Embryonic Stem Cells/enzymology/metabolism ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/*genetics ; Genome/*genetics ; Genomics ; Histone-Lysine N-Methyltransferase/deficiency/genetics/metabolism ; Histones/chemistry/metabolism ; Lysine/metabolism ; Mice ; Promoter Regions, Genetic/genetics ; Protein Binding ; Protein Structure, Tertiary ; Protein Transport ; Transcription, Genetic/genetics
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  • 59
    Publication Date: 2015-01-09
    Description: Intracellular pathogens are responsible for much of the world-wide morbidity and mortality due to infectious diseases. To colonize their hosts successfully, pathogens must sense their environment and regulate virulence gene expression appropriately. Accordingly, on entry into mammalian cells, the facultative intracellular bacterial pathogen Listeria monocytogenes remodels its transcriptional program by activating the master virulence regulator PrfA. Here we show that bacterial and host-derived glutathione are required to activate PrfA. In this study a genetic selection led to the identification of a bacterial mutant in glutathione synthase that exhibited reduced virulence gene expression and was attenuated 150-fold in mice. Genome sequencing of suppressor mutants that arose spontaneously in vivo revealed a single nucleotide change in prfA that locks the protein in the active conformation (PrfA*) and completely bypassed the requirement for glutathione during infection. Biochemical and genetic studies support a model in which glutathione-dependent PrfA activation is mediated by allosteric binding of glutathione to PrfA. Whereas glutathione and other low-molecular-weight thiols have important roles in redox homeostasis in all forms of life, here we demonstrate that glutathione represents a critical signalling molecule that activates the virulence of an intracellular pathogen.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305340/" 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/PMC4305340/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reniere, Michelle L -- Whiteley, Aaron T -- Hamilton, Keri L -- John, Sonya M -- Lauer, Peter -- Brennan, Richard G -- Portnoy, Daniel A -- 1P01AI63302/AI/NIAID NIH HHS/ -- 1R01 AI27655/AI/NIAID NIH HHS/ -- F32AI104247/AI/NIAID NIH HHS/ -- F32GM008487/GM/NIGMS NIH HHS/ -- P01 AI063302/AI/NIAID NIH HHS/ -- R01 AI027655/AI/NIAID NIH HHS/ -- S10RR027303/RR/NCRR NIH HHS/ -- S10RR029668/RR/NCRR NIH HHS/ -- England -- Nature. 2015 Jan 8;517(7533):170-3. doi: 10.1038/nature14029.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA. ; Graduate Group in Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, California 94720, USA. ; Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA. ; Aduro BioTech, Inc. Berkeley, California 94710, USA. ; 1] Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA [2] School of Public Health, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25567281" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/drug effects ; Bacterial Proteins/metabolism ; DNA/metabolism ; Gene Expression Regulation, Bacterial/drug effects/*genetics ; Glutathione/*metabolism/pharmacology ; Intracellular Space/drug effects/*metabolism/*microbiology ; Listeria monocytogenes/drug effects/*genetics/*pathogenicity ; Macrophages/metabolism ; Mutation/genetics ; Peptide Termination Factors/metabolism ; Protein Binding ; Selection, Genetic/genetics ; Suppression, Genetic/genetics ; Virulence/genetics
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  • 60
    Publication Date: 2015-07-16
    Description: Major depressive disorder (MDD), one of the most frequently encountered forms of mental illness and a leading cause of disability worldwide, poses a major challenge to genetic analysis. To date, no robustly replicated genetic loci have been identified, despite analysis of more than 9,000 cases. Here, using low-coverage whole-genome sequencing of 5,303 Chinese women with recurrent MDD selected to reduce phenotypic heterogeneity, and 5,337 controls screened to exclude MDD, we identified, and subsequently replicated in an independent sample, two loci contributing to risk of MDD on chromosome 10: one near the SIRT1 gene (P = 2.53 x 10(-10)), the other in an intron of the LHPP gene (P = 6.45 x 10(-12)). Analysis of 4,509 cases with a severe subtype of MDD, melancholia, yielded an increased genetic signal at the SIRT1 locus. We attribute our success to the recruitment of relatively homogeneous cases with severe illness.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522619/" 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/PMC4522619/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉CONVERGE consortium -- 083240/Wellcome Trust/United Kingdom -- MH-100549/MH/NIMH NIH HHS/ -- R01 MH100549/MH/NIMH NIH HHS/ -- WT083573/Z/07/Z/Wellcome Trust/United Kingdom -- WT089269/Z/09/Z/Wellcome Trust/United Kingdom -- WT090532/Z/09/Z/Wellcome Trust/United Kingdom -- WT097307/Wellcome Trust/United Kingdom -- England -- Nature. 2015 Jul 30;523(7562):588-91. doi: 10.1038/nature14659. Epub 2015 Jul 15.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26176920" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Asian Continental Ancestry Group/genetics ; China ; Chromosomes, Human, Pair 10/genetics ; Cohort Studies ; Depressive Disorder/genetics ; Depressive Disorder, Major/*genetics ; Female ; Genetic Loci/*genetics ; Genome, Human/genetics ; *Genome-Wide Association Study ; Humans ; Inorganic Pyrophosphatase/genetics ; Introns/genetics ; Middle Aged ; Sequence Analysis, DNA ; Sirtuin 1/genetics ; Young Adult
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  • 61
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sweeney, David -- Fleming, Nic -- England -- Nature. 2015 Apr 30;520(7549):S21. doi: 10.1038/520S21a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924195" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Great Britain ; Research/*economics/organization & administration/*standards ; Research Support as Topic/*economics/*organization & administration
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  • 62
    Publication Date: 2015-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barnett, Jon -- Rogers, Sarah -- Webber, Michael -- Finlayson, Brian -- Wang, Mark -- England -- Nature. 2015 Nov 19;527(7578):295-7. doi: 10.1038/527295a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Geography, University of Melbourne, Victoria, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26581275" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Cities ; Conservation of Natural Resources/economics/*methods/trends ; Environmental Policy/legislation & jurisprudence/trends ; Rain ; Recycling ; Resource Allocation/*methods ; Waste Water ; Water Supply/economics/*methods
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  • 63
    Publication Date: 2015-05-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- Reardon, Sara -- England -- Nature. 2015 Apr 30;520(7549):593-4. doi: 10.1038/520593a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25925450" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *CRISPR-Cas Systems ; China ; Embryo Research/*ethics/legislation & jurisprudence ; Embryo, Mammalian/embryology/*metabolism ; Genetic Engineering/*ethics/legislation & jurisprudence/methods ; Humans
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  • 64
    Publication Date: 2015-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Zhenwu -- Huang, Qifei -- Yang, Yufei -- England -- Nature. 2015 Sep 24;525(7570):455. doi: 10.1038/525455d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉North China Electric Power University, Beijing, China. ; Chinese Research Academy of Environmental Sciences, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26399819" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Explosions/legislation & jurisprudence/prevention & control ; *Government Regulation ; *Hazardous Substances/chemistry ; Humans ; Safety/*legislation & jurisprudence
