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  • Amino Acid Sequence  (55)
  • American Association for the Advancement of Science (AAAS)  (55)
  • American Association of Petroleum Geologists (AAPG)
  • 2010-2014  (55)
  • 1950-1954
  • 2012  (55)
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  • American Association for the Advancement of Science (AAAS)  (55)
  • American Association of Petroleum Geologists (AAPG)
  • Nature Publishing Group (NPG)  (37)
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  • 2010-2014  (55)
  • 1950-1954
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  • 1
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    MARF1 regulates essential oogenic processes in mice (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-24
    Description: Development of fertilization-competent oocytes depends on integrated processes controlling meiosis, cytoplasmic development, and maintenance of genomic integrity. We show that meiosis arrest female 1 (MARF1) is required for these processes in mammalian oocytes. Mutations of Marf1 cause female infertility characterized by up-regulation of a cohort of transcripts, increased retrotransposon expression, defective cytoplasmic maturation, and meiotic arrest. Up-regulation of protein phosphatase 2 catalytic subunit (PPP2CB) is key to the meiotic arrest phenotype. Moreover, Iap and Line1 retrotransposon messenger RNAs are also up-regulated, and, concomitantly, DNA double-strand breaks are elevated in mutant oocytes. Therefore MARF1, by suppressing levels of specific transcripts, is an essential regulator of important oogenic processes leading to female fertility and the development of healthy offspring.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612990/" 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/PMC3612990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, You-Qiang -- Sugiura, Koji -- Sun, Fengyun -- Pendola, Janice K -- Cox, Gregory A -- Handel, Mary Ann -- Schimenti, John C -- Eppig, John J -- CA34196/CA/NCI NIH HHS/ -- HD42137/HD/NICHD NIH HHS/ -- P01 HD042137/HD/NICHD NIH HHS/ -- P30 CA034196/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 23;335(6075):1496-9. doi: 10.1126/science.1214680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Jackson Laboratory, Bar Harbor, ME 04609, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22442484" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; DNA Breaks, Double-Stranded ; Embryonic Development ; Female ; *Fertility ; Meiosis ; Mice ; Molecular Sequence Data ; Mutation ; Oocytes/*physiology ; *Oogenesis ; Phenotype ; Protein Phosphatase 2/genetics/metabolism ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Retroelements ; Transcription, Genetic ; Transcriptome ; Up-Regulation
    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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  • 2
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    Secreted kinase phosphorylates extracellular proteins that regulate biomineralization (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-15
    Description: Protein phosphorylation is a fundamental mechanism regulating nearly every aspect of cellular life. Several secreted proteins are phosphorylated, but the kinases responsible are unknown. We identified a family of atypical protein kinases that localize within the Golgi apparatus and are secreted. Fam20C appears to be the Golgi casein kinase that phosphorylates secretory pathway proteins within S-x-E motifs. Fam20C phosphorylates the caseins and several secreted proteins implicated in biomineralization, including the small integrin-binding ligand, N-linked glycoproteins (SIBLINGs). Consequently, mutations in Fam20C cause an osteosclerotic bone dysplasia in humans known as Raine syndrome. Fam20C is thus a protein kinase dedicated to the phosphorylation of extracellular proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3754843/" 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/PMC3754843/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tagliabracci, Vincent S -- Engel, James L -- Wen, Jianzhong -- Wiley, Sandra E -- Worby, Carolyn A -- Kinch, Lisa N -- Xiao, Junyu -- Grishin, Nick V -- Dixon, Jack E -- DK018024-37/DK/NIDDK NIH HHS/ -- DK018849-36/DK/NIDDK NIH HHS/ -- GM094575/GM/NIGMS NIH HHS/ -- R01 DK018849/DK/NIDDK NIH HHS/ -- R37 DK018024/DK/NIDDK NIH HHS/ -- T32 CA009523/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1150-3. doi: 10.1126/science.1217817. Epub 2012 May 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0721, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582013" target="_blank"〉PubMed〈/a〉
    Keywords: Abnormalities, Multiple/genetics/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Calcification, Physiologic ; Casein Kinase I ; Casein Kinases/metabolism ; Caseins/*metabolism ; Cattle ; Cell Line, Tumor ; Cleft Palate/genetics/metabolism ; Exophthalmos/genetics/metabolism ; Extracellular Matrix Proteins/chemistry/genetics/*metabolism/secretion ; Glycoproteins/metabolism ; Golgi Apparatus/*enzymology ; HEK293 Cells ; HeLa Cells ; Humans ; Microcephaly/genetics/metabolism ; Milk/enzymology ; Molecular Sequence Data ; Mutation ; Osteopontin ; Osteosclerosis/genetics/metabolism ; Phosphorylation ; Protein Sorting Signals ; Recombinant Fusion Proteins/chemistry/metabolism/secretion ; *Secretory Pathway ; Substrate Specificity
    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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  • 3
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    Mutations in the neverland gene turned Drosophila pachea into an obligate specialist species (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-29
    Description: Most living species exploit a limited range of resources. However, little is known about how tight associations build up during evolution between such specialist species and the hosts they use. We examined the dependence of Drosophila pachea on its single host, the senita cactus. Several amino acid changes in the Neverland oxygenase rendered D. pachea unable to transform cholesterol into 7-dehydrocholesterol (the first reaction in the steroid hormone biosynthetic pathway in insects) and thus made D. pachea dependent on the uncommon sterols of its host plant. The neverland mutations increase survival on the cactus's unusual sterols and are in a genomic region that faced recent positive selection. This study illustrates how relatively few genetic changes in a single gene may restrict the ecological niche of a species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729188/" 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/PMC4729188/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lang, Michael -- Murat, Sophie -- Clark, Andrew G -- Gouppil, Geraldine -- Blais, Catherine -- Matzkin, Luciano M -- Guittard, Emilie -- Yoshiyama-Yanagawa, Takuji -- Kataoka, Hiroshi -- Niwa, Ryusuke -- Lafont, Rene -- Dauphin-Villemant, Chantal -- Orgogozo, Virginie -- AI064950/AI/NIAID NIH HHS/ -- R01 AI064950/AI/NIAID NIH HHS/ -- R01 HG003229/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1658-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR7592, Universite Paris Diderot, Sorbonne Paris Cite, Institut Jacques Monod, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019649" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cactaceae/*metabolism ; Cholesterol/metabolism ; Conserved Sequence ; Dehydrocholesterols/metabolism ; Drosophila/genetics/*physiology ; Drosophila Proteins/chemistry/*genetics/metabolism ; *Food Chain ; Molecular Sequence Data ; *Mutation ; Oxygenases/chemistry/*genetics/metabolism ; Protein Conformation ; RNA Interference ; Selection, Genetic ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 4
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    Identification and functional expression of the mitochondrial pyruvate carrier (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-26
    Description: The transport of pyruvate, the end product of glycolysis, into mitochondria is an essential process that provides the organelle with a major oxidative fuel. Although the existence of a specific mitochondrial pyruvate carrier (MPC) has been anticipated, its molecular identity remained unknown. We report that MPC is a heterocomplex formed by two members of a family of previously uncharacterized membrane proteins that are conserved from yeast to mammals. Members of the MPC family were found in the inner mitochondrial membrane, and yeast mutants lacking MPC proteins showed severe defects in mitochondrial pyruvate uptake. Coexpression of mouse MPC1 and MPC2 in Lactococcus lactis promoted transport of pyruvate across the membrane. These observations firmly establish these proteins as essential components of the MPC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herzig, Sebastien -- Raemy, Etienne -- Montessuit, Sylvie -- Veuthey, Jean-Luc -- Zamboni, Nicola -- Westermann, Benedikt -- Kunji, Edmund R S -- Martinou, Jean-Claude -- MC_U105663139/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):93-6. doi: 10.1126/science.1218530. Epub 2012 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, University of Geneva, Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628554" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Biological Transport ; Biosynthetic Pathways ; Culture Media ; Lactococcus lactis/genetics/metabolism ; Leucine/metabolism ; Mice ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondrial Membranes/*metabolism ; Molecular Sequence Data ; Proprotein Convertase 1/chemistry/genetics/*metabolism ; Proprotein Convertase 2 ; Pyruvic Acid/*metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/genetics/growth & development/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Thioctic Acid/biosynthesis/metabolism ; Valine/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 5
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    Highly conserved protective epitopes on influenza B viruses (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-11
    Description: Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538841/" 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/PMC3538841/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dreyfus, Cyrille -- Laursen, Nick S -- Kwaks, Ted -- Zuijdgeest, David -- Khayat, Reza -- Ekiert, Damian C -- Lee, Jeong Hyun -- Metlagel, Zoltan -- Bujny, Miriam V -- Jongeneelen, Mandy -- van der Vlugt, Remko -- Lamrani, Mohammed -- Korse, Hans J W M -- Geelen, Eric -- Sahin, Ozcan -- Sieuwerts, Martijn -- Brakenhoff, Just P J -- Vogels, Ronald -- Li, Olive T W -- Poon, Leo L M -- Peiris, Malik -- Koudstaal, Wouter -- Ward, Andrew B -- Wilson, Ian A -- Goudsmit, Jaap -- Friesen, Robert H E -- GM080209/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- RR017573/RR/NCRR NIH HHS/ -- T32 GM080209/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 14;337(6100):1343-8. doi: 10.1126/science.1222908. Epub 2012 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22878502" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/chemistry/*immunology ; Antibodies, Neutralizing/chemistry/immunology ; Conserved Sequence ; Hemagglutinin Glycoproteins, Influenza Virus/*immunology ; Humans ; Immunodominant Epitopes/chemistry/*immunology ; Influenza B virus/*immunology ; Influenza Vaccines/*immunology ; Mice ; Molecular Sequence Data ; Neutralization Tests ; Orthomyxoviridae Infections/*prevention & control ; Protein Conformation
    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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  • 6
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    Identification of small molecule activators of cryptochrome (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-07-17
    Description: Impairment of the circadian clock has been associated with numerous disorders, including metabolic disease. Although small molecules that modulate clock function might offer therapeutic approaches to such diseases, only a few compounds have been identified that selectively target core clock proteins. From an unbiased cell-based circadian phenotypic screen, we identified KL001, a small molecule that specifically interacts with cryptochrome (CRY). KL001 prevented ubiquitin-dependent degradation of CRY, resulting in lengthening of the circadian period. In combination with mathematical modeling, our studies using KL001 revealed that CRY1 and CRY2 share a similar functional role in the period regulation. Furthermore, KL001-mediated CRY stabilization inhibited glucagon-induced gluconeogenesis in primary hepatocytes. KL001 thus provides a tool to study the regulation of CRY-dependent physiology and aid development of clock-based therapeutics of diabetes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589997/" 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/PMC3589997/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hirota, Tsuyoshi -- Lee, Jae Wook -- St John, Peter C -- Sawa, Mariko -- Iwaisako, Keiko -- Noguchi, Takako -- Pongsawakul, Pagkapol Y -- Sonntag, Tim -- Welsh, David K -- Brenner, David A -- Doyle, Francis J 3rd -- Schultz, Peter G -- Kay, Steve A -- GM074868/GM/NIGMS NIH HHS/ -- GM085764/GM/NIGMS NIH HHS/ -- GM096873/GM/NIGMS NIH HHS/ -- MH051573/MH/NIMH NIH HHS/ -- MH082945/MH/NIMH NIH HHS/ -- P50 GM085764/GM/NIGMS NIH HHS/ -- R01 GM041804/GM/NIGMS NIH HHS/ -- R01 GM074868/GM/NIGMS NIH HHS/ -- R01 GM096873/GM/NIGMS NIH HHS/ -- R01 MH051573/MH/NIMH NIH HHS/ -- R01 MH082945/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1094-7. doi: 10.1126/science.1223710. Epub 2012 Jul 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798407" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3 Cells ; Amino Acid Sequence ; Animals ; Carbazoles/chemistry/isolation & purification/*pharmacology ; Cell Line, Tumor ; Circadian Clocks/*drug effects ; Cryptochromes/*agonists/metabolism ; Gluconeogenesis/drug effects/genetics ; Glucose-6-Phosphatase/genetics ; HEK293 Cells ; Hepatocytes/drug effects/metabolism ; Humans ; Liver/cytology/drug effects/metabolism ; Mice ; Molecular Sequence Data ; Phosphoenolpyruvate Carboxykinase (GTP)/genetics ; Protein Stability/drug effects ; Proteolysis/drug effects ; *Small Molecule Libraries ; Sulfonamides/chemistry/isolation & purification/*pharmacology
    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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  • 7
