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  • Animals  (5)
  • JGR
  • Surface physics, nanoscale physics, low-dimensional systems
  • Nature Publishing Group (NPG)  (5)
  • 1
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    Innate immune and chemically triggered oxidative stress modifies translational fidelity (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-11-27
    Description: Translational fidelity, essential for protein and cell function, requires accurate transfer RNA (tRNA) aminoacylation. Purified aminoacyl-tRNA synthetases exhibit a fidelity of one error per 10,000 to 100,000 couplings. The accuracy of tRNA aminoacylation in vivo is uncertain, however, and might be considerably lower. Here we show that in mammalian cells, approximately 1% of methionine (Met) residues used in protein synthesis are aminoacylated to non-methionyl-tRNAs. Remarkably, Met-misacylation increases up to tenfold upon exposing cells to live or non-infectious viruses, toll-like receptor ligands or chemically induced oxidative stress. Met is misacylated to specific non-methionyl-tRNA families, and these Met-misacylated tRNAs are used in translation. Met-misacylation is blocked by an inhibitor of cellular oxidases, implicating reactive oxygen species (ROS) as the misacylation trigger. Among six amino acids tested, tRNA misacylation occurs exclusively with Met. As Met residues are known to protect proteins against ROS-mediated damage, we propose that Met-misacylation functions adaptively to increase Met incorporation into proteins to protect cells against oxidative stress. In demonstrating an unexpected conditional aspect of decoding mRNA, our findings illustrate the importance of considering alternative iterations of the genetic code.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785853/" 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/PMC2785853/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Netzer, Nir -- Goodenbour, Jeffrey M -- David, Alexandre -- Dittmar, Kimberly A -- Jones, Richard B -- Schneider, Jeffrey R -- Boone, David -- Eves, Eva M -- Rosner, Marsha R -- Gibbs, James S -- Embry, Alan -- Dolan, Brian -- Das, Suman -- Hickman, Heather D -- Berglund, Peter -- Bennink, Jack R -- Yewdell, Jonathan W -- Pan, Tao -- Z01 AI000542-20/Intramural NIH HHS/ -- Z01 AI000653-16/Intramural NIH HHS/ -- Z01 AI000658-16/Intramural NIH HHS/ -- Z01 AI001014-01/Intramural NIH HHS/ -- England -- Nature. 2009 Nov 26;462(7272):522-6. doi: 10.1038/nature08576.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940929" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/physiology ; Animals ; Genetic Code ; HeLa Cells ; Humans ; *Immunity, Innate ; Ligands ; Methionine/genetics/*metabolism ; Mice ; Models, Genetic ; NADPH Oxidase/metabolism ; Orthomyxoviridae/physiology ; Oxidative Stress/drug effects/genetics/*physiology ; RNA, Transfer, Met/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Substrate Specificity ; Toll-Like Receptors/immunology/metabolism ; Transfer RNA Aminoacylation/drug effects/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Peptide neurotransmitters activate a cation channel complex of NALCN and UNC-80 (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-12-19
    Description: Several neurotransmitters act through G-protein-coupled receptors to evoke a 'slow' excitation of neurons. These include peptides, such as substance P and neurotensin, as well as acetylcholine and noradrenaline. Unlike the fast (approximately millisecond) ionotropic actions of small-molecule neurotransmitters, the slow excitation is not well understood at the molecular level, but can be mainly attributed to suppressing K(+) currents and/or activating a non-selective cation channel. The molecular identity of this cation channel has yet to be determined; similarly, how the channel is activated and its relative contribution to neuronal excitability induced by the neuropeptides are unknown. Here we show that, in the mouse hippocampal and ventral tegmental area neurons, substance P and neurotensin activate a channel complex containing NALCN and a large previously unknown protein UNC-80. The activation by substance P through TACR1 (a G-protein-coupled receptor for substance P) occurs by means of a unique mechanism: it does not require G-protein activation but is dependent on Src family kinases. These findings identify NALCN as the cation channel activated by substance P receptor, and suggest that UNC-80 and Src family kinases, rather than a G protein, are involved in the coupling from receptor to channel.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810458/" 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/PMC2810458/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Boxun -- Su, Yanhua -- Das, Sudipto -- Wang, Haikun -- Wang, Yan -- Liu, Jin -- Ren, Dejian -- R01 NS055293/NS/NINDS NIH HHS/ -- R01 NS055293-01A1/NS/NINDS NIH HHS/ -- England -- Nature. 