Foundations of Molecular Biologydtv2.Pptx
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Biochemistrystanford00kornrich.Pdf
University of California Berkeley Regional Oral History Office University of California The Bancroft Library Berkeley, California Program in the History of the Biosciences and Biotechnology Arthur Kornberg, M.D. BIOCHEMISTRY AT STANFORD, BIOTECHNOLOGY AT DNAX With an Introduction by Joshua Lederberg Interviews Conducted by Sally Smith Hughes, Ph.D. in 1997 Copyright 1998 by The Regents of the University of California Since 1954 the Regional Oral History Office has been interviewing leading participants in or well-placed witnesses to major events in the development of Northern California, the West, and the Nation. Oral history is a method of collecting historical information through tape-recorded interviews between a narrator with firsthand knowledge of historically significant events and a well- informed interviewer, with the goal of preserving substantive additions to the historical record. The tape recording is transcribed, lightly edited for continuity and clarity, and reviewed by the interviewee. The corrected manuscript is indexed, bound with photographs and illustrative materials, and placed in The Bancroft Library at the University of California, Berkeley, and in other research collections for scholarly use. Because it is primary material, oral history is not intended to present the final, verified, or complete narrative of events. It is a spoken account, offered by the interviewee in response to questioning, and as such it is reflective, partisan, deeply involved, and irreplaceable. ************************************ All uses of this manuscript are covered by a legal agreement between The Regents of the University of California and Arthur Kornberg, M.D., dated June 18, 1997. The manuscript is thereby made available for research purposes. All literary rights in the manuscript, including the right to publish, are reserved to The Bancroft Library of the University of California, Berkeley. -
Lecture Program
EARL W. SUTHERLAND LECTURE EARL W. SUTHERLAND LECTURE The Earl W. Sutherland Lecture Series was established by the SPONSORED BY: Department of Molecular Physiology and Biophysics in 1997 DEPARTMENT OF MOLECULAR PHYSIOLOGY AND BIOPHYSICS to honor Dr. Sutherland, a former member of this department and winner of the 1971 Nobel Prize in Physiology or Medicine. This series highlights important advances in cell signaling. ROBERT J. LEFKOWITZ, MD NOBEL PRIZE IN CHEMISTRY, 2012 SPEAKERS IN THIS SERIES HAVE INCLUDED: SEVEN TRANSMEMBRANE RECEPTORS Edmond H. Fischer (1997) Alfred G. Gilman (1999) Ferid Murad (2001) Louis J. Ignarro (2003) MARCH 31, 2016 Paul Greengard (2007) 4:00 P.M. 208 LIGHT HALL Eric Kandel (2009) Roger Tsien (2011) Michael S. Brown (2013) 867-2923-Institution-Discovery Lecture Series-Lefkowitz-BK-CH.indd 1 3/11/16 9:39 AM EARL W. SUTHERLAND, 1915-1974 ROBERT J. LEFKOWITZ, MD JAMES B. DUKE PROFESSOR, Earl W. Sutherland grew up in Burlingame, Kansas, a small farming community DUKE UNIVERSITY MEDICAL CENTER that nourished his love for the outdoors and fishing, which he retained throughout INVESTIGATOR, HOWARD HUGHES MEDICAL INSTITUTE his life. He graduated from Washburn College in 1937 and then received his MEMBER, NATIONAL ACADEMY OF SCIENCES M.D. from Washington University School of Medicine in 1942. After serving as a MEMBER, INSTITUTE OF MEDICINE medical officer during World War II, he returned to Washington University to train NOBEL PRIZE IN CHEMISTRY, 2012 with Carl and Gerty Cori. During those years he was influenced by his interactions with such eminent scientists as Louis Leloir, Herman Kalckar, Severo Ochoa, Arthur Kornberg, Christian deDuve, Sidney Colowick, Edwin Krebs, Theodore Robert J. -
Mito-Cytosolic Translational Balance Increased Cytoprotection And