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    Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-11
    Description: Sodium/calcium (Na(+)/Ca(2+)) exchangers (NCX) are membrane transporters that play an essential role in maintaining the homeostasis of cytosolic Ca(2+) for cell signaling. We demonstrated the Na(+)/Ca(2+)-exchange function of an NCX from Methanococcus jannaschii (NCX_Mj) and report its 1.9 angstrom crystal structure in an outward-facing conformation. Containing 10 transmembrane helices, the two halves of NCX_Mj share a similar structure with opposite orientation. Four ion-binding sites cluster at the center of the protein: one specific for Ca(2+) and three that likely bind Na(+). Two passageways allow for Na(+) and Ca(2+) access to the central ion-binding sites from the extracellular side. Based on the symmetry of NCX_Mj and its ability to catalyze bidirectional ion-exchange reactions, we propose a structure model for the inward-facing NCX_Mj.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Jun -- Li, Hua -- Zeng, Weizhong -- Sauer, David B -- Belmares, Ricardo -- Jiang, Youxing -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):686-90. doi: 10.1126/science.1215759.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323814" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Calcium/*metabolism ; Crystallization ; Crystallography, X-Ray ; Ion Transport ; Ligands ; Methanococcales/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sodium/*metabolism ; Sodium-Calcium Exchanger/*chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 8
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    Crystal structure of the heterodimeric CLOCK:BMAL1 transcriptional activator complex (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-02
    Description: The circadian clock in mammals is driven by an autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete. A key component of this mechanism is a heterodimeric transcriptional activator consisting of two basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain protein subunits, CLOCK and BMAL1. Here, we report the crystal structure of a complex containing the mouse CLOCK:BMAL1 bHLH-PAS domains at 2.3 A resolution. The structure reveals an unusual asymmetric heterodimer with the three domains in each of the two subunits--bHLH, PAS-A, and PAS-B--tightly intertwined and involved in dimerization interactions, resulting in three distinct protein interfaces. Mutations that perturb the observed heterodimer interfaces affect the stability and activity of the CLOCK:BMAL1 complex as well as the periodicity of the circadian oscillator. The structure of the CLOCK:BMAL1 complex is a starting point for understanding at an atomic level the mechanism driving the mammalian circadian clock.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694778/" 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/PMC3694778/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Nian -- Chelliah, Yogarany -- Shan, Yongli -- Taylor, Clinton A -- Yoo, Seung-Hee -- Partch, Carrie -- Green, Carla B -- Zhang, Hong -- Takahashi, Joseph S -- R01 GM081875/GM/NIGMS NIH HHS/ -- R01 GM090247/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):189-94. doi: 10.1126/science.1222804. Epub 2012 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22653727" target="_blank"〉PubMed〈/a〉
    Keywords: ARNTL Transcription Factors/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Animals ; CLOCK Proteins/*chemistry/genetics/metabolism ; Cells, Cultured ; *Circadian Rhythm ; Crystallography, X-Ray ; DNA/metabolism ; HEK293 Cells ; Helix-Loop-Helix Motifs ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; *Transcriptional Activation
    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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  • 9
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    A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-17
    Description: Exocytosis is essential to the lytic cycle of apicomplexan parasites and required for the pathogenesis of toxoplasmosis and malaria. DOC2 proteins recruit the membrane fusion machinery required for exocytosis in a Ca(2+)-dependent fashion. Here, the phenotype of a Toxoplasma gondii conditional mutant impaired in host cell invasion and egress was pinpointed to a defect in secretion of the micronemes, an apicomplexan-specific organelle that contains adhesion proteins. Whole-genome sequencing identified the etiological point mutation in TgDOC2.1. A conditional allele of the orthologous gene engineered into Plasmodium falciparum was also defective in microneme secretion. However, the major effect was on invasion, suggesting that microneme secretion is dispensable for Plasmodium egress.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354045/" 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/PMC3354045/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Farrell, Andrew -- Thirugnanam, Sivasakthivel -- Lorestani, Alexander -- Dvorin, Jeffrey D -- Eidell, Keith P -- Ferguson, David J P -- Anderson-White, Brooke R -- Duraisingh, Manoj T -- Marth, Gabor T -- Gubbels, Marc-Jan -- AI057919/AI/NIAID NIH HHS/ -- AI081220/AI/NIAID NIH HHS/ -- AI087874/AI/NIAID NIH HHS/ -- AI088314/AI/NIAID NIH HHS/ -- HG004719/HG/NHGRI NIH HHS/ -- K08 AI087874/AI/NIAID NIH HHS/ -- K08 AI087874-02/AI/NIAID NIH HHS/ -- R01 AI057919/AI/NIAID NIH HHS/ -- R01 HG004719/HG/NHGRI NIH HHS/ -- R21 AI081220/AI/NIAID NIH HHS/ -- R21 AI088314/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):218-21. doi: 10.1126/science.1210829.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246776" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calcium/*metabolism ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cell Line ; *Exocytosis ; Genes, Protozoan ; Genetic Complementation Test ; Genome, Protozoan ; Humans ; Models, Molecular ; Molecular Sequence Data ; Movement ; Mutagenesis ; Organelles/*metabolism ; Plasmodium falciparum/genetics/growth & development/physiology ; Point Mutation ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Toxoplasma/genetics/growth & development/*physiology/ultrastructure
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  • 10
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    An overlapping protein-coding region in influenza A virus segment 3 modulates the host response (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-30
    Description: Influenza A virus (IAV) infection leads to variable and imperfectly understood pathogenicity. We report that segment 3 of the virus contains a second open reading frame ("X-ORF"), accessed via ribosomal frameshifting. The frameshift product, termed PA-X, comprises the endonuclease domain of the viral PA protein with a C-terminal domain encoded by the X-ORF and functions to repress cellular gene expression. PA-X also modulates IAV virulence in a mouse infection model, acting to decrease pathogenicity. Loss of PA-X expression leads to changes in the kinetics of the global host response, which notably includes increases in inflammatory, apoptotic, and T lymphocyte-signaling pathways. Thus, we have identified a previously unknown IAV protein that modulates the host response to infection, a finding with important implications for understanding IAV pathogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552242/" 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/PMC3552242/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jagger, B W -- Wise, H M -- Kash, J C -- Walters, K-A -- Wills, N M -- Xiao, Y-L -- Dunfee, R L -- Schwartzman, L M -- Ozinsky, A -- Bell, G L -- Dalton, R M -- Lo, A -- Efstathiou, S -- Atkins, J F -- Firth, A E -- Taubenberger, J K -- Digard, P -- 073126/Wellcome Trust/United Kingdom -- 088789/Wellcome Trust/United Kingdom -- G0700815/Medical Research Council/United Kingdom -- G0700815(82260)/Medical Research Council/United Kingdom -- G9800943/Medical Research Council/United Kingdom -- MR/J002232/1/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):199-204. doi: 10.1126/science.1222213. Epub 2012 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745253" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Codon ; Conserved Sequence ; Female ; *Frameshifting, Ribosomal ; Gene Expression Regulation ; Genome, Viral ; HEK293 Cells ; Humans ; Influenza A Virus, H1N1 Subtype/*genetics/growth & development/pathogenicity ; Influenza A virus/*genetics/metabolism ; Lung/pathology/virology ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Mutation ; *Open Reading Frames ; Orthomyxoviridae Infections/genetics/immunology/pathology/*virology ; Protein Interaction Domains and Motifs ; Proteome ; RNA Replicase/chemistry/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Viral/genetics/metabolism ; Reassortant Viruses/genetics ; Repressor Proteins/chemistry/*genetics/*metabolism ; Viral Nonstructural Proteins/chemistry/*genetics/*metabolism ; Viral Proteins/biosynthesis/chemistry/*genetics/*metabolism ; Virus Replication
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  • 11
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    Chitin-induced dimerization activates a plant immune receptor (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-02
    Description: Pattern recognition receptors confer plant resistance to pathogen infection by recognizing the conserved pathogen-associated molecular patterns. The cell surface receptor chitin elicitor receptor kinase 1 of Arabidopsis (AtCERK1) directly binds chitin through its lysine motif (LysM)-containing ectodomain (AtCERK1-ECD) to activate immune responses. The crystal structure that we solved of an AtCERK1-ECD complexed with a chitin pentamer reveals that their interaction is primarily mediated by a LysM and three chitin residues. By acting as a bivalent ligand, a chitin octamer induces AtCERK1-ECD dimerization that is inhibited by shorter chitin oligomers. A mutation attenuating chitin-induced AtCERK1-ECD dimerization or formation of nonproductive AtCERK1 dimer by overexpression of AtCERK1-ECD compromises AtCERK1-mediated signaling in plant cells. Together, our data support the notion that chitin-induced AtCERK1 dimerization is critical for its activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Tingting -- Liu, Zixu -- Song, Chuanjun -- Hu, Yunfei -- Han, Zhifu -- She, Ji -- Fan, Fangfang -- Wang, Jiawei -- Jin, Changwen -- Chang, Junbiao -- Zhou, Jian-Min -- Chai, Jijie -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1160-4. doi: 10.1126/science.1218867.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654057" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylglucosamine/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/immunology/*metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Chitin/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphorylation ; Plants, Genetically Modified ; Protein Multimerization ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry/genetics/*metabolism ; Receptors, Pattern Recognition/*chemistry/genetics/*metabolism ; Signal Transduction
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  • 12
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    Evolution of shape by multiple regulatory changes to a growth gene (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-01
    Description: The genetic changes responsible for morphological differences between species are largely unidentified. Such changes can involve modifications of growth that are relevant to understanding evolution, development, and disease. We identified a gene that induces male-specific wing size and shape differences between Nasonia wasp species. Fine-scale mapping and in situ hybridization reveal that changes in at least three regions (two strictly in noncoding sequence) around the gene unpaired-like (upd-like) cause changes in spatial and temporal expression of upd-like in the developing wing and corresponding changes in wing width. Upd-like shows homology to the Drosophila unpaired gene, a well-studied signaling protein that regulates cell proliferation and differentiation. Our results indicate how multiple changes in the regulation of upd-like are involved in microevolution of morphological and sex-specific differences between species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520604/" 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/PMC3520604/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loehlin, David W -- Werren, John H -- 5R01 GM070026-04/GM/NIGMS NIH HHS/ -- 5R24 GM084917-04/GM/NIGMS NIH HHS/ -- R01 GM070026/GM/NIGMS NIH HHS/ -- R24 GM084917/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):943-7. doi: 10.1126/science.1215193.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Rochester, Rochester, NY 14627, USA. loehlin@wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363002" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Cloning, Molecular ; Drosophila/genetics ; Drosophila Proteins/genetics ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genes, Insect ; Insect Proteins/*genetics/metabolism ; Male ; Molecular Sequence Data ; Morphogenesis/genetics ; Organ Size ; Quantitative Trait Loci ; Sex Characteristics ; Species Specificity ; Transcription Factors/genetics ; Wasps/anatomy & histology/*genetics/*growth & development ; Wings, Animal/*anatomy & histology/*growth & development/metabolism
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  • 13
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    Single-molecule fluorescence experiments determine protein folding transition path times (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-01
    Description: The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs as the free-energy barrier between two states is crossed. It is a single-molecule property that contains all the mechanistic information on how a process occurs. As a step toward observing transition paths in protein folding, we determined the average transition-path time for a fast- and a slow-folding protein from a photon-by-photon analysis of fluorescence trajectories in single-molecule Forster resonance energy transfer experiments. Whereas the folding rate coefficients differ by a factor of 10,000, the transition-path times differ by a factor of less than 5, which shows that a fast- and a slow-folding protein take almost the same time to fold when folding actually happens. A very simple model based on energy landscape theory can explain this result.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878298/" 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/PMC3878298/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- McHale, Kevin -- Louis, John M -- Eaton, William A -- Z99 DK999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):981-4. doi: 10.1126/science.1215768.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD 20892-0520, USA. chunghoi@niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363011" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Carrier Proteins/*chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Photons ; Protein Conformation ; *Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thermodynamics