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  • 65
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    Nature Publishing Group (NPG)
    Publication Date: 2015-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Nov 26;527(7579):410. doi: 10.1038/527410a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26607504" target="_blank"〉PubMed〈/a〉
    Keywords: Authorship ; China ; *Cooperative Behavior ; Culture ; *Dissent and Disputes ; *Research/manpower/organization & administration ; Research Personnel/*psychology ; *Trust ; Universities
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  • 66
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Chuan-Chao -- England -- Nature. 2015 Apr 30;520(7549):S36. doi: 10.1038/520S36a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fudan University in Shanghai. In June 2015, he will become a postdoctoral researcher at the Max Planck Institute for the Science of Human History in Jena, Germany. He won the Ray Wu Prize in 2012.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924199" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Awards and Prizes ; China ; Emigration and Immigration/statistics & numerical data ; Internationality ; Motivation ; *Personnel Selection ; Research Personnel/*economics/psychology/standards
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  • 67
    Publication Date: 2015-02-14
    Description: A new docodontan mammaliaform from the Middle Jurassic of China has skeletal features for climbing and dental characters indicative of an omnivorous diet that included plant sap. This fossil expands the range of known locomotor adaptations in docodontans to include climbing, in addition to digging and swimming. It further shows that some docodontans had a diet with a substantial herbivorous component, distinctive from the faunivorous diets previously reported in other members of this clade. This reveals a greater ecological diversity in an early mammaliaform clade at a more fundamental taxonomic level not only between major clades as previously thought.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meng, Qing-Jin -- Ji, Qiang -- Zhang, Yu-Guang -- Liu, Di -- Grossnickle, David M -- Luo, Zhe-Xi -- New York, N.Y. -- Science. 2015 Feb 13;347(6223):764-8. doi: 10.1126/science.1260879.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beijing Museum of Natural History, Beijing 100050 China. ; Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, China. ; Committee on Evolutionary Biology, The University of Chicago, Chicago, IL 60637, USA. ; Committee on Evolutionary Biology, The University of Chicago, Chicago, IL 60637, USA. Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA. zxluo@uchicago.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25678661" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Feed ; Animals ; *Biodiversity ; China ; Cuspid/anatomy & histology/immunology ; *Dentition ; Forelimb/anatomy & histology/growth & development ; *Herbivory ; Incisor/anatomy & histology/growth & development ; Mammals/anatomy & histology/*classification/*growth & development ; Mandible/anatomy & histology/growth & development ; Phylogeny
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  • 68
    Publication Date: 2015-06-06
    Description: Circadian and metabolic physiology are intricately intertwined, as illustrated by Rev-erbalpha, a transcription factor (TF) that functions both as a core repressive component of the cell-autonomous clock and as a regulator of metabolic genes. Here, we show that Rev-erbalpha modulates the clock and metabolism by different genomic mechanisms. Clock control requires Rev-erbalpha to bind directly to the genome at its cognate sites, where it competes with activating ROR TFs. By contrast, Rev-erbalpha regulates metabolic genes primarily by recruiting the HDAC3 co-repressor to sites to which it is tethered by cell type-specific transcription factors. Thus, direct competition between Rev-erbalpha and ROR TFs provides a universal mechanism for self-sustained control of the molecular clock across all tissues, whereas Rev-erbalpha uses lineage-determining factors to convey a tissue-specific epigenomic rhythm that regulates metabolism tailored to the specific need of that tissue.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4613749/" 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/PMC4613749/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Yuxiang -- Fang, Bin -- Emmett, Matthew J -- Damle, Manashree -- Sun, Zheng -- Feng, Dan -- Armour, Sean M -- Remsberg, Jarrett R -- Jager, Jennifer -- Soccio, Raymond E -- Steger, David J -- Lazar, Mitchell A -- F30 DK104513/DK/NIDDK NIH HHS/ -- F32 DK102284/DK/NIDDK NIH HHS/ -- K08 DK094968/DK/NIDDK NIH HHS/ -- P30 DK019525/DK/NIDDK NIH HHS/ -- P30 DK050306/DK/NIDDK NIH HHS/ -- P30 DK19525/DK/NIDDK NIH HHS/ -- R00 DK099443/DK/NIDDK NIH HHS/ -- R01 DK045586/DK/NIDDK NIH HHS/ -- R01 DK098542/DK/NIDDK NIH HHS/ -- R01 DK45586/DK/NIDDK NIH HHS/ -- T32 GM0008275/GM/NIGMS NIH HHS/ -- T32 GM008275/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jun 26;348(6242):1488-92. doi: 10.1126/science.aab3021. Epub 2015 Jun 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Department of Genetics, and the Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. ; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Department of Genetics, and the Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Molecular and Cellular Biology, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA. ; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Department of Genetics, and the Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. lazar@mail.med.upenn.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26044300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CLOCK Proteins/*genetics ; Circadian Clocks/*genetics ; Circadian Rhythm/*genetics ; *Gene Expression Regulation ; Hepatocyte Nuclear Factor 6/metabolism ; Histone Deacetylases/*metabolism ; Lipid Metabolism/genetics ; Liver/metabolism ; Male ; Metabolism/*genetics ; Mice, Inbred C57BL ; Mice, Knockout ; Nuclear Receptor Subfamily 1, Group D, Member 1/genetics/*metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 1/metabolism ; Organ Specificity ; Protein Binding ; Tissue Distribution
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  • 69
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-06-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hao, Rongzhang -- Zhao, Rongtao -- Qiu, Shaofu -- Wang, Ligui -- Song, Hongbin -- New York, N.Y. -- Science. 2015 Jun 5;348(6239):1100-1. doi: 10.1126/science.348.6239.1100-d. Epub 2015 Jun 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China. ; Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China. hongbinsong@263.net.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26045427" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Bacterial Agents/*analysis ; China ; *Drug Resistance, Bacterial ; Food Contamination/*prevention & control ; Humans ; Livestock ; Meat/analysis ; Swine ; Waste Water/analysis ; Water Pollution/*prevention & control ; Water Supply/analysis
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  • 70
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larson, Christina -- New York, N.Y. -- Science. 2015 Oct 9;350(6257):150-2. doi: 10.1126/science.350.6257.150.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26450191" target="_blank"〉PubMed〈/a〉
    Keywords: *Animal Migration ; Animals ; *Birds ; China ; Ecosystem ; Oceans and Seas ; Population Dynamics ; Wetlands