Graphical Abstract Worms Human cells Mice Mito-cytosolic translational balance Genetically mrps-5 RNAi Mitochondrial Cytosolic ribosomes ribosomes ATF4/atf-5 Doxycycline Pharmacologically Increased cytoprotection and longevity Manuscript A conserved mito-cytosolic translational balance links two longevity pathways Marte Molenaars1*, Georges E. Janssens1*, Evan G. Williams2, Aldo Jongejan3, Jiayi Lan2, Sylvie Rabot4, Fatima Joly4, Perry D. Moerland3, Bauke V. Schomakers1,5, Marco Lezzerini1 Yasmine J. Liu1, Mark A. McCormick6,7, Brian K. Kennedy8,9, Michel van Weeghel1,5, Antoine H.C. van Kampen3, Ruedi Aebersold2,10, Alyson W. MacInnes1, Riekelt H. Houtkooper1,11# 1Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands 2Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland 3Bioinformatics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands 4Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France 5Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands. 6 Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, USA 7Autophagy, Inflammation, and Metabolism Center of Biological Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, USA 8Buck Institute for Research on Aging, Novato, USA 9Departments -
Mitochondrial Misreading in Skeletal Muscle Accelerates Metabolic Aging and Confers Lipid Accumulation and Increased Inflammation
Downloaded from rnajournal.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press REPORT Mitochondrial misreading in skeletal muscle accelerates metabolic aging and confers lipid accumulation and increased inflammation DIMITRI SHCHERBAKOV,1,4 STEFAN DUSCHA,1,4 REDA JUSKEVICIENE,1 LISA M. RESTELLI,2 STEPHAN FRANK,2 ENDRE LACZKO,3 and ERIK C. BÖTTGER1 1Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland 2Division of Neuropathology, Institute of Medical Genetics and Pathology, Basel University Hospital, 4031 Basel, Switzerland 3Functional Genomics Center Zurich, ETH Zürich und Universität Zürich, 8057 Zürich, Switzerland ABSTRACT We have recently reported on an experimental model of mitochondrial mistranslation conferred by amino acid exchange V338Y in mitochondrial ribosomal protein MrpS5. Here we used a combination of RNA-seq and metabolic profiling of ho- mozygous transgenic Mrps5V338Y/V338Y mice to analyze the changes associated with the V338Y mutation in postmitotic skeletal muscle. Metabolome analysis demonstrated enhanced levels of age-associated metabolites in the mutant V338Y animals accompanied by increased glycolysis, lipid desaturation and eicosanoid biosynthesis, and alterations of the pentose phosphate pathway. In addition, transcriptome signatures of aged V338Y mutant muscle pointed to elevated inflammation, likely reflecting the increased levels of bioactive lipids. Our findings indicate that mistranslation-mediated impairment of mitochondrial function affects specific bioenergetic processes in muscle in an age-dependent manner. Keywords: mitochondria; misreading; skeletal muscle; aging; metabolome INTRODUCTION express a mtDNA mutator phenotype, with a threefold to fivefold increase in the levels of random point mutations A decline in mitochondrial function has been associated in mtDNA, display respiratory chain dysfunction and fea- with aging and complex age-related changes in metabo- tures of accelerated aging (Trifunovic et al. -
Nucleolin and Its Role in Ribosomal Biogenesis
NUCLEOLIN: A NUCLEOLAR RNA-BINDING PROTEIN INVOLVED IN RIBOSOME BIOGENESIS Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf vorgelegt von Julia Fremerey aus Hamburg Düsseldorf, April 2016 2 Gedruckt mit der Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf Referent: Prof. Dr. A. Borkhardt Korreferent: Prof. Dr. H. Schwender Tag der mündlichen Prüfung: 20.07.2016 3 Die vorgelegte Arbeit wurde von Juli 2012 bis März 2016 in der Klinik für Kinder- Onkologie, -Hämatologie und Klinische Immunologie des Universitätsklinikums Düsseldorf unter Anleitung von Prof. Dr. A. Borkhardt und in Kooperation mit dem ‚Laboratory of RNA Molecular Biology‘ an der Rockefeller Universität unter Anleitung von Prof. Dr. T. Tuschl angefertigt. 4 Dedicated to my family TABLE OF CONTENTS 5 TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................... 5 LIST OF FIGURES ......................................................................................................10 LIST OF TABLES .......................................................................................................12 ABBREVIATION .........................................................................................................13 ABSTRACT ................................................................................................................19 ZUSAMMENFASSUNG -