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  • 14
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    The amyloid precursor protein has a flexible transmembrane domain and binds cholesterol (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-02
    Description: C99 is the transmembrane carboxyl-terminal domain of the amyloid precursor protein that is cleaved by gamma-secretase to release the amyloid-beta polypeptides, which are associated with Alzheimer's disease. Nuclear magnetic resonance and electron paramagnetic resonance spectroscopy show that the extracellular amino terminus of C99 includes a surface-embedded "N-helix" followed by a short "N-loop" connecting to the transmembrane domain (TMD). The TMD is a flexibly curved alpha helix, making it well suited for processive cleavage by gamma-secretase. Titration of C99 reveals a binding site for cholesterol, providing mechanistic insight into how cholesterol promotes amyloidogenesis. Membrane-buried GXXXG motifs (G, Gly; X, any amino acid), which have an established role in oligomerization, were also shown to play a key role in cholesterol binding. The structure and cholesterol binding properties of C99 may aid in the design of Alzheimer's therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528355/" 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/PMC3528355/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barrett, Paul J -- Song, Yuanli -- Van Horn, Wade D -- Hustedt, Eric J -- Schafer, Johanna M -- Hadziselimovic, Arina -- Beel, Andrew J -- Sanders, Charles R -- F31 NS077681/NS/NINDS NIH HHS/ -- P01 GM080513/GM/NIGMS NIH HHS/ -- T32 GM008320/GM/NIGMS NIH HHS/ -- T32 GM08320/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1168-71. doi: 10.1126/science.1219988.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654059" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amyloid beta-Protein Precursor/*chemistry/genetics/*metabolism ; Binding Sites ; Cholesterol/*metabolism ; Electron Spin Resonance Spectroscopy ; Humans ; Micelles ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 15
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    Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-17
    Description: In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377438/" 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/PMC3377438/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gagnon, Matthieu G -- Seetharaman, Sai V -- Bulkley, David -- Steitz, Thomas A -- GM022778/GM/NIGMS NIH HHS/ -- P01 GM022778/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1370-2. doi: 10.1126/science.1217443.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422986" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carboxylic Ester Hydrolases/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; Protein Structure, Tertiary ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; RNA, Transfer, Met/chemistry/metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry/metabolism/ultrastructure
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    Assembly of an evolutionarily new pathway for alpha-pyrone biosynthesis in Arabidopsis (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-08-28
    Description: Plants possess arrays of functionally diverse specialized metabolites, many of which are distributed taxonomically. Here, we describe the evolution of a class of substituted alpha-pyrone metabolites in Arabidopsis, which we have named arabidopyrones. The biosynthesis of arabidopyrones requires a cytochrome P450 enzyme (CYP84A4) to generate the catechol-substituted substrate for an extradiol ring-cleavage dioxygenase (AtLigB). Unlike other ring-cleavage-derived plant metabolites made from tyrosine, arabidopyrones are instead derived from phenylalanine through the early steps of phenylpropanoid metabolism. Whereas CYP84A4, an Arabidopsis-specific paralog of the lignin-biosynthetic enzyme CYP84A1, has neofunctionalized relative to its ancestor, AtLigB homologs are widespread among land plants and many bacteria. This study exemplifies the rapid evolution of a biochemical pathway formed by the addition of a new biological activity into an existing metabolic infrastructure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weng, Jing-Ke -- Li, Yi -- Mo, Huaping -- Chapple, Clint -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):960-4. doi: 10.1126/science.1221614.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923580" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/enzymology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Biosynthetic Pathways ; Catalytic Domain ; Cytochrome P-450 Enzyme System/chemistry/genetics/*metabolism ; Dioxygenases/genetics/metabolism ; Evolution, Molecular ; Gene Duplication ; Genome, Plant ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phenylalanine/metabolism ; Phylogeny ; Plant Stems/metabolism ; Plants, Genetically Modified ; Pyrones/chemistry/*metabolism
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    Structural basis for prereceptor modulation of plant hormones by GH3 proteins (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-05-26
    Description: Acyl acid amido synthetases of the GH3 family act as critical prereceptor modulators of plant hormone action; however, the molecular basis for their hormone selectivity is unclear. Here, we report the crystal structures of benzoate-specific Arabidopsis thaliana AtGH3.12/PBS3 and jasmonic acid-specific AtGH3.11/JAR1. These structures, combined with biochemical analysis, define features for the conjugation of amino acids to diverse acyl acid substrates and highlight the importance of conformational changes in the carboxyl-terminal domain for catalysis. We also identify residues forming the acyl acid binding site across the GH3 family and residues critical for amino acid recognition. Our results demonstrate how a highly adaptable three-dimensional scaffold is used for the evolution of promiscuous activity across an enzyme family for modulation of plant signaling molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westfall, Corey S -- Zubieta, Chloe -- Herrmann, Jonathan -- Kapp, Ulrike -- Nanao, Max H -- Jez, Joseph M -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1708-11. doi: 10.1126/science.1221863. Epub 2012 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Washington University, St. Louis, MO 63130, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628555" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Arabidopsis ; Arabidopsis Proteins/*chemistry/metabolism ; Benzoates/chemistry ; Binding Sites ; Crystallography, X-Ray ; Cyclopentanes/chemistry ; Indoleacetic Acids/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleotidyltransferases/*chemistry/metabolism ; Oxylipins/chemistry ; Plant Growth Regulators/chemistry/metabolism ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Substrate Specificity
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  • 18
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    The crystal structure of TAL effector PthXo1 bound to its DNA target (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-10
    Description: DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427646/" 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/PMC3427646/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mak, Amanda Nga-Sze -- Bradley, Philip -- Cernadas, Raul A -- Bogdanove, Adam J -- Stoddard, Barry L -- R01 GM049857/GM/NIGMS NIH HHS/ -- R01 GM088277/GM/NIGMS NIH HHS/ -- R01 GM098861/GM/NIGMS NIH HHS/ -- R01GM098861/GM/NIGMS NIH HHS/ -- RL1 0CA833133/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):716-9. doi: 10.1126/science.1216211. Epub 2012 Jan 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025 Seattle, WA 98019, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223736" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; DNA, Plant/*chemistry/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; High-Throughput Screening Assays ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Processes ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repetitive Sequences, Amino Acid ; Virulence Factors/*chemistry/*metabolism ; Xanthomonas/*chemistry/pathogenicity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 19
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    Imaginal discs secrete insulin-like peptide 8 to mediate plasticity of growth and maturation (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-05
    Description: Developing animals frequently adjust their growth programs and/or their maturation or metamorphosis to compensate for growth disturbances (such as injury or tumor) and ensure normal adult size. Such plasticity entails tissue and organ communication to preserve their proportions and symmetry. Here, we show that imaginal discs autonomously activate DILP8, a Drosophila insulin-like peptide, to communicate abnormal growth and postpone maturation. DILP8 delays metamorphosis by inhibiting ecdysone biosynthesis, slowing growth in the imaginal discs, and generating normal-sized animals. Loss of dilp8 yields asymmetric individuals with an unusually large variation in size and a more varied time of maturation. Thus, DILP8 is a fundamental element of the hitherto ill-defined machinery governing the plasticity that ensures developmental stability and robustness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garelli, Andres -- Gontijo, Alisson M -- Miguela, Veronica -- Caparros, Esther -- Dominguez, Maria -- New York, N.Y. -- Science. 2012 May 4;336(6081):579-82. doi: 10.1126/science.1216735.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas-Universidad Miguel Hernandez de Elche, Sant Joan d'Alacant, 03550 Alicante, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556250" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apoptosis ; Drosophila Proteins/chemistry/*genetics/*metabolism ; Drosophila melanogaster/*genetics/*growth & development/metabolism ; Ecdysone/biosynthesis ; Ethyl Methanesulfonate/pharmacology ; Gene Expression Regulation, Developmental ; Genes, Insect ; Imaginal Discs/growth & development/*physiology ; Intercellular Signaling Peptides and Proteins/chemistry/*genetics/metabolism ; Intracellular Signaling Peptides and Proteins/genetics/metabolism ; Larva/growth & development ; *Metamorphosis, Biological/genetics ; Molecular Sequence Data ; Neoplasms, Experimental/genetics/metabolism/pathology ; Peptide Initiation Factors/genetics/metabolism ; Pupa/growth & development ; Regeneration
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  • 20
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    Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-18
    Description: It is held as a paradigm that ribosomally synthesized peptides and proteins contain only l-amino acids. We demonstrate a ribosomal origin of the marine sponge-derived polytheonamides, exceptionally potent, giant natural-product toxins. Isolation of the biosynthetic genes from the sponge metagenome revealed a bacterial gene architecture. Only six candidate enzymes were identified for 48 posttranslational modifications, including 18 epimerizations and 17 methylations of nonactivated carbon centers. Three enzymes were functionally validated, which showed that a radical S-adenosylmethionine enzyme is responsible for the unidirectional epimerization of multiple and different amino acids. Collectively, these complex alterations create toxins that function as unimolecular minimalistic ion channels with near-femtomolar activity. This study broadens the biosynthetic scope of ribosomal systems and creates new opportunities for peptide and protein bioengineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freeman, Michael F -- Gurgui, Cristian -- Helf, Maximilian J -- Morinaka, Brandon I -- Uria, Agustinus R -- Oldham, Neil J -- Sahl, Hans-Georg -- Matsunaga, Shigeki -- Piel, Jorn -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):387-90. doi: 10.1126/science.1226121. Epub 2012 Sep 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22983711" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Ion Channels/biosynthesis/*metabolism ; Marine Toxins/biosynthesis/*metabolism ; *Metagenome ; Methylation ; Molecular Sequence Data ; Protein Biosynthesis ; *Protein Processing, Post-Translational ; Proteins/*metabolism ; Ribosomes/metabolism ; S-Adenosylmethionine/metabolism ; Theonella/*microbiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 21
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    Oxytocin/vasopressin-related peptides have an ancient role in reproductive behavior (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-01
    Description: Many biological functions are conserved, but the extent to which conservation applies to integrative behaviors is unknown. Vasopressin and oxytocin neuropeptides are strongly implicated in mammalian reproductive and social behaviors, yet rodent loss-of-function mutants have relatively subtle behavioral defects. Here we identify an oxytocin/vasopressin-like signaling system in Caenorhabditis elegans, consisting of a peptide and two receptors that are expressed in sexually dimorphic patterns. Males lacking the peptide or its receptors perform poorly in reproductive behaviors, including mate search, mate recognition, and mating, but other sensorimotor behaviors are intact. Quantitative analysis indicates that mating motor patterns are fragmented and inefficient in mutants, suggesting that oxytocin/vasopressin peptides increase the coherence of mating behaviors. These results indicate that conserved molecules coordinate diverse behavioral motifs in reproductive behavior.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597094/" 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/PMC3597094/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garrison, Jennifer L -- Macosko, Evan Z -- Bernstein, Samantha -- Pokala, Navin -- Albrecht, Dirk R -- Bargmann, Cornelia I -- GM07739/GM/NIGMS NIH HHS/ -- K99 GM092859/GM/NIGMS NIH HHS/ -- K99GM092859/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Oct 26;338(6106):540-3. doi: 10.1126/science.1226201.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23112335" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; CHO Cells ; Caenorhabditis elegans/genetics/*physiology ; Caenorhabditis elegans ; Proteins/agonists/chemistry/genetics/pharmacology/*physiology ; Cricetinae ; Humans ; Male ; Neuropeptides/chemistry/genetics/pharmacology/*physiology ; Oxytocin/chemistry/genetics/pharmacology/*physiology ; Receptors, G-Protein-Coupled/agonists/genetics/*physiology ; Reproduction ; Sexual Behavior, Animal/*physiology ; Vasopressins/chemistry/genetics/pharmacology/*physiology