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larson, Christina -- New York, N.Y. -- Science. 2015 Sep 25;349(6255):1434. doi: 10.1126/science.349.6255.1434.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26404805" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; China ; *Coral Reefs ; *Environment Design ; *Fisheries ; *Islands ; Politics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larson, Christina -- New York, N.Y. -- Science. 2015 Feb 13;347(6223):704. doi: 10.1126/science.347.6223.704.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25678639" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/drug effects/genetics/isolation & purification ; China ; *Drug Resistance, Bacterial ; Food Industry ; Humans ; Lakes/*microbiology ; Manure/*microbiology ; *Meat ; Swine
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  • 73
    Publication Date: 2015-03-07
    Description: Chemokines are small proteins that function as immune modulators through activation of chemokine G protein-coupled receptors (GPCRs). Several viruses also encode chemokines and chemokine receptors to subvert the host immune response. How protein ligands activate GPCRs remains unknown. We report the crystal structure at 2.9 angstrom resolution of the human cytomegalovirus GPCR US28 in complex with the chemokine domain of human CX3CL1 (fractalkine). The globular body of CX3CL1 is perched on top of the US28 extracellular vestibule, whereas its amino terminus projects into the central core of US28. The transmembrane helices of US28 adopt an active-state-like conformation. Atomic-level simulations suggest that the agonist-independent activity of US28 may be due to an amino acid network evolved in the viral GPCR to destabilize the receptor's inactive state.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445376/" 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/PMC4445376/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burg, John S -- Ingram, Jessica R -- Venkatakrishnan, A J -- Jude, Kevin M -- Dukkipati, Abhiram -- Feinberg, Evan N -- Angelini, Alessandro -- Waghray, Deepa -- Dror, Ron O -- Ploegh, Hidde L -- Garcia, K Christopher -- DP1 GM106409/GM/NIGMS NIH HHS/ -- R01 GM097015/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Mar 6;347(6226):1113-7. doi: 10.1126/science.aaa5026.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. ; Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. ; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Computer Science, Stanford University, Stanford, CA 94305, USA. Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA. ; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. ; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. kcgarcia@stanford.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25745166" target="_blank"〉PubMed〈/a〉
    Keywords: CCR5 Receptor Antagonists/chemistry ; Chemokine CX3CL1/*chemistry ; Crystallography, X-Ray ; Cyclohexanes/chemistry ; Humans ; Ligands ; Piperidines/chemistry ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, CXCR4/antagonists & inhibitors ; Receptors, Chemokine/agonists/*chemistry ; Triazoles/chemistry ; Viral Proteins/agonists/*chemistry
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  • 74
    Publication Date: 2015-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cao, Ling -- Naylor, Rosamond -- Henriksson, Patrik -- Leadbitter, Duncan -- Metian, Marc -- Troell, Max -- Zhang, Wenbo -- New York, N.Y. -- Science. 2015 Jan 9;347(6218):133-5. doi: 10.1126/science.1260149.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stanford University, Stanford, CA 94035, USA. ; Stanford University, Stanford, CA 94035, USA. roz@stanford.edu. ; Leiden University, 2333 CC Leiden, the Netherlands. ; University of Wollongong, Wollongong NSW 2522, Australia. ; Stockholm University, 106 91 Stockholm, Sweden. ; Stockholm University, 106 91 Stockholm, Sweden. The Royal Swedish Academy of Sciences, 104 05 Stockholm, Sweden. ; University of Stirling, FK9 4LA, UK. Shanghai Ocean University, Shanghai 201306, PR China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25574011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aquaculture/*trends ; China ; Fisheries ; *Fishes ; *Food Supply
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  • 75
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-10-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, Dennis -- New York, N.Y. -- Science. 2015 Oct 16;350(6258):265. doi: 10.1126/science.350.6258.265.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26472888" target="_blank"〉PubMed〈/a〉
    Keywords: Antimalarials/therapeutic use ; Artemisinins/therapeutic use ; China ; Drug Discovery/*methods ; Humans ; Lactones/therapeutic use ; Malaria/drug therapy ; Medicine, Chinese Traditional/*trends ; *Nobel Prize
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-10-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Z Josh -- Luo, Liqun -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Oct 2;350(6256):42-4. doi: 10.1126/science.aad4120. Epub 2015 Oct 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. huangj@cshl.edu lluo@stanford.edu. ; HHMI/Department of Biology, Stanford University, Stanford, CA 94305, USA. huangj@cshl.edu lluo@stanford.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26430110" target="_blank"〉PubMed〈/a〉
    Keywords: Brain/*physiology ; China ; Europe ; Humans ; *International Cooperation ; Japan ; Neurosciences/*trends ; Republic of Korea ; United States
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-09-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Haotian -- Long, Erping -- Chen, Weirong -- Liu, Yizhi -- New York, N.Y. -- Science. 2015 Sep 4;349(6252):1064. doi: 10.1126/science.349.6252.1064-b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China. ; The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China. yizhi_liu@aliyun.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26339020" target="_blank"〉PubMed〈/a〉
    Keywords: Cataract/*congenital/*therapy ; Child, Preschool ; China ; Clinical Trials as Topic ; Humans ; Pilot Projects ; Rare Diseases/*congenital/*therapy ; Translational Medical Research/economics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 78
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvistendahl, Mara -- New York, N.Y. -- Science. 2015 Feb 13;347(6223):700-1. doi: 10.1126/science.347.6223.700.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25678636" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Zoo/*virology ; Breeding ; China ; Disease Outbreaks/prevention & control/*veterinary ; Distemper/mortality/*prevention & control/*transmission ; *Distemper Virus, Canine ; Dogs ; *Endangered Species ; Female ; Male ; Ursidae/*virology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 79
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Jun -- Normile, Dennis -- New York, N.Y. -- Science. 2015 Jul 31;349(6247):463. doi: 10.1126/science.349.6247.463.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26228121" target="_blank"〉PubMed〈/a〉
    Keywords: Artificial Intelligence/*utilization ; China ; *Genome ; Genomics/*methods ; Human Genome Project ; Humans ; Oryza/genetics
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 80
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-05-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Jianguo -- New York, N.Y. -- Science. 2015 May 8;348(6235):642. doi: 10.1126/science.348.6235.642-a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA. liuji@msu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25953997" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Climate Change ; *Endangered Species ; Herbivory ; Population ; Reproduction ; *Ursidae
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 81