Moore Noller
2002 Ada Doisy Lectures Ada Doisy Lecturers 2003 in BIOCHEMISTRY Sponsored by the Department of Biochemistry • University of Illinois at Urbana-Champaign Dr. Peter B. 1970-71 Charles Huggins* and Elwood V. Jensen A76 1972-73 Paul Berg* and Walter Gilbert* Moore 1973-74 Saul Roseman and Bruce Ames Department of Molecular carbonyl Biophysics & Biochemistry Phe 1974-75 Arthur Kornberg* and Osamu Hayaishi Yale University C75 1976-77 Luis F. Leloir* New Haven, Connecticutt 1977-78 Albert L. Lehninger and Efraim Racker 2' OH attacking 1978-79 Donald D. Brown and Herbert Boyer amino N3 Tyr 1979-80 Charles Yanofsky A76 4:00 p.m. A2486 1980-81 Leroy E. Hood Thursday, May 1, 2003 (2491) 1983-84 Joseph L. Goldstein* and Michael S. Brown* Medical Sciences Auditorium 1984-85 Joan Steitz and Phillip Sharp* Structure and Function in 1985-86 Stephen J. Benkovic and Jeremy R. Knowles the Large Ribosomal Subunit 1986-87 Tom Maniatis and Mark Ptashne 1988-89 J. Michael Bishop* and Harold E. Varmus* 1989-90 Kurt Wüthrich Dr. Harry F. 1990-91 Edmond H. Fischer* and Edwin G. Krebs* 1993-94 Bert W. O’Malley Noller 1994-95 Earl W. Davie and John W. Suttie Director, Center for Molecular Biology of RNA 1995-96 Richard J. Roberts* University of California, Santa Cruz 1996-97 Ronald M. Evans Santa Cruz, California 1998-99 Elizabeth H. Blackburn 1999-2000 Carl R. Woese and Norman R. Pace 2000-01 Willem P. C. Stemmer and Ronald W. Davis 2001-02 Janos K. Lanyi and Sir John E. Walker* 12:00 noon 2002-03 Peter B. -
USP16 Counteracts Mono-Ubiquitination of Rps27a And
RESEARCH ARTICLE USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit Christian Montellese1†, Jasmin van den Heuvel1,2, Caroline Ashiono1, Kerstin Do¨ rner1,2, Andre´ Melnik3‡, Stefanie Jonas1§, Ivo Zemp1, Paola Picotti3, Ludovic C Gillet1, Ulrike Kutay1* 1Institute of Biochemistry, ETH Zurich, Zurich, Switzerland; 2Molecular Life Sciences Ph.D. Program, Zurich, Switzerland; 3Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland Abstract Establishment of translational competence represents a decisive cytoplasmic step in the biogenesis of 40S ribosomal subunits. This involves final 18S rRNA processing and release of residual biogenesis factors, including the protein kinase RIOK1. To identify novel proteins promoting the final maturation of human 40S subunits, we characterized pre-ribosomal subunits trapped on RIOK1 by mass spectrometry, and identified the deubiquitinase USP16 among the captured factors. We demonstrate that USP16 constitutes a component of late cytoplasmic pre-40S subunits that promotes the removal of ubiquitin from an internal lysine of ribosomal protein *For correspondence: RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, manifesting in [email protected] incomplete processing of 18S rRNA and retarded recycling of late-acting ribosome biogenesis Present address: †CSL Behring, factors, revealing an unexpected contribution of USP16 to the ultimate step of 40S synthesis. CSL Biologics Research Center, Finally, ubiquitination of RPS27a appears to depend on active translation, pointing at a potential ‡ Bern, Switzerland; MSD Merck connection between 40S maturation and protein synthesis. Sharp & Dohme AG, Lucerne, Switzerland; §Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland Introduction Ribosomes stand at the center of translation in all kingdoms of life, catalyzing the synthesis of pro- Competing interests: The teins by reading a messenger RNA (mRNA) template. -
Hexosamine Biosynthetic Pathway-Derived O-Glcnacylation Is Critical for RANKL-Mediated Osteoclast Differentiation