    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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  • 22
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    An exon splice enhancer primes IGF2:IGF2R binding site structure and function evolution (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-01
    Description: Placental development and genomic imprinting coevolved with parental conflict over resource distribution to mammalian offspring. The imprinted genes IGF2 and IGF2R code for the growth promoter insulin-like growth factor 2 (IGF2) and its inhibitor, mannose 6-phosphate (M6P)/IGF2 receptor (IGF2R), respectively. M6P/IGF2R of birds and fish do not recognize IGF2. In monotremes, which lack imprinting, IGF2 specifically bound M6P/IGF2R via a hydrophobic CD loop. We show that the DNA coding the CD loop in monotremes functions as an exon splice enhancer (ESE) and that structural evolution of binding site loops (AB, HI, FG) improved therian IGF2 affinity. We propose that ESE evolution led to the fortuitous acquisition of IGF2 binding by M6P/IGF2R that drew IGF2R into parental conflict; subsequent imprinting may then have accelerated affinity maturation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658703/" 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/PMC4658703/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Christopher -- Hoppe, Hans-Jurgen -- Rezgui, Dellel -- Strickland, Madeleine -- Forbes, Briony E -- Grutzner, Frank -- Frago, Susana -- Ellis, Rosamund Z -- Wattana-Amorn, Pakorn -- Prince, Stuart N -- Zaccheo, Oliver J -- Nolan, Catherine M -- Mungall, Andrew J -- Jones, E Yvonne -- Crump, Matthew P -- Hassan, A Bassim -- 082352/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 9891/Cancer Research UK/United Kingdom -- A13295/Cancer Research UK/United Kingdom -- A9891/Cancer Research UK/United Kingdom -- C375/Cancer Research UK/United Kingdom -- C429/Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1209-13. doi: 10.1126/science.1228633.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organic and Biological Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197533" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Animals ; Binding Sites/genetics ; Conserved Sequence ; Enhancer Elements, Genetic/*genetics ; *Evolution, Molecular ; *Exons ; Genomic Imprinting ; Humans ; Insulin-Like Growth Factor II/*chemistry/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Receptor, IGF Type 2/*chemistry/classification/genetics ; Species Specificity
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  • 23
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    Vasopressin/oxytocin-related signaling regulates gustatory associative learning in C. elegans (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-11-01
    Description: Vasopressin- and oxytocin-related neuropeptides are key regulators of animal physiology, including water balance and reproduction. Although these neuropeptides also modulate social behavior and cognition in mammals, the mechanism for influencing behavioral plasticity and the evolutionary origin of these effects are not well understood. Here, we present a functional vasopressin- and oxytocin-like signaling system in the nematode Caenorhabditis elegans. Through activation of its receptor NTR-1, a vasopressin/oxytocin-related neuropeptide, designated nematocin, facilitates the experience-driven modulation of salt chemotaxis, a type of gustatory associative learning in C. elegans. Our study suggests that vasopressin and oxytocin neuropeptides have ancient roles in modulating sensory processing in neural circuits that underlie behavioral plasticity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beets, Isabel -- Janssen, Tom -- Meelkop, Ellen -- Temmerman, Liesbet -- Suetens, Nick -- Rademakers, Suzanne -- Jansen, Gert -- Schoofs, Liliane -- New York, N.Y. -- Science. 2012 Oct 26;338(6106):543-5. doi: 10.1126/science.1226860.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Functional Genomics and Proteomics Unit, KU Leuven, 3000 Leuven, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23112336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biological Evolution ; Caenorhabditis elegans/genetics/*physiology ; Caenorhabditis elegans ; Proteins/agonists/chemistry/genetics/metabolism/pharmacology/*physiology ; Learning/drug effects/*physiology ; Male ; Molecular Sequence Data ; Neuropeptides/chemistry/genetics/pharmacology/*physiology ; Oxytocin/chemistry/genetics/pharmacology/*physiology ; Receptors, G-Protein-Coupled/agonists/genetics/metabolism/*physiology ; Signal Transduction ; Taste/drug effects/*physiology ; Vasopressins/chemistry/genetics/pharmacology/*physiology
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  • 24
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    The structure and catalytic cycle of a sodium-pumping pyrophosphatase (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-07-28
    Description: Membrane-integral pyrophosphatases (M-PPases) are crucial for the survival of plants, bacteria, and protozoan parasites. They couple pyrophosphate hydrolysis or synthesis to Na(+) or H(+) pumping. The 2.6-angstrom structure of Thermotoga maritima M-PPase in the resting state reveals a previously unknown solution for ion pumping. The hydrolytic center, 20 angstroms above the membrane, is coupled to the gate formed by the conserved Asp(243), Glu(246), and Lys(707) by an unusual "coupling funnel" of six alpha helices. Comparison with our 4.0-angstrom resolution structure of the product complex suggests that helix 12 slides down upon substrate binding to open the gate by a simple binding-change mechanism. Below the gate, four helices form the exit channel. Superimposing helices 3 to 6, 9 to 12, and 13 to 16 suggests that M-PPases arose through gene triplication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kellosalo, Juho -- Kajander, Tommi -- Kogan, Konstantin -- Pokharel, Kisun -- Goldman, Adrian -- New York, N.Y. -- Science. 2012 Jul 27;337(6093):473-6. doi: 10.1126/science.1222505.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology and Biophysics Program, Institute of Biotechnology, Post Office Box 65, University of Helsinki, FIN-00014, Finland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22837527" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/metabolism ; Biocatalysis ; Calcium/chemistry ; Catalytic Domain ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Diphosphates/*metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Pyrophosphatases/*chemistry/genetics/*metabolism ; Sodium/*metabolism ; Sodium-Potassium-Exchanging ATPase/*chemistry/genetics/metabolism ; Thermotoga maritima/*enzymology
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  • 25
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    Natural variation in a chloride channel subunit confers avermectin resistance in C. elegans (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-04
    Description: Resistance of nematodes to anthelmintics such as avermectins has emerged as a major global health and agricultural problem, but genes conferring natural resistance to avermectins are unknown. We show that a naturally occurring four-amino-acid deletion in the ligand-binding domain of GLC-1, the alpha-subunit of a glutamate-gated chloride channel, confers resistance to avermectins in the model nematode Caenorhabditis elegans. We also find that the same variant confers resistance to the avermectin-producing bacterium Streptomyces avermitilis. Population-genetic analyses identified two highly divergent haplotypes at the glc-1 locus that have been maintained at intermediate frequencies by long-term balancing selection. These results implicate variation in glutamate-gated chloride channels in avermectin resistance and provide a mechanism by which such resistance can be maintained.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273849/" 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/PMC3273849/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghosh, Rajarshi -- Andersen, Erik C -- Shapiro, Joshua A -- Gerke, Justin P -- Kruglyak, Leonid -- P50-GM071508/GM/NIGMS NIH HHS/ -- R01 HG004321/HG/NHGRI NIH HHS/ -- R01 HG004321-03/HG/NHGRI NIH HHS/ -- R01-HG004321/HG/NHGRI NIH HHS/ -- R37- MH59520/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 3;335(6068):574-8. doi: 10.1126/science.1214318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lewis-Sigler Institute for Integrative Genomics, Department of Ecology and Evolutionary Biology, and Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22301316" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Antinematodal Agents/*pharmacology ; Caenorhabditis elegans/*drug effects/*genetics/physiology ; Caenorhabditis elegans Proteins/chemistry/*genetics/metabolism ; Chloride Channels/chemistry/*genetics/metabolism ; Crosses, Genetic ; Drug Resistance/genetics ; Genes, Helminth ; Genome-Wide Association Study ; Ivermectin/*analogs & derivatives/*pharmacology ; Ligands ; Molecular Sequence Data ; Mutation ; Polymorphism, Single Nucleotide ; Protein Structure, Tertiary ; Quantitative Trait Loci ; Selection, Genetic ; Streptomyces/physiology
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  • 26
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    Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-10-16
    Description: The rhg1-b allele of soybean is widely used for resistance against soybean cyst nematode (SCN), the most economically damaging pathogen of soybeans in the United States. Gene silencing showed that genes in a 31-kilobase segment at rhg1-b, encoding an amino acid transporter, an alpha-SNAP protein, and a WI12 (wound-inducible domain) protein, each contribute to resistance. There is one copy of the 31-kilobase segment per haploid genome in susceptible varieties, but 10 tandem copies are present in an rhg1-b haplotype. Overexpression of the individual genes in roots was ineffective, but overexpression of the genes together conferred enhanced SCN resistance. Hence, SCN resistance mediated by the soybean quantitative trait locus Rhg1 is conferred by copy number variation that increases the expression of a set of dissimilar genes in a repeated multigene segment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cook, David E -- Lee, Tong Geon -- Guo, Xiaoli -- Melito, Sara -- Wang, Kai -- Bayless, Adam M -- Wang, Jianping -- Hughes, Teresa J -- Willis, David K -- Clemente, Thomas E -- Diers, Brian W -- Jiang, Jiming -- Hudson, Matthew E -- Bent, Andrew F -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1206-9. doi: 10.1126/science.1228746. Epub 2012 Oct 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23065905" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Animals ; *Gene Dosage ; Gene Expression Regulation, Plant ; *Genetic Loci ; Genetic Variation ; Haplotypes ; Male ; Molecular Sequence Data ; Plant Diseases/*genetics/*parasitology ; Plant Proteins/*genetics ; Plant Roots/genetics/parasitology ; Protein Structure, Tertiary/genetics ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins/genetics ; Soybeans/*genetics/*parasitology ; *Tylenchoidea
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  • 27
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    iRhom2 regulation of TACE controls TNF-mediated protection against Listeria and responses to LPS (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-17
    Description: Innate immune responses are vital for pathogen defense but can result in septic shock when excessive. A key mediator of septic shock is tumor necrosis factor-alpha (TNFalpha), which is shed from the plasma membrane after cleavage by the TNFalpha convertase (TACE). We report that the rhomboid family member iRhom2 interacted with TACE and regulated TNFalpha shedding. iRhom2 was critical for TACE maturation and trafficking to the cell surface in hematopoietic cells. Gene-targeted iRhom2-deficient mice showed reduced serum TNFalpha in response to lipopolysaccharide (LPS) and could survive a lethal LPS dose. Furthermore, iRhom2-deficient mice failed to control the replication of Listeria monocytogenes. Our study has identified iRhom2 as a regulator of innate immunity that may be an important target for modulating sepsis and pathogen defense.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250273/" 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/PMC4250273/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McIlwain, David R -- Lang, Philipp A -- Maretzky, Thorsten -- Hamada, Koichi -- Ohishi, Kazuhito -- Maney, Sathish Kumar -- Berger, Thorsten -- Murthy, Aditya -- Duncan, Gordon -- Xu, Haifeng C -- Lang, Karl S -- Haussinger, Dieter -- Wakeham, Andrew -- Itie-Youten, Annick -- Khokha, Rama -- Ohashi, Pamela S -- Blobel, Carl P -- Mak, Tak W -- GM64750/GM/NIGMS NIH HHS/ -- R01 GM064750/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):229-32. doi: 10.1126/science.1214448.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Campell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network (UHN), 620 University Avenue, Toronto, Ontario M5G 2C1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246778" target="_blank"〉PubMed〈/a〉