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Jiaqi -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):195. doi: 10.1126/science.348.6231.195-b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 200032, Shanghai, China. liujiaqi1213@yahoo.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859039" target="_blank"〉PubMed〈/a〉
    Keywords: China ; *Community Health Services ; Community-Institutional Relations ; *Health Fairs ; *Health Promotion ; Humans ; *Trust
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 82
    Publication Date: 2015-02-01
    Description: During virus infection, the adaptor proteins MAVS and STING transduce signals from the cytosolic nucleic acid sensors RIG-I and cGAS, respectively, to induce type I interferons (IFNs) and other antiviral molecules. Here we show that MAVS and STING harbor two conserved serine and threonine clusters that are phosphorylated by the kinases IKK and/or TBK1 in response to stimulation. Phosphorylated MAVS and STING then bind to a positively charged surface of interferon regulatory factor 3 (IRF3) and thereby recruit IRF3 for its phosphorylation and activation by TBK1. We further show that TRIF, an adaptor protein in Toll-like receptor signaling, activates IRF3 through a similar phosphorylation-dependent mechanism. These results reveal that phosphorylation of innate adaptor proteins is an essential and conserved mechanism that selectively recruits IRF3 to activate the type I IFN pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Siqi -- Cai, Xin -- Wu, Jiaxi -- Cong, Qian -- Chen, Xiang -- Li, Tuo -- Du, Fenghe -- Ren, Junyao -- Wu, You-Tong -- Grishin, Nick V -- Chen, Zhijian J -- AI-93967/AI/NIAID NIH HHS/ -- GM-094575/GM/NIGMS NIH HHS/ -- GM-63692/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Mar 13;347(6227):aaa2630. doi: 10.1126/science.aaa2630. Epub 2015 Jan 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. ; Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. ; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. Howard Hughes Medical Institute (HHMI), University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. ; Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. Howard Hughes Medical Institute (HHMI), University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. ; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. Howard Hughes Medical Institute (HHMI), University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. zhijian.chen@utsouthwestern.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25636800" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/chemistry/*metabolism ; Adaptor Proteins, Vesicular Transport/chemistry/*metabolism ; Amino Acid Sequence ; Animals ; Cell Line ; Humans ; I-kappa B Kinase/metabolism ; Interferon Regulatory Factor-3/chemistry/*metabolism ; Interferon-alpha/biosynthesis ; Interferon-beta/biosynthesis ; Membrane Proteins/chemistry/*metabolism ; Mice ; Molecular Sequence Data ; Phosphorylation ; Protein Binding ; Protein Multimerization ; Protein-Serine-Threonine Kinases/metabolism ; Recombinant Proteins/metabolism ; Sendai virus/physiology ; Serine/metabolism ; Signal Transduction ; Ubiquitination ; Vesiculovirus/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 83
    Publication Date: 2015-06-13
    Description: The spindle checkpoint of the cell division cycle senses kinetochores that are not attached to microtubules and prevents precocious onset of anaphase, which can lead to aneuploidy. The nuclear division cycle 80 complex (Ndc80C) is a major microtubule receptor at the kinetochore. Ndc80C also mediates the kinetochore recruitment of checkpoint proteins. We found that the checkpoint protein kinase monopolar spindle 1 (Mps1) directly bound to Ndc80C through two independent interactions. Both interactions involved the microtubule-binding surfaces of Ndc80C and were directly inhibited in the presence of microtubules. Elimination of one such interaction in human cells caused checkpoint defects expected from a failure to detect unattached kinetochores. Competition between Mps1 and microtubules for Ndc80C binding thus constitutes a direct mechanism for the detection of unattached kinetochores.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ji, Zhejian -- Gao, Haishan -- Yu, Hongtao -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Jun 12;348(6240):1260-4. doi: 10.1126/science.aaa4029.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 74390, USA. ; Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 74390, USA. hongtao.yu@utsouthwestern.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26068854" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding, Competitive ; *Cell Cycle ; Cell Cycle Proteins/genetics/*metabolism ; HeLa Cells ; Humans ; Kinetochores/*metabolism ; Microtubules/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/*metabolism ; Protein Binding ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Protein-Tyrosine Kinases/genetics/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 84
    Publication Date: 2015-10-17
    Description: Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the cryo-electron microscopy structure of Tetrahymena telomerase at ~9 angstrom resolution. In addition to seven known holoenzyme proteins, we identify two additional proteins that form a complex (TEB) with single-stranded telomere DNA-binding protein Teb1, paralogous to heterotrimeric replication protein A (RPA). The p75-p45-p19 subcomplex is identified as another RPA-related complex, CST (CTC1-STN1-TEN1). This study reveals the paths of TER in the TERT-TER-p65 catalytic core and single-stranded DNA exit; extensive subunit interactions of the TERT essential N-terminal domain, p50, and TEB; and other subunit identities and structures, including p19 and p45C crystal structures. Our findings provide structural and mechanistic insights into telomerase holoenzyme function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687456/" 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/PMC4687456/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Jiansen -- Chan, Henry -- Cash, Darian D -- Miracco, Edward J -- Ogorzalek Loo, Rachel R -- Upton, Heather E -- Cascio, Duilio -- O'Brien Johnson, Reid -- Collins, Kathleen -- Loo, Joseph A -- Zhou, Z Hong -- Feigon, Juli -- GM007185/GM/NIGMS NIH HHS/ -- GM048123/GM/NIGMS NIH HHS/ -- GM071940/GM/NIGMS NIH HHS/ -- GM101874/GM/NIGMS NIH HHS/ -- GM103479/GM/NIGMS NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- P41 RR015301/RR/NCRR NIH HHS/ -- R01 GM048123/GM/NIGMS NIH HHS/ -- R01 GM054198/GM/NIGMS NIH HHS/ -- R01 GM071940/GM/NIGMS NIH HHS/ -- R01 GM103479/GM/NIGMS NIH HHS/ -- R01GM054198/GM/NIGMS NIH HHS/ -- S10OD018111/OD/NIH HHS/ -- S10RR23057/RR/NCRR NIH HHS/ -- UL1TR000124/TR/NCATS NIH HHS/ -- New York, N.Y. -- Science. 2015 Oct 30;350(6260):aab4070. doi: 10.1126/science.aab4070. Epub 2015 Oct 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA. California Nanosystems Institute, UCLA, Los Angeles, CA 90095, USA. ; Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. ; Department of Biological Chemistry, UCLA, Los Angeles, CA 90095, USA. ; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA. ; Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. Department of Biological Chemistry, UCLA, Los Angeles, CA 90095, USA. UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA. ; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA. California Nanosystems Institute, UCLA, Los Angeles, CA 90095, USA. ; Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. California Nanosystems Institute, UCLA, Los Angeles, CA 90095, USA. UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA. feigon@mbi.ucla.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26472759" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA, Single-Stranded/chemistry ; Holoenzymes/chemistry ; Protein Binding ; Protein Conformation ; Protein Subunits/chemistry ; RNA/*chemistry ; Replication Protein A/chemistry ; Telomerase/*chemistry ; Telomere/chemistry ; Telomere Homeostasis ; Telomere-Binding Proteins ; Tetrahymena/*enzymology