2009 Feb 5;457(7230):741-4. doi: 10.1038/nature07579. Epub 2008 Dec 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Pennsylvania, 415 S. University Avenue, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092807" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Electric Conductivity ; Guanosine Triphosphate/metabolism ; Heterotrimeric GTP-Binding Proteins ; Hippocampus/cytology ; Humans ; Ion Channels/agonists/genetics/*metabolism ; Mice ; Molecular Sequence Data ; Nerve Tissue Proteins/agonists/genetics/*metabolism ; Neurons/metabolism ; Neurotensin/pharmacology ; Neurotransmitter Agents/*pharmacology ; Receptors, Neurokinin-1/metabolism ; Substance P/pharmacology ; Transfection ; Ventral Tegmental Area/cytology ; src-Family Kinases/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Continued clearance of apoptotic cells critically depends on the phagocyte Ucp2 protein (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-08-23
    Description: Rapid and efficient removal of apoptotic cells by phagocytes is important during development, tissue homeostasis and in immune responses. Efficient clearance depends on the capacity of a single phagocyte to ingest multiple apoptotic cells successively, and to process the corpse-derived cellular material. However, the factors that influence continued clearance by phagocytes are not known. Here we show that the mitochondrial membrane potential of the phagocyte critically controls engulfment capacity, with lower potential enhancing engulfment and vice versa. The mitochondrial membrane protein Ucp2, which acts to lower the mitochondrial membrane potential, was upregulated in phagocytes engulfing apoptotic cells. Loss of Ucp2 reduced phagocytic capacity, whereas Ucp2 overexpression enhanced engulfment. Mutational and pharmacological studies indicated a direct role for Ucp2-mediated mitochondrial function in phagocytosis. Macrophages from Ucp2-deficient mice were impaired in phagocytosis in vitro, and Ucp2-deficient mice showed profound in vivo defects in clearing dying cells in the thymus and testes. Collectively, these data indicate that mitochondrial membrane potential and Ucp2 are key molecular determinants of apoptotic cell clearance. As Ucp2 is linked to metabolic diseases and atherosclerosis, this newly discovered role for Ucp2 in apoptotic cell clearance has implications for the complex aetiology and pathogenesis of these diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3513690/" 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/PMC3513690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Daeho -- Han, Claudia Z -- Elliott, Michael R -- Kinchen, Jason M -- Trampont, Paul C -- Das, Soumita -- Collins, Sheila -- Lysiak, Jeffrey J -- Hoehn, Kyle L -- Ravichandran, Kodi S -- R01 GM064709/GM/NIGMS NIH HHS/ -- R01 HD057242/HD/NICHD NIH HHS/ -- T32 GM008136/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 Aug 21;477(7363):220-4. doi: 10.1038/nature10340.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cell Clearance, University of Virginia, Charlottesville, Virginia 22908, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21857682" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Apoptosis ; Cell Line ; Cell Size/drug effects ; Cells, Cultured ; Ion Channels/deficiency/genetics/*metabolism ; Membrane Potential, Mitochondrial/drug effects/physiology ; Mice ; Mitochondrial Proteins/deficiency/genetics/*metabolism ; Phagocytes/*cytology/drug effects/*metabolism ; Phagocytosis/drug effects/*physiology ; Thymus Gland/cytology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Evolutionary implications of a third lymphocyte lineage in lampreys (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-08-13
    Description: Jawed vertebrates (gnathostomes) and jawless vertebrates (cyclostomes) have different adaptive immune systems. Gnathostomes use T- and B-cell antigen receptors belonging to the immunoglobulin superfamily. Cyclostomes, the lampreys and hagfish, instead use leucine-rich repeat proteins to construct variable lymphocyte receptors (VLRs), two types of which, VLRA and VLRB, are reciprocally expressed by lymphocytes resembling gnathostome T and B cells. Here we define another lineage of T-cell-like lymphocytes that express the recently identified VLRC receptors. Both VLRC(+) and VLRA(+) lymphocytes express orthologues of genes that gnathostome gammadelta and alphabeta T cells use for their differentiation, undergo VLRC and VLRA assembly and repertoire diversification in the 'thymoid' gill region, and express their VLRs solely as cell-surface proteins. Our findings suggest that the genetic programmes for two primordial T-cell lineages and a prototypic B-cell lineage were already present in the last common vertebrate ancestor approximately 500 million years ago. We propose that functional specialization of distinct T-cell-like lineages was an