    Keywords: ADAM Proteins/genetics/*metabolism ; Amino Acid Sequence ; Animals ; B-Lymphocytes/immunology/metabolism ; Base Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cell Membrane/metabolism ; Gene Deletion ; *Immunity, Innate ; Lipopolysaccharides/*immunology ; Listeria monocytogenes/immunology/physiology ; Listeriosis/*immunology/metabolism/microbiology/pathology ; Macrophages/immunology/metabolism ; Macrophages, Peritoneal/immunology/metabolism/microbiology ; Mice ; Molecular Sequence Data ; Protein Transport ; Shock, Septic/*immunology/metabolism ; Spleen/cytology ; Tumor Necrosis Factor-alpha/blood/genetics/*metabolism
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    Catalysis and sulfa drug resistance in dihydropteroate synthase (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-03
    Description: The sulfonamide antibiotics inhibit dihydropteroate synthase (DHPS), a key enzyme in the folate pathway of bacteria and primitive eukaryotes. However, resistance mutations have severely compromised the usefulness of these drugs. We report structural, computational, and mutagenesis studies on the catalytic and resistance mechanisms of DHPS. By performing the enzyme-catalyzed reaction in crystalline DHPS, we have structurally characterized key intermediates along the reaction pathway. Results support an S(N)1 reaction mechanism via formation of a novel cationic pterin intermediate. We also show that two conserved loops generate a substructure during catalysis that creates a specific binding pocket for p-aminobenzoic acid, one of the two DHPS substrates. This substructure, together with the pterin-binding pocket, explains the roles of the conserved active-site residues and reveals how sulfonamide resistance arises.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531234/" 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/PMC3531234/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yun, Mi-Kyung -- Wu, Yinan -- Li, Zhenmei -- Zhao, Ying -- Waddell, M Brett -- Ferreira, Antonio M -- Lee, Richard E -- Bashford, Donald -- White, Stephen W -- AI070721/AI/NIAID NIH HHS/ -- CA21765/CA/NCI NIH HHS/ -- P30 CA021765/CA/NCI NIH HHS/ -- R01 AI070721/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1110-4. doi: 10.1126/science.1214641.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383850" target="_blank"〉PubMed〈/a〉
    Keywords: 4-Aminobenzoic Acid/chemistry/metabolism ; Amino Acid Sequence ; Anti-Bacterial Agents/chemistry/metabolism/*pharmacology ; Bacillus anthracis/drug effects/enzymology ; Biocatalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Dihydropteroate Synthase/*chemistry/genetics/*metabolism ; Diphosphates/chemistry/metabolism ; *Drug Resistance, Bacterial ; Magnesium/chemistry ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Parabens/chemistry/metabolism ; Protein Conformation ; Sulfamethoxazole/chemistry/metabolism/*pharmacology ; Sulfathiazoles/chemistry/metabolism/*pharmacology ; Yersinia pestis/drug effects/enzymology
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    A mutation in EGF repeat-8 of Notch discriminates between Serrate/Jagged and Delta family ligands (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-12-01
    Description: Notch signaling affects many developmental and cellular processes and has been implicated in congenital disorders, stroke, and numerous cancers. The Notch receptor binds its ligands Delta and Serrate and is able to discriminate between them in different contexts. However, the specific domains in Notch responsible for this selectivity are poorly defined. Through genetic screens in Drosophila, we isolated a mutation, Notch(jigsaw), that affects Serrate- but not Delta-dependent signaling. Notch(jigsaw) carries a missense mutation in epidermal growth factor repeat-8 (EGFr-8) and is defective in Serrate binding. A homologous point mutation in mammalian Notch2 also exhibits defects in signaling of a mammalian Serrate homolog, Jagged1. Hence, an evolutionarily conserved valine in EGFr-8 is essential for ligand selectivity and provides a molecular handle to study numerous Notch-dependent signaling events.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663443/" 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/PMC3663443/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamamoto, Shinya -- Charng, Wu-Lin -- Rana, Nadia A -- Kakuda, Shinako -- Jaiswal, Manish -- Bayat, Vafa -- Xiong, Bo -- Zhang, Ke -- Sandoval, Hector -- David, Gabriela -- Wang, Hao -- Haltiwanger, Robert S -- Bellen, Hugo J -- 1RC4GM096355-01/GM/NIGMS NIH HHS/ -- 5K12GM084897/GM/NIGMS NIH HHS/ -- 5P30HD024064/HD/NICHD NIH HHS/ -- 5R01GM061126-12/GM/NIGMS NIH HHS/ -- 5R01GM067858/GM/NIGMS NIH HHS/ -- 5T32-HD055200/HD/NICHD NIH HHS/ -- K12 GM084897/GM/NIGMS NIH HHS/ -- P30 HD024064/HD/NICHD NIH HHS/ -- R01 GM061126/GM/NIGMS NIH HHS/ -- R01 GM067858/GM/NIGMS NIH HHS/ -- RC4 GM096355/GM/NIGMS NIH HHS/ -- T32 HD055200/HD/NICHD NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1229-32. doi: 10.1126/science.1228745.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197537" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Calcium-Binding Proteins/*metabolism ; Cells, Cultured ; DNA Mutational Analysis ; Drosophila Proteins/*genetics/*metabolism ; Drosophila melanogaster/genetics/*metabolism ; Epidermal Growth Factor/genetics ; Evolution, Molecular ; Humans ; Intercellular Signaling Peptides and Proteins/*metabolism ; Intracellular Signaling Peptides and Proteins/*metabolism ; Ligands ; Male ; Membrane Proteins/*metabolism ; Methionine/genetics ; Molecular Sequence Data ; Mutation ; Receptor, Notch2/genetics/metabolism ; Receptors, Notch/*genetics/*metabolism ; Tandem Repeat Sequences/genetics ; Valine/genetics ; X Chromosome/genetics
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    Botulinum neurotoxin is shielded by NTNHA in an interlocked complex (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-01
    Description: Botulinum neurotoxins (BoNTs) are highly poisonous substances that are also effective medicines. Accidental BoNT poisoning often occurs through ingestion of Clostridium botulinum-contaminated food. Here, we present the crystal structure of a BoNT in complex with a clostridial nontoxic nonhemagglutinin (NTNHA) protein at 2.7 angstroms. Biochemical and functional studies show that NTNHA provides large and multivalent binding interfaces to protect BoNT from gastrointestinal degradation. Moreover, the structure highlights key residues in BoNT that regulate complex assembly in a pH-dependent manner. Collectively, our findings define the molecular mechanisms by which NTNHA shields BoNT in the hostile gastrointestinal environment and releases it upon entry into the circulation. These results will assist in the design of small molecules for inhibiting oral BoNT intoxication and of delivery vehicles for oral administration of biologics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545708/" 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/PMC3545708/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Shenyan -- Rumpel, Sophie -- Zhou, Jie -- Strotmeier, Jasmin -- Bigalke, Hans -- Perry, Kay -- Shoemaker, Charles B -- Rummel, Andreas -- Jin, Rongsheng -- R01 AI091823/AI/NIAID NIH HHS/ -- U54 AI057159/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):977-81. doi: 10.1126/science.1214270.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neuroscience, Aging and Stem Cell Research, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363010" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Botulinum Toxins, Type A/*chemistry/metabolism ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Multiprotein Complexes/chemistry/metabolism ; Mutagenesis ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary
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    Structure and allostery of the PKA RIIbeta tetrameric holoenzyme (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-11
    Description: In its physiological state, cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is a tetramer that contains a regulatory (R) subunit dimer and two catalytic (C) subunits. We describe here the 2.3 angstrom structure of full-length tetrameric RIIbeta(2):C(2) holoenzyme. This structure showing a dimer of dimers provides a mechanistic understanding of allosteric activation by cAMP. The heterodimers are anchored together by an interface created by the beta4-beta5 loop in the RIIbeta subunit, which docks onto the carboxyl-terminal tail of the adjacent C subunit, thereby forcing the C subunit into a fully closed conformation in the absence of nucleotide. Diffusion of magnesium adenosine triphosphate (ATP) into these crystals trapped not ATP, but the reaction products, adenosine diphosphate and the phosphorylated RIIbeta subunit. This complex has implications for the dissociation-reassociation cycling of PKA. The quaternary structure of the RIIbeta tetramer differs appreciably from our model of the RIalpha tetramer, confirming the small-angle x-ray scattering prediction that the structures of each PKA tetramer are different.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985767/" 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/PMC3985767/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Ping -- Smith-Nguyen, Eric V -- Keshwani, Malik M -- Deal, Michael S -- Kornev, Alexandr P -- Taylor, Susan S -- GM34921/GM/NIGMS NIH HHS/ -- R01 GM034921/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):712-6. doi: 10.1126/science.1213979.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093-0654, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323819" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Allosteric Site ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/metabolism ; Cyclic AMP-Dependent Protein Kinase Catalytic Subunits/*chemistry/*metabolism ; Cyclic AMP-Dependent Protein Kinase RIIbeta Subunit/*chemistry/*metabolism ; Holoenzymes/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Folding ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Rats
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    Parallel molecular evolution in an herbivore community (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-29
    Description: Numerous insects have independently evolved the ability to feed on plants that produce toxic secondary compounds called cardenolides and can sequester these compounds for use in their defense. We surveyed the protein target for cardenolides, the alpha subunit of the sodium pump, Na(+),K(+)-ATPase (ATPalpha), in 14 species that feed on cardenolide-producing plants and 15 outgroups spanning three insect orders. Despite the large number of potential targets for modulating cardenolide sensitivity, amino acid substitutions associated with host-plant specialization are highly clustered, with many parallel substitutions. Additionally, we document four independent duplications of ATPalpha with convergent tissue-specific expression patterns. We find that unique substitutions are disproportionately associated with recent duplications relative to parallel substitutions. Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3770729/" 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/PMC3770729/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhen, Ying -- Aardema, Matthew L -- Medina, Edgar M -- Schumer, Molly -- Andolfatto, Peter -- R01 GM083228/GM/NIGMS NIH HHS/ -- R01-GM083228/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1634-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019645" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological/*genetics ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Apocynaceae/*metabolism/parasitology ; Cardenolides/*metabolism ; *Evolution, Molecular ; Genetic Pleiotropy ; Herbivory/*genetics ; Host-Parasite Interactions/*genetics ; Insects/enzymology/*genetics/physiology ; Molecular Sequence Data ; Organ Specificity ; Sodium-Potassium-Exchanging ATPase/chemistry/*genetics/metabolism
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    EF-P is essential for rapid synthesis of proteins containing consecutive proline residues (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-12-15
    Description: Elongation factor P (EF-P) is a translation factor of unknown function that has been implicated in a great variety of cellular processes. Here, we show that EF-P prevents ribosome from stalling during synthesis of proteins containing consecutive prolines, such as PPG, PPP, or longer proline strings, in natural and engineered model proteins. EF-P promotes peptide-bond formation and stabilizes the peptidyl-transfer RNA in the catalytic center of the ribosome. EF-P is posttranslationally modified by a hydroxylated beta-lysine attached to a lysine residue. The modification enhances the catalytic proficiency of the factor mainly by increasing its affinity to the ribosome. We propose that EF-P and its eukaryotic homolog, eIF5A, are essential for the synthesis of a subset of proteins containing proline stretches in all cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doerfel, Lili K -- Wohlgemuth, Ingo -- Kothe, Christina -- Peske, Frank -- Urlaub, Henning -- Rodnina, Marina V -- New York, N.Y. -- Science. 2013 Jan 4;339(6115):85-8. doi: 10.1126/science.1229017. Epub 2012 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23239624" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Escherichia coli/genetics/*metabolism ; Lysine/metabolism ; Molecular Sequence Data ; Peptide Elongation Factors/*metabolism ; Proline/genetics/*metabolism ; Protein Biosynthesis ; Protein Processing, Post-Translational ; Ribosomes/*metabolism
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    Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-12-22