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  • 85
    Publication Date: 2015-02-24
    Description: Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease with no effective treatment. We report the results of a moderate-scale sequencing study aimed at increasing the number of genes known to contribute to predisposition for ALS. We performed whole-exome sequencing of 2869 ALS patients and 6405 controls. Several known ALS genes were found to be associated, and TBK1 (the gene encoding TANK-binding kinase 1) was identified as an ALS gene. TBK1 is known to bind to and phosphorylate a number of proteins involved in innate immunity and autophagy, including optineurin (OPTN) and p62 (SQSTM1/sequestosome), both of which have also been implicated in ALS. These observations reveal a key role of the autophagic pathway in ALS and suggest specific targets for therapeutic intervention.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437632/" 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/PMC4437632/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cirulli, Elizabeth T -- Lasseigne, Brittany N -- Petrovski, Slave -- Sapp, Peter C -- Dion, Patrick A -- Leblond, Claire S -- Couthouis, Julien -- Lu, Yi-Fan -- Wang, Quanli -- Krueger, Brian J -- Ren, Zhong -- Keebler, Jonathan -- Han, Yujun -- Levy, Shawn E -- Boone, Braden E -- Wimbish, Jack R -- Waite, Lindsay L -- Jones, Angela L -- Carulli, John P -- Day-Williams, Aaron G -- Staropoli, John F -- Xin, Winnie W -- Chesi, Alessandra -- Raphael, Alya R -- McKenna-Yasek, Diane -- Cady, Janet -- Vianney de Jong, J M B -- Kenna, Kevin P -- Smith, Bradley N -- Topp, Simon -- Miller, Jack -- Gkazi, Athina -- FALS Sequencing Consortium -- Al-Chalabi, Ammar -- van den Berg, Leonard H -- Veldink, Jan -- Silani, Vincenzo -- Ticozzi, Nicola -- Shaw, Christopher E -- Baloh, Robert H -- Appel, Stanley -- Simpson, Ericka -- Lagier-Tourenne, Clotilde -- Pulst, Stefan M -- Gibson, Summer -- Trojanowski, John Q -- Elman, Lauren -- McCluskey, Leo -- Grossman, Murray -- Shneider, Neil A -- Chung, Wendy K -- Ravits, John M -- Glass, Jonathan D -- Sims, Katherine B -- Van Deerlin, Vivianna M -- Maniatis, Tom -- Hayes, Sebastian D -- Ordureau, Alban -- Swarup, Sharan -- Landers, John -- Baas, Frank -- Allen, Andrew S -- Bedlack, Richard S -- Harper, J Wade -- Gitler, Aaron D -- Rouleau, Guy A -- Brown, Robert -- Harms, Matthew B -- Cooper, Gregory M -- Harris, Tim -- Myers, Richard M -- Goldstein, David B -- 089701/Wellcome Trust/United Kingdom -- K08 NS075094/NS/NINDS NIH HHS/ -- P01 AG017586/AG/NIA NIH HHS/ -- P01 AG032953/AG/NIA NIH HHS/ -- P50 AG025688/AG/NIA NIH HHS/ -- R37 NS033123/NS/NINDS NIH HHS/ -- R37 NS083524/NS/NINDS NIH HHS/ -- T32 GM007754/GM/NIGMS NIH HHS/ -- TL1 TR001066/TR/NCATS NIH HHS/ -- UL1 TR001067/TR/NCATS NIH HHS/ -- New York, N.Y. -- Science. 2015 Mar 27;347(6229):1436-41. doi: 10.1126/science.aaa3650. Epub 2015 Feb 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27708, USA. ; HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA. ; Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA. ; Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA. ; Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada. ; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. ; Duke University School of Medicine, Durham, NC 27708, USA. ; Biogen Idec, Cambridge, MA 02142, USA. ; Neurogenetics DNA Diagnostic Laboratory, Center for Human Genetics Research, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA. ; Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA. ; Department of Genome Analysis, Academic Medical Center, Meibergdreef 9, 1105AZ Amsterdam, Netherlands. ; Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland. ; Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK. ; Department of Neurology, Brain Center Rudolf Magnus, University Medical Centre Utrecht, 3508 GA Utrecht, Netherlands. ; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy, and Department of Pathophysiology and Transplantation, Dino Ferrari Center, Universita degli Studi di Milano, Milan 20122, Italy. ; Cedars Sinai Medical Center, Los Angeles, CA 90048, USA. ; Houston Methodist Hospital, Houston, TX 77030, USA, and Weill Cornell Medical College of Cornell University, New York, NY 10065, USA. ; Ludwig Institute for Cancer Research and Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA. ; Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA. ; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. ; Department of Neurology, Penn ALS Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. ; Department of Neurology, Penn Frontotemporal Degeneration Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. ; Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA. ; Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA. ; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA. ; Department of Neurology, Emory University, Atlanta, GA 30322, USA. ; Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10027, USA. ; Biogen Idec, Cambridge, MA 02142, USA. Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. ; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. ; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708, USA. ; Duke ALS Clinic and Durham VA Medical Center, Durham, NC 27708, USA. ; Biogen Idec, Cambridge, MA 02142, USA. tim.harris@biogenidec.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700176" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/genetics/metabolism ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Amyotrophic Lateral Sclerosis/*genetics ; Autophagy/*genetics ; Exome/*genetics ; Female ; Genes ; Genetic Association Studies ; *Genetic Predisposition to Disease ; Humans ; Male ; Middle Aged ; Protein Binding ; Protein-Serine-Threonine Kinases/*genetics/metabolism ; Risk ; Sequence Analysis, DNA ; Transcription Factor TFIIIA/genetics/metabolism ; Young Adult
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  • 86
    Publication Date: 2015-04-11
    Description: To address how the configuration of conjugated ubiquitins determines the recognition of substrates by the proteasome, we analyzed the degradation kinetics of substrates with chemically defined ubiquitin configurations. Contrary to the view that a tetraubiquitin chain is the minimal signal for efficient degradation, we find that distributing the ubiquitins as diubiquitin chains provides a more efficient signal. To understand how the proteasome actually discriminates among ubiquitin configurations, we developed single-molecule assays that distinguished intermediate steps of degradation kinetically. The level of ubiquitin on a substrate drives proteasome-substrate interaction, whereas the chain structure of ubiquitin affects translocation into the axial channel on the proteasome. Together these two features largely determine the susceptibility of substrates for proteasomal degradation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450770/" 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/PMC4450770/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Ying -- Lee, Byung-hoon -- King, Randall W -- Finley, Daniel -- Kirschner, Marc W -- GM43601/GM/NIGMS NIH HHS/ -- GM66492/GM/NIGMS NIH HHS/ -- R01 GM039023/GM/NIGMS NIH HHS/ -- R01 GM066492/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):1250834. doi: 10.1126/science.1250834.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. ; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. ; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. marc@hms.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859050" target="_blank"〉PubMed〈/a〉