ancient feature of a primordial immune system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901013/" 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/PMC3901013/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hirano, Masayuki -- Guo, Peng -- McCurley, Nathanael -- Schorpp, Michael -- Das, Sabyasachi -- Boehm, Thomas -- Cooper, Max D -- R01 AI072435/AI/NIAID NIH HHS/ -- R01 GM100151/GM/NIGMS NIH HHS/ -- R01AI072435/AI/NIAID NIH HHS/ -- R01GM100151/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Sep 19;501(7467):435-8. doi: 10.1038/nature12467. Epub 2013 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, Georgia 30322, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23934109" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens/immunology ; *Biological Evolution ; Cell Differentiation ; *Cell Lineage ; Gene Expression Profiling ; Lampreys/*immunology ; Mitogens/immunology ; Molecular Sequence Data ; Poly I-C/immunology ; Proteins/genetics/immunology/metabolism ; T-Lymphocyte Subsets/*cytology/*immunology/metabolism ; Transcription, Genetic
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  • 5
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    NANOG-dependent function of TET1 and TET2 in establishment of pluripotency (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-02-12
    Description: Molecular control of the pluripotent state is thought to reside in a core circuitry of master transcription factors including the homeodomain-containing protein NANOG, which has an essential role in establishing ground state pluripotency during somatic cell reprogramming. Whereas the genomic occupancy of NANOG has been extensively investigated, comparatively little is known about NANOG-associated proteins and their contribution to the NANOG-mediated reprogramming process. Using enhanced purification techniques and a stringent computational algorithm, we identify 27 high-confidence protein interaction partners of NANOG in mouse embryonic stem cells. These consist of 19 previously unknown partners of NANOG that have not been reported before, including the ten-eleven translocation (TET) family methylcytosine hydroxylase TET1. We confirm physical association of NANOG with TET1, and demonstrate that TET1, in synergy with NANOG, enhances the efficiency of reprogramming. We also find physical association and reprogramming synergy of TET2 with NANOG, and demonstrate that knockdown of TET2 abolishes the reprogramming synergy of NANOG with a catalytically deficient mutant of TET1. These results indicate that the physical interaction between NANOG and TET1/TET2 proteins facilitates reprogramming in a manner that is dependent on the catalytic activity of TET1/TET2. TET1 and NANOG co-occupy genomic loci of genes associated with both maintenance of pluripotency and lineage commitment in embryonic stem cells, and TET1 binding is reduced upon NANOG depletion. Co-expression of NANOG and TET1 increases 5-hydroxymethylcytosine levels at the top-ranked common target loci Esrrb and Oct4 (also called Pou5f1), resulting in priming of their expression before reprogramming to naive pluripotency. We propose that TET1 is recruited by NANOG to enhance the expression of a subset of key reprogramming target genes. These results provide an insight into the reprogramming mechanism of NANOG and uncover a new role for 5-methylcytosine hydroxylases in the establishment of naive pluripotency.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606645/" 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/PMC3606645/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Costa, Yael -- Ding, Junjun -- Theunissen, Thorold W -- Faiola, Francesco -- Hore, Timothy A -- Shliaha, Pavel V -- Fidalgo, Miguel -- Saunders, Arven -- Lawrence, Moyra -- Dietmann, Sabine -- Das, Satyabrata -- Levasseur, Dana N -- Li, Zhe -- Xu, Mingjiang -- Reik, Wolf -- Silva, Jose C R -- Wang, Jianlong -- 079249/Wellcome Trust/United Kingdom -- 086692/Wellcome Trust/United Kingdom -- 095645/Wellcome Trust/United Kingdom -- 1R01-GM095942-01A1/GM/NIGMS NIH HHS/ -- BB/H008071/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0700098/Medical Research Council/United Kingdom -- R01 GM095942/GM/NIGMS NIH HHS/ -- R01 HL112294/HL/NHLBI NIH HHS/ -- WT079249/Wellcome Trust/United Kingdom -- WT086692MA/Wellcome Trust/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2013 Mar 21;495(7441):370-4. doi: 10.1038/nature11925. Epub 2013 Feb 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23395962" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cellular Reprogramming/*physiology ; DNA-Binding Proteins/genetics/*metabolism ; Embryonic Stem Cells ; Gene Expression Regulation, Developmental ; Genome ; Homeodomain Proteins/genetics/*metabolism ; Mice ; Protein Binding ; Proto-Oncogene Proteins/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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