    Description: The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers host immune responses such as the production of type I interferons. Cytosolic DNA induces interferons through the production of cyclic guanosine monophosphate-adenosine monophosphate (cyclic GMP-AMP, or cGAMP), which binds to and activates the adaptor protein STING. Through biochemical fractionation and quantitative mass spectrometry, we identified a cGAMP synthase (cGAS), which belongs to the nucleotidyltransferase family. Overexpression of cGAS activated the transcription factor IRF3 and induced interferon-beta in a STING-dependent manner. Knockdown of cGAS inhibited IRF3 activation and interferon-beta induction by DNA transfection or DNA virus infection. cGAS bound to DNA in the cytoplasm and catalyzed cGAMP synthesis. These results indicate that cGAS is a cytosolic DNA sensor that induces interferons by producing the second messenger cGAMP.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863629/" 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/PMC3863629/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Lijun -- Wu, Jiaxi -- Du, Fenghe -- Chen, Xiang -- Chen, Zhijian J -- AI-093967/AI/NIAID NIH HHS/ -- R01 AI093967/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Feb 15;339(6121):786-91. doi: 10.1126/science.1232458. Epub 2012 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23258413" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Cell Line, Tumor ; Cyclic AMP/biosynthesis ; Cyclic GMP/biosynthesis ; Cytidine Triphosphate/metabolism ; Cytosol/enzymology/*immunology ; DNA/*immunology/metabolism ; Gene Knockdown Techniques ; HEK293 Cells ; Humans ; Interferon Type I/*biosynthesis ; Interferon-beta/*biosynthesis ; Metabolic Networks and Pathways ; Mice ; Molecular Sequence Data ; Nucleotidyltransferases/genetics/isolation & purification/*metabolism
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    The protein-folding problem, 50 years on (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-11-28
    Description: The protein-folding problem was first posed about one half-century ago. The term refers to three broad questions: (i) What is the physical code by which an amino acid sequence dictates a protein's native structure? (ii) How can proteins fold so fast? (iii) Can we devise a computer algorithm to predict protein structures from their sequences? We review progress on these problems. In a few cases, computer simulations of the physical forces in chemically detailed models have now achieved the accurate folding of small proteins. We have learned that proteins fold rapidly because random thermal motions cause conformational changes leading energetically downhill toward the native structure, a principle that is captured in funnel-shaped energy landscapes. And thanks in part to the large Protein Data Bank of known structures, predicting protein structures is now far more successful than was thought possible in the early days. What began as three questions of basic science one half-century ago has now grown into the full-fledged research field of protein physical science.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dill, Ken A -- MacCallum, Justin L -- GM34993/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 23;338(6110):1042-6. doi: 10.1126/science.1219021.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA. dill@laufercenter.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180855" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Caspase 9/chemistry ; Computer Simulation ; Models, Chemical ; Pharmaceutical Preparations/chemistry ; *Protein Conformation ; *Protein Folding ; Proteins/*chemistry
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    A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-26
    Description: Pyruvate constitutes a critical branch point in cellular carbon metabolism. We have identified two proteins, Mpc1 and Mpc2, as essential for mitochondrial pyruvate transport in yeast, Drosophila, and humans. Mpc1 and Mpc2 associate to form an ~150-kilodalton complex in the inner mitochondrial membrane. Yeast and Drosophila mutants lacking MPC1 display impaired pyruvate metabolism, with an accumulation of upstream metabolites and a depletion of tricarboxylic acid cycle intermediates. Loss of yeast Mpc1 results in defective mitochondrial pyruvate uptake, and silencing of MPC1 or MPC2 in mammalian cells impairs pyruvate oxidation. A point mutation in MPC1 provides resistance to a known inhibitor of the mitochondrial pyruvate carrier. Human genetic studies of three families with children suffering from lactic acidosis and hyperpyruvatemia revealed a causal locus that mapped to MPC1, changing single amino acids that are conserved throughout eukaryotes. These data demonstrate that Mpc1 and Mpc2 form an essential part of the mitochondrial pyruvate carrier.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690818/" 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/PMC3690818/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bricker, Daniel K -- Taylor, Eric B -- Schell, John C -- Orsak, Thomas -- Boutron, Audrey -- Chen, Yu-Chan -- Cox, James E -- Cardon, Caleb M -- Van Vranken, Jonathan G -- Dephoure, Noah -- Redin, Claire -- Boudina, Sihem -- Gygi, Steven P -- Brivet, Michele -- Thummel, Carl S -- Rutter, Jared -- K99 AR059190/AR/NIAMS NIH HHS/ -- K99AR059190/AR/NIAMS NIH HHS/ -- P30 HL101310/HL/NHLBI NIH HHS/ -- P30DK072437/DK/NIDDK NIH HHS/ -- R01 DK071962/DK/NIDDK NIH HHS/ -- R01 GM087346/GM/NIGMS NIH HHS/ -- R01 GM094232/GM/NIGMS NIH HHS/ -- R01GM083746/GM/NIGMS NIH HHS/ -- R24 DK092784/DK/NIDDK NIH HHS/ -- R24DK092784/DK/NIDDK NIH HHS/ -- RC1DK086426/DK/NIDDK NIH HHS/ -- T32GM007464/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):96-100. doi: 10.1126/science.1218099. Epub 2012 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628558" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/metabolism ; Animals ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Biological Transport ; Carbohydrate Metabolism ; Citric Acid Cycle ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster/chemistry/genetics/*metabolism ; Humans ; Metabolomics ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Point Mutation ; Pyruvic Acid/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Crystal structure of the human K2P TRAAK, a lipid- and mechano-sensitive K+ ion channel (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-28
    Description: TRAAK channels, members of the two-pore domain K(+) (potassium ion) channel family K2P, are expressed almost exclusively in the nervous system and control the resting membrane potential. Their gating is sensitive to polyunsaturated fatty acids, mechanical deformation of the membrane, and temperature changes. Physiologically, these channels appear to control the noxious input threshold for temperature and pressure sensitivity in dorsal root ganglia neurons. We present the crystal structure of human TRAAK at a resolution of 3.8 angstroms. The channel comprises two protomers, each containing two distinct pore domains, which create a two-fold symmetric K(+) channel. The extracellular surface features a helical cap, 35 angstroms tall, that creates a bifurcated pore entryway and accounts for the insensitivity of two-pore domain K(+) channels to inhibitory toxins. Two diagonally opposed gate-forming inner helices form membrane-interacting structures that may underlie this channel's sensitivity to chemical and mechanical properties of the cell membrane.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329120/" 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/PMC3329120/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brohawn, Stephen G -- del Marmol, Josefina -- MacKinnon, Roderick -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jan 27;335(6067):436-41. doi: 10.1126/science.1213808.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22282805" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; CHO Cells ; Cell Membrane/chemistry/physiology ; Cricetinae ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Lipid Bilayers/chemistry ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; Patch-Clamp Techniques ; Potassium/metabolism ; Potassium Channel Blockers/pharmacology ; Potassium Channels/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Recombinant Proteins/chemistry
    Print ISSN: 0036-8075
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  • 38
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    Atomic view of a toxic amyloid small oligomer (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-10
    Description: Amyloid diseases, including Alzheimer's, Parkinson's, and the prion conditions, are each associated with a particular protein in fibrillar form. These amyloid fibrils were long suspected to be the disease agents, but evidence suggests that smaller, often transient and polymorphic oligomers are the toxic entities. Here, we identify a segment of the amyloid-forming protein alphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: beta-sheet-rich structure, cytotoxicity, and recognition by an oligomer-specific antibody. The x-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six antiparallel protein strands, that we term a cylindrin. The cylindrin structure is compatible with a sequence segment from the beta-amyloid protein of Alzheimer's disease. Cylindrins offer models for the hitherto elusive structures of amyloid oligomers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959867/" 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/PMC3959867/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laganowsky, Arthur -- Liu, Cong -- Sawaya, Michael R -- Whitelegge, Julian P -- Park, Jiyong -- Zhao, Minglei -- Pensalfini, Anna -- Soriaga, Angela B -- Landau, Meytal -- Teng, Poh K -- Cascio, Duilio -- Glabe, Charles -- Eisenberg, David -- 016570/PHS HHS/ -- 1R01-AG029430/AG/NIA NIH HHS/ -- 5T32GM008496/GM/NIGMS NIH HHS/ -- P50 AG016570/AG/NIA NIH HHS/ -- R01 AG029430/AG/NIA NIH HHS/ -- R01 AG033069/AG/NIA NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Mar 9;335(6073):1228-31. doi: 10.1126/science.1213151.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, University of California Los Angeles (UCLA), Howard Hughes Medical Institute (HHMI), Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22403391" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amyloid/*chemistry/immunology ; Amyloid beta-Peptides/chemistry ; Antibodies/immunology ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Peptide Fragments/*chemistry/immunology ; Protein Conformation ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; alpha-Crystallin B Chain/*chemistry/immunology
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  • 39
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    Crystal structure of the human two-pore domain potassium channel K2P1 (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-28
    Description: Two-pore domain potassium (K(+)) channels (K2P channels) control the negative resting potential of eukaryotic cells and regulate cell excitability by conducting K(+) ions across the plasma membrane. Here, we present the 3.4 angstrom resolution crystal structure of a human K2P channel, K2P1 (TWIK-1). Unlike other K(+) channel structures, K2P1 is dimeric. An extracellular cap domain located above the selectivity filter forms an ion pathway in which K(+) ions flow through side portals. Openings within the transmembrane region expose the pore to the lipid bilayer and are filled with electron density attributable to alkyl chains. An interfacial helix appears structurally poised to affect gating. The structure lays a foundation to further investigate how K2P channels are regulated by diverse stimuli.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Alexandria N -- Long, Stephen B -- New York, N.Y. -- Science. 2012 Jan 27;335(6067):432-6. doi: 10.1126/science.1213274.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22282804" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Humans ; Ion Channel Gating ; Lipid Bilayers/chemistry ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; Potassium/metabolism ; Potassium Channels, Tandem Pore Domain/*chemistry/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry
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    Cis-acting transcriptional repression establishes a sharp boundary in chordate embryos (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-08-28
    Description: The function of bone morphogenetic protein (BMP) signaling in dorsoventral (DV) patterning of animal embryos is conserved among Bilateria. In vertebrates, the BMP ligand antidorsalizing morphogenetic protein (Admp) is expressed dorsally and moves to the opposite side to specify the ventral fate. Here, we show that Pinhead is an antagonist specific for Admp with a role in establishing the DV axis of the trunk epidermis in embryos of the ascidian Ciona intestinalis. Pinhead and Admp exist in tandem in the genomes of various animals from arthropods to vertebrates. This genomic configuration is important for mutually exclusive expression of these genes, because Pinhead transcription directly disturbs the action of the Admp enhancer. Our data suggest that this dual negative regulatory mechanism is widely conserved in animals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Imai, Kaoru S -- Daido, Yutaka -- Kusakabe, Takehiro G -- Satou, Yutaka -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):964-7. doi: 10.1126/science.1222488.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biodiversity, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923581" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Body Patterning ; Bone Morphogenetic Protein 2/genetics/metabolism ; Bone Morphogenetic Protein 4/genetics/metabolism ; Bone Morphogenetic Proteins/chemistry/*genetics/metabolism ; Ciona intestinalis/*embryology/genetics/metabolism ; Embryo, Nonmammalian/*metabolism ; Embryonic Development ; Enhancer Elements, Genetic ; Epidermis/embryology ; Gastrula/metabolism ; *Gene Expression Regulation, Developmental ; Molecular Sequence Data ; Oligodeoxyribonucleotides, Antisense ; Oryzias/embryology/genetics/metabolism ; Promoter Regions, Genetic ; Signal Transduction ; *Transcription, Genetic
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    Evolutionarily assembled cis-regulatory module at a human ciliopathy locus (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-28