    Keywords: Cyclin B/metabolism ; Geminin/metabolism ; Humans ; Kinetics ; Proteasome Endopeptidase Complex/chemistry/*metabolism ; Protein Binding ; Protein Transport ; *Proteolysis ; Securin/metabolism ; Stochastic Processes ; Ubiquitin/chemistry/*metabolism ; Ubiquitinated Proteins/chemistry/*metabolism ; Ubiquitination
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 87
    Publication Date: 2015-04-11
    Description: Biological processes require specific enzymatic reactions, paradoxically involving short recognition sequences. As an example, cell-cycle timing depends on a sequence of ubiquitylation events mediated by the anaphase-promoting complex (APC) based on short redundant motifs. To understand the origin of specificity, we designed single-molecule fluorescence assays that capture transient ubiquitylation reactions. We find that the APC-mediated ubiquitylation involves a highly processive initial reaction on the substrate, followed by multiple encounters and reactions at a slower rate. The initial ubiquitylation greatly enhances the substrate's binding affinity in subsequent reactions, by both increasing the on-rate and decreasing the off-rate. We postulate that these cycles of positive feedback enable high specificity for substrates with short recognition motifs in a complex cellular environment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449139/" 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/PMC4449139/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Ying -- Wang, Weiping -- Kirschner, Marc W -- 5R01GM039023-26/GM/NIGMS NIH HHS/ -- R01 GM039023/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):1248737. doi: 10.1126/science.1248737. Epub 2015 Apr 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. ; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. marc@hms.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859049" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase-Promoting Complex-Cyclosome/antagonists & ; inhibitors/chemistry/*metabolism ; Cell Cycle ; Cyclin A/metabolism ; Cyclin B/metabolism ; Feedback, Physiological ; Fluorescence ; Fluorescent Dyes ; HeLa Cells ; Humans ; Kinetics ; Protein Binding ; Protein Interaction Domains and Motifs ; SMN Complex Proteins/metabolism ; Substrate Specificity ; Ubiquitin/metabolism ; Ubiquitination
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  • 88
    Publication Date: 2015-02-24
    Description: Notch receptors guide mammalian cell fate decisions by engaging the proteins Jagged and Delta-like (DLL). The 2.3 angstrom resolution crystal structure of the interacting regions of the Notch1-DLL4 complex reveals a two-site, antiparallel binding orientation assisted by Notch1 O-linked glycosylation. Notch1 epidermal growth factor-like repeats 11 and 12 interact with the DLL4 Delta/Serrate/Lag-2 (DSL) domain and module at the N-terminus of Notch ligands (MNNL) domains, respectively. Threonine and serine residues on Notch1 are functionalized with O-fucose and O-glucose, which act as surrogate amino acids by making specific, and essential, contacts to residues on DLL4. The elucidation of a direct chemical role for O-glycans in Notch1 ligand engagement demonstrates how, by relying on posttranslational modifications of their ligand binding sites, Notch proteins have linked their functional capacity to developmentally regulated biosynthetic pathways.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445638/" 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/PMC4445638/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luca, Vincent C -- Jude, Kevin M -- Pierce, Nathan W -- Nachury, Maxence V -- Fischer, Suzanne -- Garcia, K Christopher -- 1R01-GM097015/GM/NIGMS NIH HHS/ -- R01 GM097015/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Feb 20;347(6224):847-53. doi: 10.1126/science.1261093.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. ; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. ; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. kcgarcia@stanford.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700513" target="_blank"〉PubMed〈/a〉
    Keywords: Alagille Syndrome/genetics ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Cell Line ; Conserved Sequence ; Crystallography, X-Ray ; Fucose/chemistry ; Glucose/chemistry ; Glycosylation ; Intracellular Signaling Peptides and Proteins/*chemistry/genetics ; Ligands ; Membrane Proteins/*chemistry/genetics/ultrastructure ; Molecular Sequence Data ; Molecular Targeted Therapy ; Polysaccharides/chemistry ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy/genetics ; Protein Binding ; Protein Structure, Tertiary ; Rats ; Receptor, Notch1/*chemistry/genetics/ultrastructure ; Serine/chemistry/genetics ; Threonine/chemistry/genetics
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  • 89
    Publication Date: 2015-02-24
    Description: Macromolecular function is rooted in energy landscapes, where sequence determines not a single structure but an ensemble of conformations. Hence, evolution modifies a protein's function by altering its energy landscape. Here, we recreate the evolutionary pathway between two modern human oncogenes, Src and Abl, by reconstructing their common ancestors. Our evolutionary reconstruction combined with x-ray structures of the common ancestor and pre-steady-state kinetics reveals a detailed atomistic mechanism for selectivity of the successful cancer drug Gleevec. Gleevec affinity is gained during the evolutionary trajectory toward Abl and lost toward Src, primarily by shifting an induced-fit equilibrium that is also disrupted in the clinical T315I resistance mutation. This work reveals the mechanism of Gleevec specificity while offering insights into how energy landscapes evolve.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405104/" 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/PMC4405104/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, C -- Agafonov, R V -- Hoemberger, M -- Kutter, S -- Zorba, A -- Halpin, J -- Buosi, V -- Otten, R -- Waterman, D -- Theobald, D L -- Kern, D -- GM094468/GM/NIGMS NIH HHS/ -- GM096053/GM/NIGMS NIH HHS/ -- GM100966-01/GM/NIGMS NIH HHS/ -- R01 GM094468/GM/NIGMS NIH HHS/ -- R01 GM096053/GM/NIGMS NIH HHS/ -- R01 GM100966/GM/NIGMS NIH HHS/ -- T32 EB009419/EB/NIBIB NIH HHS/ -- T32 GM007596/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Feb 20;347(6224):882-6. doi: 10.1126/science.aaa1823.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA. ; Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA. ; Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA. dkern@brandeis.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700521" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/chemistry/*pharmacology ; Benzamides/chemistry/*pharmacology ; Drug Resistance, Neoplasm/*genetics ; Entropy ; *Evolution, Molecular ; Humans ; Imatinib Mesylate ; Mutation ; Oncogene Proteins v-abl/chemistry/genetics ; Phylogeny ; Piperazines/chemistry/*pharmacology ; Protein Binding ; Protein Kinase Inhibitors/chemistry/*pharmacology ; Protein Structure, Secondary ; Pyrimidines/chemistry/*pharmacology ; src-Family Kinases/*chemistry/classification/genetics
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  • 90
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-10-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibbons, Ann -- New York, N.Y. -- Science. 2015 Oct 16;350(6258):264. doi: 10.1126/science.350.6258.264.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26472887" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; *Biological Evolution ; Caves ; China ; *Fossils ; *Human Migration ; Humans ; Tooth
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  • 91
    Publication Date: 2015-02-14