International Journal of Molecular Sciences Article Hexosamine Biosynthetic Pathway-Derived O-GlcNAcylation Is Critical for RANKL-Mediated Osteoclast Differentiation Myoung Jun Kim 1,†, Hyuk Soon Kim 2,3,† , Sangyong Lee 1, Keun Young Min 1, Wahn Soo Choi 1,4 and Jueng Soo You 1,4,* 1 School of Medicine, Konkuk University, Seoul 05029, Korea; [email protected] (M.J.K.); [email protected] (S.L.); [email protected] (K.Y.M.); [email protected] (W.S.C.) 2 Department of Biomedical Sciences, College of Natural Science, Dong-A University, Busan 49315, Korea; [email protected] 3 Department of Health Sciences, The Graduate School of Dong-A University, Busan 49315, Korea 4 KU Open Innovation Center, Research Institute of Medical Science, Konkuk University, Chungju 27478, Korea * Correspondence: [email protected]; Tel.: +82-2-2049-6235 † The first two authors are equally contributed. Abstract: O-linked-N-acetylglucosaminylation (O-GlcNAcylation) performed by O-GlcNAc trans- ferase (OGT) is a nutrient-responsive post-translational modification (PTM) via the hexosamine biosynthetic pathway (HBP). Various transcription factors (TFs) are O-GlcNAcylated, affecting their activities and significantly contributing to cellular processes ranging from survival to cellular dif- ferentiation. Given the pleiotropic functions of O-GlcNAc modification, it has been studied in various fields; however, the role of O-GlcNAcylation during osteoclast differentiation remains to be explored. Kinetic transcriptome analysis during receptor activator of nuclear factor-kappaB (NF-κB) ligand (RANKL)-mediated osteoclast differentiation revealed that the nexus of major nutri- ent metabolism, HBP was critical for this process. We observed that the critical genes related to HBP Citation: Kim, M.J.; Kim, H.S.; activation, including Nagk, Gfpt1, and Ogt, were upregulated, while the global O-GlcNAcylation was Lee, S.; Min, K.Y.; Choi, W.S.; You, J.S. -
Arthur Kornberg Discovered (The First) DNA Polymerase Four
Arthur Kornberg discovered (the first) DNA polymerase Using an “in vitro” system for DNA polymerase activity: 1. Grow E. coli 2. Break open cells 3. Prepare soluble extract 4. Fractionate extract to resolve different proteins from each other; repeat; repeat 5. Search for DNA polymerase activity using an biochemical assay: incorporate radioactive building blocks into DNA chains Four requirements of DNA-templated (DNA-dependent) DNA polymerases • single-stranded template • deoxyribonucleotides with 5’ triphosphate (dNTPs) • magnesium ions • annealed primer with 3’ OH Synthesis ONLY occurs in the 5’-3’ direction Fig 4-1 E. coli DNA polymerase I 5’-3’ polymerase activity Primer has a 3’-OH Incoming dNTP has a 5’ triphosphate Pyrophosphate (PP) is lost when dNMP adds to the chain E. coli DNA polymerase I: 3 separable enzyme activities in 3 protein domains 5’-3’ polymerase + 3’-5’ exonuclease = Klenow fragment N C 5’-3’ exonuclease Fig 4-3 E. coli DNA polymerase I 3’-5’ exonuclease Opposite polarity compared to polymerase: polymerase activity must stop to allow 3’-5’ exonuclease activity No dNTP can be re-made in reversed 3’-5’ direction: dNMP released by hydrolysis of phosphodiester backboneFig 4-4 Proof-reading (editing) of misincorporated 3’ dNMP by the 3’-5’ exonuclease Fidelity is accuracy of template-cognate dNTP selection. It depends on the polymerase active site structure and the balance of competing polymerase and exonuclease activities. A mismatch disfavors extension and favors the exonuclease.Fig 4-5 Superimposed structure of the Klenow fragment of DNA pol I with two different DNAs “Fingers” “Thumb” “Palm” red/orange helix: 3’ in red is elongating blue/cyan helix: 3’ in blue is getting edited Fig 4-6 E. -
5 Inhibitors of Protein Synthesis