    Description: Neighboring genes are often coordinately expressed within cis-regulatory modules, but evidence that nonparalogous genes share functions in mammals is lacking. Here, we report that mutation of either TMEM138 or TMEM216 causes a phenotypically indistinguishable human ciliopathy, Joubert syndrome. Despite a lack of sequence homology, the genes are aligned in a head-to-tail configuration and joined by chromosomal rearrangement at the amphibian-to-reptile evolutionary transition. Expression of the two genes is mediated by a conserved regulatory element in the noncoding intergenic region. Coordinated expression is important for their interdependent cellular role in vesicular transport to primary cilia. Hence, during vertebrate evolution of genes involved in ciliogenesis, nonparalogous genes were arranged to a functional gene cluster with shared regulatory elements.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3671610/" 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/PMC3671610/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jeong Ho -- Silhavy, Jennifer L -- Lee, Ji Eun -- Al-Gazali, Lihadh -- Thomas, Sophie -- Davis, Erica E -- Bielas, Stephanie L -- Hill, Kiley J -- Iannicelli, Miriam -- Brancati, Francesco -- Gabriel, Stacey B -- Russ, Carsten -- Logan, Clare V -- Sharif, Saghira Malik -- Bennett, Christopher P -- Abe, Masumi -- Hildebrandt, Friedhelm -- Diplas, Bill H -- Attie-Bitach, Tania -- Katsanis, Nicholas -- Rajab, Anna -- Koul, Roshan -- Sztriha, Laszlo -- Waters, Elizabeth R -- Ferro-Novick, Susan -- Woods, C Geoffrey -- Johnson, Colin A -- Valente, Enza Maria -- Zaki, Maha S -- Gleeson, Joseph G -- DK068306/DK/NIDDK NIH HHS/ -- DK072301/DK/NIDDK NIH HHS/ -- DK075972/DK/NIDDK NIH HHS/ -- DK090917/DK/NIDDK NIH HHS/ -- EY021872/EY/NEI NIH HHS/ -- G0700073/Medical Research Council/United Kingdom -- GGP08145/Telethon/Italy -- HD042601/HD/NICHD NIH HHS/ -- NS04843/NS/NINDS NIH HHS/ -- NS052455/NS/NINDS NIH HHS/ -- P30 CA023100/CA/NCI NIH HHS/ -- P30NS047101/NS/NINDS NIH HHS/ -- R01 DK068306/DK/NIDDK NIH HHS/ -- R01 DK072301/DK/NIDDK NIH HHS/ -- R01 DK075972/DK/NIDDK NIH HHS/ -- R01 EY021872/EY/NEI NIH HHS/ -- R01 HD042601/HD/NICHD NIH HHS/ -- R01 NS048453/NS/NINDS NIH HHS/ -- R01 NS052455/NS/NINDS NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):966-9. doi: 10.1126/science.1213506. Epub 2012 Jan 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neurogenetics Laboratory, Howard Hughes Medical Institute (HHMI), Department of Neurosciences, University of California, San Diego, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22282472" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cell Line ; Cerebellar Diseases/*genetics/metabolism/pathology ; Cilia/metabolism/*ultrastructure ; Conserved Sequence ; DNA, Intergenic ; *Evolution, Molecular ; Eye Abnormalities/*genetics/metabolism/pathology ; Gene Expression Profiling ; *Gene Expression Regulation ; Genetic Heterogeneity ; *Genetic Loci ; Humans ; Kidney Diseases, Cystic/*genetics/metabolism/pathology ; Membrane Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Mutation ; Mutation, Missense ; Phenotype ; Protein Transport ; *Regulatory Sequences, Nucleic Acid ; Retina/abnormalities/metabolism/pathology ; Transport Vesicles/metabolism/ultrastructure
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    Structural basis of Wnt recognition by Frizzled (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-02
    Description: Wnts are lipid-modified morphogens that play critical roles in development principally through engagement of Frizzled receptors. The 3.25 angstrom structure of Xenopus Wnt8 (XWnt8) in complex with mouse Frizzled-8 (Fz8) cysteine-rich domain (CRD) reveals an unusual two-domain Wnt structure, not obviously related to known protein folds, resembling a "hand" with "thumb" and "index" fingers extended to grasp the Fz8-CRD at two distinct binding sites. One site is dominated by a palmitoleic acid lipid group projecting from serine 187 at the tip of Wnt's thumb into a deep groove in the Fz8-CRD. In the second binding site, the conserved tip of Wnt's "index finger" forms hydrophobic amino acid contacts with a depression on the opposite side of the Fz8-CRD. The conservation of amino acids in both interfaces appears to facilitate ligand-receptor cross-reactivity, which has important implications for understanding Wnt's functional pleiotropy and for developing Wnt-based drugs for cancer and regenerative medicine.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577348/" 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/PMC3577348/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janda, Claudia Y -- Waghray, Deepa -- Levin, Aron M -- Thomas, Christoph -- Garcia, K Christopher -- R01 GM097015/GM/NIGMS NIH HHS/ -- R01-GM097015/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):59-64. doi: 10.1126/science.1222879. Epub 2012 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22653731" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Cysteine/chemistry ; Fatty Acids, Monounsaturated/chemistry ; Glycosylation ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Folding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/*chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism ; Wnt Proteins/*chemistry/metabolism ; Wnt Signaling Pathway ; Xenopus Proteins/*chemistry/metabolism ; Xenopus laevis
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    The crystal structure of human Argonaute2 (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-04-28
    Description: Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521581/" 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/PMC3521581/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schirle, Nicole T -- MacRae, Ian J -- R01 GM086701/GM/NIGMS NIH HHS/ -- U54 GM074898/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 May 25;336(6084):1037-40. doi: 10.1126/science.1221551. Epub 2012 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539551" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Argonaute Proteins/*chemistry/metabolism ; Base Pairing ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; MicroRNAs/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA Interference ; RNA, Guide/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Tryptophan/chemistry
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    MMS19 links cytoplasmic iron-sulfur cluster assembly to DNA metabolism (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-09
    Description: The function of many DNA metabolism proteins depends on their ability to coordinate an iron-sulfur (Fe-S) cluster. Biogenesis of Fe-S proteins is a multistep process that takes place in mitochondria and the cytoplasm, but how it is linked to nuclear Fe-S proteins is not known. Here, we demonstrate that MMS19 forms a complex with the cytoplasmic Fe-S assembly (CIA) proteins CIAO1, IOP1, and MIP18. Cytoplasmic MMS19 also binds to multiple nuclear Fe-S proteins involved in DNA metabolism. In the absence of MMS19, a failure to transfer Fe-S clusters to target proteins is associated with Fe-S protein instability and preimplantation death of mice in which Mms19 has been knocked out. We propose that MMS19 functions as a platform to facilitate Fe-S cluster transfer to proteins critical for DNA replication and repair.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gari, Kerstin -- Leon Ortiz, Ana Maria -- Borel, Valerie -- Flynn, Helen -- Skehel, J Mark -- Boulton, Simon J -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):243-5. doi: 10.1126/science.1219664. Epub 2012 Jun 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22678361" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/metabolism ; Cytoplasm/*metabolism ; DNA/*metabolism ; DNA Repair ; DNA Replication ; Humans ; Hydrogenase/metabolism ; Iron-Sulfur Proteins/*metabolism ; Metallochaperones/metabolism ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Protein Stability ; Saccharomyces cerevisiae/genetics/metabolism ; Transcription Factors/genetics/*metabolism ; Xeroderma Pigmentosum Group D Protein/metabolism
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    A Rab32-dependent pathway contributes to Salmonella typhi host restriction (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-20
    Description: Unlike other Salmonellae, the intracellular bacterial human pathogen Salmonella Typhi exhibits strict host specificity. The molecular bases for this restriction are unknown. Here we found that the expression of a single type III secretion system effector protein from broad-host Salmonella Typhimurium allowed Salmonella Typhi to survive and replicate within macrophages and tissues from mice, a nonpermissive host. This effector proteolytically targeted Rab32, which controls traffic to lysosome-related organelles in conjunction with components of the biogenesis of lysosome-related organelle complexes (BLOCs). RNA interference-mediated depletion of Rab32 or of an essential component of a BLOC complex was sufficient to allow S. Typhi to survive within mouse macrophages. Furthermore, S. Typhi was able to survive in macrophages from mice defective in BLOC components.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693731/" 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/PMC3693731/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spano, Stefania -- Galan, Jorge E -- AI055472/AI/NIAID NIH HHS/ -- AI079022/AI/NIAID NIH HHS/ -- R01 AI055472/AI/NIAID NIH HHS/ -- R01 AI079022/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 16;338(6109):960-3. doi: 10.1126/science.1229224.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbial Pathogenesis, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23162001" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacterial Secretion Systems/genetics/*physiology ; COS Cells ; Cercopithecus aethiops ; *Host-Pathogen Interactions ; Humans ; Lysosomes/metabolism ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; Salmonella typhi/genetics/*physiology ; rab GTP-Binding Proteins/classification/genetics/*physiology
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  • 46
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    Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-29
    Description: BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete genomes from an acetate-amended aquifer. All organisms were nonrespiring anaerobes predicted to ferment. Three augment fermentation with archaeal-like hybrid type II/III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) that couples adenosine monophosphate salvage with CO(2) fixation, a pathway not previously described in Bacteria. Members of OD1 reduce sulfur and may pump protons using archaeal-type hydrogenases. For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wrighton, Kelly C -- Thomas, Brian C -- Sharon, Itai -- Miller, Christopher S -- Castelle, Cindy J -- VerBerkmoes, Nathan C -- Wilkins, Michael J -- Hettich, Robert L -- Lipton, Mary S -- Williams, Kenneth H -- Long, Philip E -- Banfield, Jillian F -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1661-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019650" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacteria, Anaerobic/*classification/*enzymology/genetics ; Codon, Terminator/genetics ; DNA, Bacterial ; Fermentation ; Genome, Bacterial ; Hydrogen/*metabolism ; Hydrogenase/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/chemistry/genetics/*metabolism ; Sulfur/*metabolism ; Tryptophan/genetics
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    Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-28
    Description: Polycomb repressive complex 2 (PRC2)-mediated histone H3 lysine 27 (H3K27) methylation is vital for Polycomb gene silencing, a classic epigenetic phenomenon that maintains transcriptional silencing throughout cell divisions. We report that PRC2 activity is regulated by the density of its substrate nucleosome arrays. Neighboring nucleosomes activate the PRC2 complex with a fragment of their H3 histones (Ala(31) to Arg(42)). We also identified mutations on PRC2 subunit Su(z)12, which impair its binding and response to the activating peptide and its ability in establishing H3K27 trimethylation levels in vivo. In mouse embryonic stem cells, local chromatin compaction occurs before the formation of trimethylated H3K27 upon transcription cessation of the retinoic acid-regulated gene CYP26a1. We propose that PRC2 can sense the chromatin environment to exert its role in the maintenance of transcriptional states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Wen -- Wu, Tong -- Fu, Hang -- Dai, Chao -- Wu, Hui -- Liu, Nan -- Li, Xiang -- Xu, Mo -- Zhang, Zhuqiang -- Niu, Tianhui -- Han, Zhifu -- Chai, Jijie -- Zhou, Xianghong Jasmine -- Gao, Shaorong -- Zhu, Bing -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):971-5. doi: 10.1126/science.1225237.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Biological Sciences, China Agricultural University, Beijing 100094, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923582" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; CD4-Positive T-Lymphocytes ; Chromatin Immunoprecipitation ; Cytochrome P-450 Enzyme System/genetics ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster ; Embryonic Stem Cells ; Gene Silencing ; Histone-Lysine N-Methyltransferase/chemistry/genetics/*metabolism ; Histones/chemistry/genetics/*metabolism ; Humans ; Lysine/metabolism ; Methylation ; Mice ; Molecular Sequence Data ; Mutagenesis ; Nucleosomes/*metabolism/ultrastructure ; Peptide Fragments/metabolism ; Polycomb Repressive Complex 2 ; Polycomb-Group Proteins ; Repressor Proteins/chemistry/genetics/*metabolism ; *Transcription, Genetic
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    Control of nonapoptotic developmental cell death in Caenorhabditis elegans by a polyglutamine-repeat protein (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-01
    Description: Death is a vital developmental cell fate. In Caenorhabditis elegans, programmed death of the linker cell, which leads gonadal elongation, proceeds independently of caspases and apoptotic effectors. To identify genes promoting linker-cell death, we performed a genome-wide RNA interference screen. We show that linker-cell death requires the gene pqn-41, encoding an endogenous polyglutamine-repeat protein. pqn-41 functions cell-autonomously and is expressed at the onset of linker-cell death. pqn-41 expression is controlled by the mitogen-activated protein kinase kinase SEK-1, which functions in parallel to the zinc-finger protein LIN-29 to promote cellular demise. Linker-cell death is morphologically similar to cell death associated with normal vertebrate development and polyglutamine-induced neurodegeneration. Our results may therefore provide molecular inroads to understanding nonapoptotic cell death in metazoan development and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858082/" 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/PMC3858082/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blum, Elyse S -- Abraham, Mary C -- Yoshimura, Satoshi -- Lu, Yun -- Shaham, Shai -- CA09673/CA/NCI NIH HHS/ -- R01 HD042680/HD/NICHD NIH HHS/ -- R01HD042680/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):970-3. doi: 10.1126/science.1215156.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363008" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Caenorhabditis elegans/*cytology/genetics/growth & development/*metabolism ; Caenorhabditis elegans Proteins/chemistry/*genetics/*metabolism ; *Cell Death ; Cell Nucleus/ultrastructure ; Cell Survival ; DNA-Binding Proteins/genetics/metabolism ; Gene Expression Regulation ; Genes, Helminth ; Genome, Helminth ; MAP Kinase Kinase 4/genetics/metabolism ; Male ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Peptides/chemistry ; Protein Structure, Tertiary ; RNA Interference ; Sequence Deletion ; Transcription Factors/genetics/metabolism ; Transgenes