    Description: A new Late Jurassic docodontan shows specializations for a subterranean lifestyle. It is similar to extant subterranean golden moles in having reduced digit segments as compared to the ancestral phalangeal pattern of mammaliaforms and extant mammals. The reduction of digit segments can occur in mammals by fusion of the proximal and intermediate phalangeal precursors, a developmental process for which a gene and signaling network have been characterized in mouse and human. Docodontans show a positional shift of thoracolumbar ribs, a developmental variation that is controlled by Hox9 and Myf5 genes in extant mammals. We argue that these morphogenetic mechanisms of modern mammals were operating before the rise of modern mammals, driving the morphological disparity in the earliest mammaliaform diversification.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luo, Zhe-Xi -- Meng, Qing-Jin -- Ji, Qiang -- Liu, Di -- Zhang, Yu-Guang -- Neander, April I -- New York, N.Y. -- Science. 2015 Feb 13;347(6223):760-4. doi: 10.1126/science.1260880.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA. zxluo@uchicago.edu mengqingjin@bmnh.org.cn. ; Beijing Museum of Natural History, Beijing 100050, China. zxluo@uchicago.edu mengqingjin@bmnh.org.cn. ; Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, China. ; Beijing Museum of Natural History, Beijing 100050, China. ; Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25678660" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; China ; Finger Phalanges/*anatomy & histology/*growth & development ; Foot/anatomy & histology/growth & development ; Homeodomain Proteins/genetics/physiology ; Humans ; Mammals/*anatomy & histology/genetics/*growth & development ; Mice ; Morphogenesis/genetics/*physiology ; Myogenic Regulatory Factor 5/genetics/physiology
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  • 92
    Publication Date: 2015-05-16
    Description: The centrosome organizes microtubule arrays within animal cells and comprises two centrioles surrounded by an amorphous protein mass called the pericentriolar material (PCM). Despite the importance of centrosomes as microtubule-organizing centers, the mechanism and regulation of PCM assembly are not well understood. In Caenorhabditis elegans, PCM assembly requires the coiled-coil protein SPD-5. We found that recombinant SPD-5 could polymerize to form micrometer-sized porous networks in vitro. Network assembly was accelerated by two conserved regulators that control PCM assembly in vivo, Polo-like kinase-1 and SPD-2/Cep192. Only the assembled SPD-5 networks, and not unassembled SPD-5 protein, functioned as a scaffold for other PCM proteins. Thus, PCM size and binding capacity emerge from the regulated polymerization of one coiled-coil protein to form a porous network.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Woodruff, Jeffrey B -- Wueseke, Oliver -- Viscardi, Valeria -- Mahamid, Julia -- Ochoa, Stacy D -- Bunkenborg, Jakob -- Widlund, Per O -- Pozniakovsky, Andrei -- Zanin, Esther -- Bahmanyar, Shirin -- Zinke, Andrea -- Hong, Sun Hae -- Decker, Marcus -- Baumeister, Wolfgang -- Andersen, Jens S -- Oegema, Karen -- Hyman, Anthony A -- R01-GM074207/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 May 15;348(6236):808-12. doi: 10.1126/science.aaa3923.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. ; Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA. ; Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany. ; Department of Clinical Biochemistry, Copenhagen University Hospital, Hvidovre 2650, Denmark. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark. ; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark. ; Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA. hyman@mpi-cbg.de koegema@ucsd.edu. ; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. hyman@mpi-cbg.de koegema@ucsd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25977552" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*genetics/*metabolism ; Caenorhabditis elegans Proteins/chemistry/genetics/*metabolism ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; Centrosome/*metabolism/ultrasonography ; Metabolic Networks and Pathways ; Phosphorylation ; Polymerization ; Protein Binding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*metabolism ; Proto-Oncogene Proteins/*metabolism
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  • 93
    Publication Date: 2015-09-05
    Description: Fusion of intracellular transport vesicles requires soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and Sec1/Munc18-family (SM) proteins. Membrane-bridging SNARE complexes are critical for fusion, but their spontaneous assembly is inefficient and may require SM proteins in vivo. We report x-ray structures of Vps33, the SM subunit of the yeast homotypic fusion and vacuole protein-sorting (HOPS) complex, bound to two individual SNAREs. The two SNAREs, one from each membrane, are held in the correct orientation and register for subsequent complex assembly. Vps33 and potentially other SM proteins could thus act as templates for generating partially zipped SNARE assembly intermediates. HOPS was essential to mediate SNARE complex assembly at physiological SNARE concentrations. Thus, Vps33 appears to catalyze SNARE complex assembly through specific SNARE motif recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727825/" 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/PMC4727825/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Richard W -- Jeffrey, Philip D -- Zick, Michael -- Phillips, Ben P -- Wickner, William T -- Hughson, Frederick M -- GM071574/GM/NIGMS NIH HHS/ -- GM23377/GM/NIGMS NIH HHS/ -- R01 GM071574/GM/NIGMS NIH HHS/ -- T32 GM007388/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Sep 4;349(6252):1111-4. doi: 10.1126/science.aac7906.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. ; Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. ; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. hughson@princeton.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26339030" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Membrane Proteins/chemistry/metabolism ; Munc18 Proteins/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Qa-SNARE Proteins/*metabolism ; R-SNARE Proteins/*metabolism ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism/ultrastructure ; Synaptosomal-Associated Protein 25/chemistry/metabolism ; Vesicular Transport Proteins/chemistry/*metabolism/ultrastructure
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  • 94
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-05-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xue, Bing -- New York, N.Y. -- Science. 2015 May 22;348(6237):872. doi: 10.1126/science.348.6237.872-a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Applied Ecology, Chinese Academy of Sciences, 110016, Shenyang, China; Institute for Advanced Sustainability Studies (IASS), 14467, Potsdam, Germany; and Bohai University, 121013, Jinzhou, China. xuebing@iae.ac.cn bing.xue@iass-potsdam.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25999498" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Greenhouse Effect/*prevention & control
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  • 95
    Publication Date: 2015-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Hong -- Huang, Xianjin -- Thompson, Julian R -- Flower, Roger J -- New York, N.Y. -- Science. 2015 Feb 20;347(6224):834-5. doi: 10.1126/science.347.6224.834-d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CEES, Department of Biosciences, University of Oslo, Blindern, 0316, Oslo, Norway. hongyanghy@gmail.com hxj369@nju.edu.cn. ; School of Geographic and Oceanographic Science, Xianlin Campus, Nanjing University, Nanjing, 210023, China. hongyanghy@gmail.com hxj369@nju.edu.cn. ; Wetland Research Unit/Environmental Change Research Centre, UCL Department of Geography, University College London, London, WC1E 6BT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700509" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollutants/standards ; Air Pollution/*legislation & jurisprudence ; Carbon Dioxide/standards ; China ; Conservation of Natural Resources/*legislation & jurisprudence ; Water Pollutants/standards ; Water Pollution/*legislation & jurisprudence