5 Inhibitors of protein synthesis Many antimicrobial substances inhibit protein biosynthesis. In most cases the inhibition involved one or other of the events which take place on the ribosomes. Only a few agents inhibit either amino acid activation or the attachment of the activated amino acid to the terminal adenylic acid residue of transfer RNA (tRNA). There are many chemical types to be found among the inhibitors of prolein synthesis, a fa ct which has increased the difficulty of unders tanding the molecular nature of their inhibitory effects. Indeed, while the reaction which is inhibited has been ideIHified with some precision in certain instances, the nature of the molecular interaction between the sensitive site and inhibi tor remains generally elusive. The reason lies in the complexity of the reactions leading to the for mation of correctly sequenced polypeptides on the ribosome and also in the complex. ity of the structure of the ribosome itself. Our intention is to provide an outline of the current knowledge of the steps in protein biosynthesis. More detailed discussion is given to those specific reactions which are blocked by the inhibitors of protein biosynthesis. RIBOSOMES These remarkable organelles are the machines upon which polypeptides are elaborated. There are three main classes of ribosomes identified by their sedimentation coefficients. The 80S ribosomes are apparently confined to eukaryotic cells, while 70S ribosomes are found in both prokaryotic and euk aryotic cells. A unique species of50-55S ribosome found only in mamma· tian mitochondria resembles bacterial ribosomes in functional organization and antibiotic sensitivity. The 80S particle dissociates reversibly into 60S and 405 subunits and the 70S into 505 and 305 subunits as the Mg:2+ concentration of the solution is reduced. -
Micrornas Mediated Regulation of the Ribosomal Proteins and Its Consequences on the Global Translation of Proteins
cells Review microRNAs Mediated Regulation of the Ribosomal Proteins and Its Consequences on the Global Translation of Proteins Abu Musa Md Talimur Reza 1,2 and Yu-Guo Yuan 1,3,* 1 Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; [email protected] 2 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawi´nskiego5a, 02-106 Warsaw, Poland 3 Jiangsu Key Laboratory of Zoonosis/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China * Correspondence: [email protected]; Tel.: +86-514-8797-9228 Abstract: Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional 0 gene expression, miRNAs regulate gene expression by targeting the 3 untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 50 untranslated region, Citation: Reza, A.M.M.T.; Yuan, Y.-G. -
The Role of Human Ribosomal Proteins in the Maturation of Rrna and Ribosome Production
JOBNAME: RNA 14#9 2008 PAGE: 1 OUTPUT: Friday August 8 17:34:50 2008 csh/RNA/164293/rna11320 Downloaded from rnajournal.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press The role of human ribosomal proteins in the maturation of rRNA and ribosome production SARA ROBLEDO,1,3 RACHEL A. IDOL,1,3 DAN L. CRIMMINS,2 JACK H. LADENSON,2 PHILIP J. MASON,1,4 and MONICA BESSLER1,4 1Department of Internal Medicine, Division of Hematology, Washington University School of Medicine, St. Louis, Missouri 63110, USA 2Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA ABSTRACT Production of ribosomes is a fundamental process that occurs in all dividing cells. It is a complex process consisting of the coordinated synthesis and assembly of four ribosomal RNAs (rRNA) with about 80 ribosomal proteins (r-proteins) involving more than 150 nonribosomal proteins and other factors. Diamond Blackfan anemia (DBA) is an inherited red cell aplasia caused by mutations in one of several r-proteins. How defects in r-proteins, essential for proliferation in all cells, lead to a human disease with a specific defect in red cell development is unknown. Here, we investigated the role of r-proteins in ribosome biogenesis in order to find out whether those mutated in DBA have any similarities. We depleted HeLa cells using siRNA for several individual r-proteins of the small (RPS6, RPS7, RPS15, RPS16, RPS17, RPS19, RPS24, RPS25, RPS28) or large subunit (RPL5, RPL7, RPL11, RPL14, RPL26, RPL35a) and studied the effect on rRNA processing and ribosome production.