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    Egg cell-secreted EC1 triggers sperm cell activation during double fertilization (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-28
    Description: Double fertilization is the defining characteristic of flowering plants. However, the molecular mechanisms regulating the fusion of one sperm with the egg and the second sperm with the central cell are largely unknown. We show that gamete interactions in Arabidopsis depend on small cysteine-rich EC1 (EGG CELL 1) proteins accumulating in storage vesicles of the egg cell. Upon sperm arrival, EC1-containing vesicles are exocytosed. The sperm endomembrane system responds to exogenously applied EC1 peptides by redistributing the potential gamete fusogen HAP2/GCS1 (HAPLESS 2/GENERATIVE CELL SPECIFIC 1) to the cell surface. Furthermore, fertilization studies with ec1 quintuple mutants show that successful male-female gamete interactions are necessary to prevent multiple-sperm cell delivery. Our findings provide evidence that mutual gamete activation, regulated exocytosis, and sperm plasma membrane modifications govern flowering plant gamete interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sprunck, Stefanie -- Rademacher, Svenja -- Vogler, Frank -- Gheyselinck, Jacqueline -- Grossniklaus, Ueli -- Dresselhaus, Thomas -- New York, N.Y. -- Science. 2012 Nov 23;338(6110):1093-7. doi: 10.1126/science.1223944.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitatsstrasse 31, D-93053 Regensburg, Germany. stefanie.sprunck@biologie.uni-regensburg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180860" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/metabolism/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; Carrier Proteins/metabolism ; Cell Membrane/metabolism ; *Exocytosis ; *Fertilization ; Flowers/genetics/metabolism/physiology ; Gene Expression Regulation, Plant ; Genes, Plant ; Molecular Sequence Data ; Multigene Family ; Ovule/genetics/metabolism/physiology ; Pollen/genetics/metabolism/*physiology ; Protein Sorting Signals ; Transcription, Genetic
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    A killer-protector system regulates both hybrid sterility and segregation distortion in rice (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-18
    Description: Hybrid sterility is a major form of postzygotic reproductive isolation that restricts gene flow between populations. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica; inter-subspecific hybrids are usually sterile. We show that a killer-protector system at the S5 locus encoded by three tightly linked genes [Open Reading Frame 3 (ORF3) to ORF5] regulates fertility in indica-japonica hybrids. During female sporogenesis, the action of ORF5+ (killer) and ORF4+ (partner) causes endoplasmic reticulum (ER) stress. ORF3+ (protector) prevents ER stress and produces normal gametes, but ORF3- cannot prevent ER stress, resulting in premature programmed cell death and leads to embryo-sac abortion. Preferential transmission of ORF3+ gametes results in segregation distortion in the progeny. These results add to our understanding of differences between indica and japonica rice and may aid in rice genetic improvement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Jiangyi -- Zhao, Xiaobo -- Cheng, Ke -- Du, Hongyi -- Ouyang, Yidan -- Chen, Jiongjiong -- Qiu, Shuqing -- Huang, Jianyan -- Jiang, Yunhe -- Jiang, Liwen -- Ding, Jihua -- Wang, Jia -- Xu, Caiguo -- Li, Xianghua -- Zhang, Qifa -- New York, N.Y. -- Science. 2012 Sep 14;337(6100):1336-40. doi: 10.1126/science.1223702.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22984070" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chimera/*genetics ; Endoplasmic Reticulum Stress/genetics ; Germ Cells, Plant/metabolism ; Molecular Sequence Data ; Open Reading Frames/genetics ; Oryza/cytology/*genetics ; Plant Infertility/*genetics
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    A gain-of-function polymorphism controlling complex traits and fitness in nature (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-01
    Description: Identification of the causal genes that control complex trait variation remains challenging, limiting our appreciation of the evolutionary processes that influence polymorphisms in nature. We cloned a quantitative trait locus that controls plant defensive chemistry, damage by insect herbivores, survival, and reproduction in the natural environments where this polymorphism evolved. These ecological effects are driven by duplications in the BCMA (branched-chain methionine allocation) loci controlling this variation and by two selectively favored amino acid changes in the glucosinolate-biosynthetic cytochrome P450 proteins that they encode. These changes cause a gain of novel enzyme function, modulated by allelic differences in catalytic rate and gene copy number. Ecological interactions in diverse environments likely contribute to the widespread polymorphism of this biochemical function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872477/" 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/PMC3872477/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prasad, Kasavajhala V S K -- Song, Bao-Hua -- Olson-Manning, Carrie -- Anderson, Jill T -- Lee, Cheng-Ruei -- Schranz, M Eric -- Windsor, Aaron J -- Clauss, Maria J -- Manzaneda, Antonio J -- Naqvi, Ibtehaj -- Reichelt, Michael -- Gershenzon, Jonathan -- Rupasinghe, Sanjeewa G -- Schuler, Mary A -- Mitchell-Olds, Thomas -- R01 GM086496/GM/NIGMS NIH HHS/ -- R01-GM079530/GM/NIGMS NIH HHS/ -- R01-GM086496/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1081-4. doi: 10.1126/science.1221636.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936775" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Amino Acid Substitution ; Arabidopsis/genetics/metabolism/parasitology ; *Brassicaceae/genetics/metabolism/parasitology ; Cytochrome P-450 Enzyme System/*genetics ; Gene Dosage ; Gene-Environment Interaction ; Glucosinolates/biosynthesis/*genetics ; Herbivory/physiology ; Methionine/genetics/metabolism ; Molecular Sequence Data ; Plant Leaves/genetics/metabolism/parasitology ; Plants, Genetically Modified/genetics/metabolism/parasitology ; Polymorphism, Genetic ; *Quantitative Trait Loci ; *Quantitative Trait, Heritable ; *Selection, Genetic
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    Synchronizing nuclear import of ribosomal proteins with ribosome assembly (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-11-03
    Description: Ribosomal proteins are synthesized in the cytoplasm, before nuclear import and assembly with ribosomal RNA (rRNA). Little is known about coordination of nucleocytoplasmic transport with ribosome assembly. Here, we identify a transport adaptor, symportin 1 (Syo1), that facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11. In vitro studies revealed that Syo1 concomitantly binds Rpl5-Rpl11 and furthermore recruits the import receptor Kap104. The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP and can be directly transferred onto the 5S rRNA. Syo1 can shuttle back to the cytoplasm by interaction with phenylalanine-glycine nucleoporins. X-ray crystallography uncovered how the alpha-solenoid symportin accommodates the Rpl5 amino terminus, normally bound to 5S rRNA, in an extended groove. Symportin-mediated coimport of Rpl5-Rpl11 could ensure coordinated and stoichiometric incorporation of these proteins into pre-60S ribosomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kressler, Dieter -- Bange, Gert -- Ogawa, Yutaka -- Stjepanovic, Goran -- Bradatsch, Bettina -- Pratte, Dagmar -- Amlacher, Stefan -- Strauss, Daniela -- Yoneda, Yoshihiro -- Katahira, Jun -- Sinning, Irmgard -- Hurt, Ed -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):666-71. doi: 10.1126/science.1226960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany. dieter.kressler@unifr.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23118189" target="_blank"〉PubMed〈/a〉
    Keywords: *Active Transport, Cell Nucleus ; Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*metabolism ; Chaetomium/metabolism ; Crystallography, X-Ray ; Fungal Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; RNA, Fungal/metabolism ; RNA, Ribosomal, 5S/metabolism ; RNA-Binding Proteins/chemistry/*metabolism ; Ribosomal Proteins/chemistry/*metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; beta Karyopherins/metabolism
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    Structural basis for sequence-specific recognition of DNA by TAL effectors (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-01-10
    Description: TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586824/" 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/PMC3586824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deng, Dong -- Yan, Chuangye -- Pan, Xiaojing -- Mahfouz, Magdy -- Wang, Jiawei -- Zhu, Jian-Kang -- Shi, Yigong -- Yan, Nieng -- R01 GM070795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):720-3. doi: 10.1126/science.1215670. Epub 2012 Jan 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Bio-Membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223738" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Processes ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Virulence Factors/*chemistry/*metabolism ; Xanthomonas/chemistry/pathogenicity
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    Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-01
    Description: The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786669/" 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/PMC3786669/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redecke, Lars -- Nass, Karol -- DePonte, Daniel P -- White, Thomas A -- Rehders, Dirk -- Barty, Anton -- Stellato, Francesco -- Liang, Mengning -- Barends, Thomas R M -- Boutet, Sebastien -- Williams, Garth J -- Messerschmidt, Marc -- Seibert, M Marvin -- Aquila, Andrew -- Arnlund, David -- Bajt, Sasa -- Barth, Torsten -- Bogan, Michael J -- Caleman, Carl -- Chao, Tzu-Chiao -- Doak, R Bruce -- Fleckenstein, Holger -- Frank, Matthias -- Fromme, Raimund -- Galli, Lorenzo -- Grotjohann, Ingo -- Hunter, Mark S -- Johansson, Linda C -- Kassemeyer, Stephan -- Katona, Gergely -- Kirian, Richard A -- Koopmann, Rudolf -- Kupitz, Chris -- Lomb, Lukas -- Martin, Andrew V -- Mogk, Stefan -- Neutze, Richard -- Shoeman, Robert L -- Steinbrener, Jan -- Timneanu, Nicusor -- Wang, Dingjie -- Weierstall, Uwe -- Zatsepin, Nadia A -- Spence, John C H -- Fromme, Petra -- Schlichting, Ilme -- Duszenko, Michael -- Betzel, Christian -- Chapman, Henry N -- 1R01GM095583/GM/NIGMS NIH HHS/ -- R01 GM095583/GM/NIGMS NIH HHS/ -- U54 GM094599/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jan 11;339(6116):227-30. doi: 10.1126/science.1229663. Epub 2012 Nov 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lubeck, at Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23196907" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Cathepsin B/antagonists & inhibitors/*chemistry ; Crystallization ; Crystallography, X-Ray ; Enzyme Precursors/chemistry ; Glycosylation ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protozoan Proteins/antagonists & inhibitors/*chemistry ; Sf9 Cells ; Spodoptera ; Trypanosoma brucei brucei/*enzymology ; X-Rays
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Comparative analysis of bat genomes provides insight into the evolution of flight and immunity (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-22
    Description: Bats are the only mammals capable of sustained flight and are notorious reservoir hosts for some of the world's most highly pathogenic viruses, including Nipah, Hendra, Ebola, and severe acute respiratory syndrome (SARS). To identify genetic changes associated with the development of bat-specific traits, we performed whole-genome sequencing and comparative analyses of two distantly related species, fruit bat Pteropus alecto and insectivorous bat Myotis davidii. We discovered an unexpected concentration of positively selected genes in the DNA damage checkpoint and nuclear factor kappaB pathways that may be related to the origin of flight, as well as expansion and contraction of important gene families. Comparison of bat genomes with other mammalian species has provided new insights into bat biology and evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guojie -- Cowled, Christopher -- Shi, Zhengli -- Huang, Zhiyong -- Bishop-Lilly, Kimberly A -- Fang, Xiaodong -- Wynne, James W -- Xiong, Zhiqiang -- Baker, Michelle L -- Zhao, Wei -- Tachedjian, Mary -- Zhu, Yabing -- Zhou, Peng -- Jiang, Xuanting -- Ng, Justin -- Yang, Lan -- Wu, Lijun -- Xiao, Jin -- Feng, Yue -- Chen, Yuanxin -- Sun, Xiaoqing -- Zhang, Yong -- Marsh, Glenn A -- Crameri, Gary -- Broder, Christopher C -- Frey, Kenneth G -- Wang, Lin-Fa -- Wang, Jun -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):456-60. doi: 10.1126/science.1230835. Epub 2012 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BGI-Shenzhen, Shenzhen, 518083, China. zhanggj@genomics.org.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23258410" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Chiroptera/*genetics/immunology/physiology ; DNA Damage/genetics ; DNA Repair/genetics ; Echolocation ; Evolution, Molecular ; *Flight, Animal ; Genetic Speciation ; *Genome ; Hibernation/genetics ; High-Throughput Nucleotide Sequencing ; Immunity, Innate/*genetics ; Male ; Molecular Sequence Data ; Phylogeny ; Reactive Oxygen Species/metabolism ; Selection, Genetic ; *Sequence Analysis, DNA ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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