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  • 96
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-05-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2015 May 8;348(6235):617. doi: 10.1126/science.348.6235.617.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25953986" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds/*anatomy & histology/*physiology ; China ; Feathers/*physiology ; *Flight, Animal ; Fossils
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  • 97
    Publication Date: 2015-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- Vogel, Gretchen -- New York, N.Y. -- Science. 2015 Oct 9;350(6257):144-5. doi: 10.1126/science.350.6257.144.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26450186" target="_blank"〉PubMed〈/a〉
    Keywords: Antimalarials/*therapeutic use ; Artemisinins/*therapeutic use ; China ; Humans ; Malaria/*drug therapy ; *Medicine, Chinese Traditional ; Neglected Diseases/*drug therapy ; *Nobel Prize ; Onchocerciasis, Ocular/drug therapy ; *Tropical Medicine
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  • 98
    Publication Date: 2015-01-24
    Description: Chemokines and their receptors control cell migration during development, immune system responses, and in numerous diseases, including inflammation and cancer. The structural basis of receptor:chemokine recognition has been a long-standing unanswered question due to the challenges of structure determination for membrane protein complexes. Here, we report the crystal structure of the chemokine receptor CXCR4 in complex with the viral chemokine antagonist vMIP-II at 3.1 angstrom resolution. The structure revealed a 1:1 stoichiometry and a more extensive binding interface than anticipated from the paradigmatic two-site model. The structure helped rationalize a large body of mutagenesis data and together with modeling provided insights into CXCR4 interactions with its endogenous ligand CXCL12, its ability to recognize diverse ligands, and the specificity of CC and CXC receptors for their respective chemokines.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362693/" 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/PMC4362693/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qin, Ling -- Kufareva, Irina -- Holden, Lauren G -- Wang, Chong -- Zheng, Yi -- Zhao, Chunxia -- Fenalti, Gustavo -- Wu, Huixian -- Han, Gye Won -- Cherezov, Vadim -- Abagyan, Ruben -- Stevens, Raymond C -- Handel, Tracy M -- ACB-12002/PHS HHS/ -- AGM-12006/PHS HHS/ -- R01 GM071872/GM/NIGMS NIH HHS/ -- R01 GM081763/GM/NIGMS NIH HHS/ -- R21 AI101687/AI/NIAID NIH HHS/ -- U01 GM094612/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Mar 6;347(6226):1117-22. doi: 10.1126/science.1261064. Epub 2015 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA. ; University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA. thandel@ucsd.edu stevens@usc.edu ikufareva@ucsd.edu. ; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. ; Department of Chemistry, Bridge Institute. Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA. ; Department of Chemistry, Bridge Institute. ; Department of Chemistry, Bridge Institute. Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA. thandel@ucsd.edu stevens@usc.edu ikufareva@ucsd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25612609" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chemokine CXCL12/chemistry ; Chemokines/*chemistry ; Crystallography, X-Ray ; Drug Design ; Humans ; Models, Chemical ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Receptors, CXCR4/agonists/antagonists & inhibitors/*chemistry ; Structural Homology, Protein
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  • 99
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-06-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- New York, N.Y. -- Science. 2015 Jun 12;348(6240):1185. doi: 10.1126/science.348.6240.1185.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26068817" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Climate ; *Dinosaurs ; *Extinction, Biological ; *Geologic Sediments ; *Global Warming ; *Greenhouse Effect ; *Lakes ; Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2015-05-16
    Description: Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, which are fundamental steps in the initiation of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBMs), harbor highly recurrent TERT promoter mutations of unknown function but specific to two nucleotide positions. We identified the functional consequence of these mutations in GBMs to be recruitment of the multimeric GA-binding protein (GABP) transcription factor specifically to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared mechanism underlying TERT reactivation. Tandem flanking native E26 transformation-specific motifs critically cooperate with these mutations to activate TERT, probably by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456397/" 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/PMC4456397/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, Robert J A -- Rube, H Tomas -- Kreig, Alex -- Mancini, Andrew -- Fouse, Shaun D -- Nagarajan, Raman P -- Choi, Serah -- Hong, Chibo -- He, Daniel -- Pekmezci, Melike -- Wiencke, John K -- Wrensch, Margaret R -- Chang, Susan M -- Walsh, Kyle M -- Myong, Sua -- Song, Jun S -- Costello, Joseph F -- DP2 GM105453/GM/NIGMS NIH HHS/ -- P01 CA118816/CA/NCI NIH HHS/ -- P01CA118816-06/CA/NCI NIH HHS/ -- P50CA097257/CA/NCI NIH HHS/ -- R01 CA163336/CA/NCI NIH HHS/ -- R01 CA169316/CA/NCI NIH HHS/ -- R01CA163336/CA/NCI NIH HHS/ -- R01CA169316-01/CA/NCI NIH HHS/ -- R01CA52689/CA/NCI NIH HHS/ -- R25CA112355/CA/NCI NIH HHS/ -- T32 GM008568/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 May 29;348(6238):1036-9. doi: 10.1126/science.aab0015. Epub 2015 May 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurological Surgery, University of California, San Francisco, CA. Department of Biostatistics and Epidemiology, University of California, San Francisco, CA. ; Department of Physics, University of Illinois, Urbana-Champaign, IL. Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. ; Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL. ; Department of Neurological Surgery, University of California, San Francisco, CA. ; Department of Radiation Oncology, University of California San Francisco, San Francisco, CA. ; Department of Anatomic Pathology, University of California San Francisco Medical School, San Francisco, CA 94143, USA. ; Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA. Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA. ; Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA. ; Department of Biostatistics and Epidemiology, University of California, San Francisco, CA. Department of Physics, University of Illinois, Urbana-Champaign, IL. Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL. songj@illinois.edu joseph.costello@ucsf.edu. ; Department of Neurological Surgery, University of California, San Francisco, CA. songj@illinois.edu joseph.costello@ucsf.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25977370" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Cell Line, Tumor ; GA-Binding Protein Transcription Factor/*metabolism ; *Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Neoplastic ; Glioblastoma/*genetics ; Humans ; Promoter Regions, Genetic ; Protein Binding ; Protein Multimerization ; Telomerase/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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